@article {pmid38014190,
year = {2023},
author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD},
title = {Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.13.566841},
pmid = {38014190},
abstract = {Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f 3 -statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P -values of qpAdm models, and f 3 -statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f 2 -statistics, demonstrating the improved demographic inference that could be achieved with advancements in f -statistic estimations.},
}
@article {pmid38012935,
year = {2023},
author = {Jäger, HY and Atz Zanotelli, D and Maixner, F and Nicklisch, N and Alt, KW and Meller, H and Pap, I and Szikossy, I and Pálfi, G and Zink, AR},
title = {Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {143S},
number = {},
pages = {102392},
doi = {10.1016/j.tube.2023.102392},
pmid = {38012935},
issn = {1873-281X},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Tuberculosis/microbiology ; Bone and Bones ; DNA ; DNA, Ancient ; },
abstract = {Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.},
}
@article {pmid38012931,
year = {2023},
author = {Zink, A and Maixner, F and Jäger, HY and Szikossy, I and Pálfi, G and Pap, I},
title = {Tuberculosis in mummies - New findings, perspectives and limitations.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {143S},
number = {},
pages = {102371},
doi = {10.1016/j.tube.2023.102371},
pmid = {38012931},
issn = {1873-281X},
abstract = {The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges.},
}
@article {pmid38012918,
year = {2023},
author = {Kharlamova, N and Ogarkov, O and Berdnikov, I and Berdnikova, N and Galeev, R and Mokrousov, I},
title = {Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {143S},
number = {},
pages = {102368},
doi = {10.1016/j.tube.2023.102368},
pmid = {38012918},
issn = {1873-281X},
abstract = {In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates.},
}
@article {pmid38006200,
year = {2023},
author = {Houldcroft, CJ and Underdown, S},
title = {Infectious disease in the Pleistocene: Old friends or old foes?.},
journal = {American journal of biological anthropology},
volume = {182},
number = {4},
pages = {513-531},
doi = {10.1002/ajpa.24737},
pmid = {38006200},
issn = {2692-7691},
support = {//Oxford Brookes University/ ; },
mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; },
abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.},
}
@article {pmid38002979,
year = {2023},
author = {Uricoechea Patiño, D and Collins, A and Romero García, OJ and Santos Vecino, G and Aristizábal Espinosa, P and Bernal Villegas, JE and Benavides Benitez, E and Vergara Muñoz, S and Briceño Balcázar, I},
title = {Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
pmid = {38002979},
issn = {2073-4425},
support = {Convocatoria interna de 2013 (Internal Call of 2013) as per acta 809 de la comisión de asuntos generales, proyecto MED-168-2013.//Universidad de La Sabana/ ; },
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Genetics, Population ; Mitochondria/genetics ; North America ; Human Migration ; },
abstract = {This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.},
}
@article {pmid37993617,
year = {2023},
author = {Izarraras-Gomez, A and Ortega-Del Vecchyo, D},
title = {Ancient DNA uncovers past migrations in California.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37993617},
issn = {1476-4687},
}
@article {pmid37992125,
year = {2023},
author = {Di Santo, LN and Quilodran, CS and Currat, M},
title = {Temporal variation in introgressed segments' length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad252},
pmid = {37992125},
issn = {1537-1719},
abstract = {Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed six summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions and related measures. The first two statistics could confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.},
}
@article {pmid37971141,
year = {2023},
author = {Pečnerová, P and Lord, E and Garcia-Erill, G and Hanghøj, K and Rasmussen, MS and Meisner, J and Liu, X and van der Valk, T and Santander, CG and Quinn, L and Lin, L and Liu, S and Carøe, C and Dalerum, F and Götherström, A and Måsviken, J and Vartanyan, S and Raundrup, K and Al-Chaer, A and Rasmussen, L and Hvilsom, C and Heide-Jørgensen, MP and Sinding, MS and Aastrup, P and Van Coeverden de Groot, PJ and Schmidt, NM and Albrechtsen, A and Dalén, L and Heller, R and Moltke, I and Siegismund, HR},
title = {Population genomics of the muskox' resilience in the near absence of genetic variation.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17205},
pmid = {37971141},
issn = {1365-294X},
support = {CF20-0539//Carlsbergfondet/ ; 8021-00344B//Danmarks Frie Forskningsfond/ ; },
abstract = {Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.},
}
@article {pmid37955570,
year = {2023},
author = {Harning, DJ and Sacco, S and Anamthawat-Jónsson, K and Ardenghi, N and Thordarson, T and Raberg, JH and Sepúlveda, J and Geirsdóttir, Á and Shapiro, B and Miller, GH},
title = {Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37955570},
issn = {2050-084X},
mesh = {*Betula ; Ecosystem ; Iceland ; Betulaceae ; Biodiversity ; DNA, Ancient ; *Tracheophyta ; },
abstract = {As the Arctic continues to warm, woody shrubs are expected to expand northward. This process, known as 'shrubification,' has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While the future rate of shrubification remains poorly constrained, past records of plant immigration to newly deglaciated landscapes in the Arctic may serve as useful analogs. We provide one new postglacial Holocene sedimentary ancient DNA (sedaDNA) record of vascular plants from Iceland and place a second Iceland postglacial sedaDNA record on an improved geochronology; both show Salicaceae present shortly after deglaciation, whereas Betulaceae first appears more than 1000 y later. We find a similar pattern of delayed Betulaceae colonization in eight previously published postglacial sedaDNA records from across the glaciated circum North Atlantic. In nearly all cases, we find that Salicaceae colonizes earlier than Betulaceae and that Betulaceae colonization is increasingly delayed for locations farther from glacial-age woody plant refugia. These trends in Salicaceae and Betulaceae colonization are consistent with the plant families' environmental tolerances, species diversity, reproductive strategies, seed sizes, and soil preferences. As these reconstructions capture the efficiency of postglacial vascular plant migration during a past period of high-latitude warming, a similarly slow response of some woody shrubs to current warming in glaciated regions, and possibly non-glaciated tundra, may delay Arctic shrubification and future changes in the structure of tundra ecosystems and temperature amplification.},
}
@article {pmid37955431,
year = {2023},
author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA},
title = {Large variance in inbreeding within the Iberian wolf population.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esad071},
pmid = {37955431},
issn = {1465-7333},
abstract = {The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300-350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here we measured changes on genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared to other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.},
}
@article {pmid37955259,
year = {2023},
author = {},
title = {Neolithic Community Revealed Using Ancient DNA Data.},
journal = {American journal of medical genetics. Part A},
volume = {191},
number = {12},
pages = {2797-2798},
doi = {10.1002/ajmg.a.62840},
pmid = {37955259},
issn = {1552-4833},
}
@article {pmid37953960,
year = {2023},
author = {Coia, V and Paladin, A and Zingale, S and Wurst, C and Croze, M and Maixner, F and Zink, A},
title = {Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps.},
journal = {iScience},
volume = {26},
number = {11},
pages = {108215},
pmid = {37953960},
issn = {2589-0042},
abstract = {In South Tyrol (Eastern Italian Alps), during Late Antiquity-Early Middle Ages, archeological records indicate cultural hybridization among alpine groups and peoples of various origin. Using paleogenomics, we reconstructed the ancestry of 20 individuals (4[th]-7[th] cent. AD) from a cemetery to analyze whether they had heterogeneous or homogeneous ancestry and to study their social organization. The results revealed a primary genetic ancestry from southern Europe and additional ancestries from south-western, western, and northern Europe, suggesting that cultural hybridization was accompanied by complex genetic admixture. Kinship analyses found no genetic relatedness between the only two individuals buried with grave goods. Instead, a father-son pair was discovered in one multiple grave, together with unrelated individuals and one possible non-local female. These genetic findings indicate the presence of a high social status familia, which is supported by the cultural materials and the proximity of the grave to the most sacred area of the church.},
}
@article {pmid37949985,
year = {2023},
author = {Callaway, E},
title = {How to keep wildcats wild: ancient DNA offers fresh insights.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37949985},
issn = {1476-4687},
}
@article {pmid37935117,
year = {2023},
author = {Jamieson, A and Carmagnini, A and Howard-McCombe, J and Doherty, S and Hirons, A and Dimopoulos, E and Lin, AT and Allen, R and Anderson-Whymark, H and Barnett, R and Batey, C and Beglane, F and Bowden, W and Bratten, J and De Cupere, B and Drew, E and Foley, NM and Fowler, T and Fox, A and Geigl, EM and Gotfredsen, AB and Grange, T and Griffiths, D and Groß, D and Haruda, A and Hjermind, J and Knapp, Z and Lebrasseur, O and Librado, P and Lyons, LA and Mainland, I and McDonnell, C and Muñoz-Fuentes, V and Nowak, C and O'Connor, T and Peters, J and Russo, IM and Ryan, H and Sheridan, A and Sinding, MS and Skoglund, P and Swali, P and Symmons, R and Thomas, G and Trolle Jensen, TZ and Kitchener, AC and Senn, H and Lawson, D and Driscoll, C and Murphy, WJ and Beaumont, M and Ottoni, C and Sykes, N and Larson, G and Frantz, L},
title = {Limited historical admixture between European wildcats and domestic cats.},
journal = {Current biology : CB},
volume = {33},
number = {21},
pages = {4751-4760.e14},
doi = {10.1016/j.cub.2023.08.031},
pmid = {37935117},
issn = {1879-0445},
support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Cats/genetics ; Animals ; Cattle ; Bees ; Sheep ; Swine ; *Hybridization, Genetic ; Chickens ; *Felis/genetics ; Europe ; Gene Flow ; },
abstract = {Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.},
}
@article {pmid37935112,
year = {2023},
author = {Schurr, TG and Shengelia, R and Shamoon-Pour, M and Chitanava, D and Laliashvili, S and Laliashvili, I and Kibret, R and Kume-Kangkolo, Y and Akhvlediani, I and Bitadze, L and Mathieson, I and Yardumian, A},
title = {Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad198},
pmid = {37935112},
issn = {1759-6653},
abstract = {To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian-speaking. From these DNA samples, we generated mtDNA control region sequences for all 485 participants (female and male), Y-STR haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal SNPs plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, W. X2), as well as low frequencies of East Eurasian haplogroups (A, C, D, F, G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared to ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.},
}
@article {pmid37928683,
year = {2023},
author = {Roche, K and Dalle, F and Capelli, N and Borne, R and Jouffroy-Bapicot, I and Valot, B and Grenouillet, F and Le Bailly, M},
title = {From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1249884},
pmid = {37928683},
issn = {1664-302X},
abstract = {Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.},
}
@article {pmid37927550,
year = {2023},
author = {Childebayeva, A and Zavala, EI},
title = {Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics.},
journal = {iScience},
volume = {26},
number = {11},
pages = {108066},
pmid = {37927550},
issn = {2589-0042},
abstract = {Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.},
}
@article {pmid37923262,
year = {2023},
author = {Fracasso, I and Zaccone, C and Oskolkov, N and Da Ros, L and Dinella, A and Marchesini, LB and Buzzini, P and Sannino, C and Turchetti, B and Cesco, S and Le Roux, G and Tonon, G and Vernesi, C and Mimmo, T and Ventura, M and Borruso, L},
title = {Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168159},
doi = {10.1016/j.scitotenv.2023.168159},
pmid = {37923262},
issn = {1879-1026},
abstract = {Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify organic remains, including their morphological description. However, this is strongly constrained by the researcher's ability to identify residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.},
}
@article {pmid37909055,
year = {2023},
author = {Seeber, PA and Palmer, Z and Schmidt, A and Chagas, A and Kitagawa, K and Marinova-Wolff, E and Tafelmaier, Y and Epp, LS},
title = {The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation.},
journal = {Biology letters},
volume = {19},
number = {11},
pages = {20230343},
pmid = {37909055},
issn = {1744-957X},
mesh = {Animals ; Phylogeny ; *Hyaenidae/genetics ; *Genome, Mitochondrial ; DNA ; Perissodactyla/genetics/metabolism ; Fossils ; },
abstract = {The woolly rhinoceros (Coelodonta antiquitatis) is an iconic species of the Eurasian Pleistocene megafauna, which was abundant in Eurasia in the Pleistocene until its demise beginning approximately 10 000 years ago. Despite the early recovery of several specimens from well-known European archaeological sites, including its type specimen (Blumenbach 1799), no genomes of European populations were available so far, and all available genomic data originated exclusively from Siberian populations. Using coprolites of cave hyenas (Crocuta crocuta spelea) recovered from Middle Palaeolithic layers of two caves in Germany (Bockstein-Loch and Hohlenstein-Stadel), we isolated and enriched predator and prey DNA to assemble the first European woolly rhinoceros mitogenomes, in addition to cave hyena mitogenomes. Both coprolite samples produced copious sequences assigned to C. crocuta (27% and 59% mitogenome coverage, respectively) and woolly rhinoceros (Coelodonta antiquitatis; 27% and 81% coverage, respectively). The sequences suggested considerable DNA degradation, which may limit the conclusions to be drawn; however, the mitogenomes of European woolly rhinoceros are genetically distinct from the Siberian woolly rhinoceros, and analyses of the more complete mitogenome suggest a split of the populations potentially coinciding with the earliest fossil records of woolly rhinoceros in Europe.},
}
@article {pmid37908771,
year = {2023},
author = {Zhur, KV and Sharko, FS and Sedov, VV and Dobrovolskaya, MV and Volkov, VG and Maksimov, NG and Seslavine, AN and Makarov, NA and Prokhortchouk, EB},
title = {The Rurikids: The First Experience of Reconstructing the Genetic Portrait of the Ruling Family of Medieval Rus' Based on Paleogenomic Data.},
journal = {Acta naturae},
volume = {15},
number = {3},
pages = {50-65},
pmid = {37908771},
issn = {2075-8251},
abstract = {The Rurikids were the reigning house of Rus', its principalities and, ultimately the Tsardom of Russia, for seven centuries: from the IX to the end of the XVI century. According to the Primary Chronicle (the Tale of Bygone Years), the main chronicle of Rus', the Rurik dynasty was founded by the Varangian prince Rurik, invited to reign in Novgorod in 862, but still there is no direct genetic evidence of the origin of the early Rurikids. This research, for the first time, provides a genome-wide paleogenetic analysis of bone remains belonging to one of the Rurikids, Prince Dmitry Alexandrovich (?-1294), the son of the Grand Prince of Vladimir Alexander Yaroslavich Nevsky (1221-1263). It has been established that his Y chromosome belongs to the N1a haplogroup. Most of the modern Rurikids, according to their genealogies, belonging to the N1a haplogroup, have the most similar variants of Y chromosomes to each other, as well as to the Y chromosome of Prince Dmitry Alexandrovich. Genome-wide data of the medieval and modern Rurikids unequivocally indicates that they belong to the N1a haplogroup of the Y chromosome, starting at least from the XI century (since the time of Prince Yaroslav the Wise). All the other alleged Rurikids, both ancient and modern, being carriers of other haplogroups (R1a, I2a), possess high heterogeneity of the sequence of Y chromosomes, meaning that we cannot confirm their common ancestry. The most probable ancestors of Prince Dmitry Alexandrovich in the male line were the men who left the burial ground Bolshoy Oleny Island on the coast of the Kola Peninsula about 3,600 years ago. The reconstruction of the genome of Prince Dmitry Alexandrovich indicates the contribution of three ancestral components to his origin: (1) the early medieval population of the east of Scandinavia from the island of Oland, (2) representatives of the steppe nomadic peoples of the Eurasian steppes of the Iron Age or the early medieval population of central Europe (steppe nomads from the territory of Hungary), and (3) the ancient East-Eurasian component. Reliable statistics were also obtained when the Scandinavians were replaced with the Medieval Russian Slavic populations of the XI century. Thus, for the first time, we have shown the complex nature of interethnic interactions in the formation of the nobility of medieval Rus' on the example of the ancient Rurikid.},
}
@article {pmid37803274,
year = {2023},
author = {Pittman, M and Wang, Y},
title = {Paleoecology of extinct species.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {59},
pmid = {37803274},
issn = {2730-7182},
mesh = {*DNA, Ancient ; },
abstract = {Recent developments, including new imaging and ancient environmental DNA (aeDNA) technologies, are providing unprecedented insights into the past, which can also help researchers predict future ecological change. BMC Ecology and Evolution has launched a new article Collection on the "Paleoecology of extinct species" to provide an open-access resource for all interested in this multidisciplinary field.},
}
@article {pmid37907573,
year = {2023},
author = {Zedda, N and Meheux, K and Blöcher, J and Diekmann, Y and Gorelik, AV and Kalle, M and Klein, K and Titze, AL and Winkelbach, L and Naish, E and Brou, L and Valotteau, F and Le Brun-Ricalens, F and Burger, J and Brami, M},
title = {Biological and substitute parents in Beaker period adult-child graves.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {18765},
pmid = {37907573},
issn = {2045-2322},
support = {788616//HORIZON EUROPE European Research Council/ ; 466680522//Deutsche Forschungsgemeinschaft/ ; 466680522//Deutsche Forschungsgemeinschaft/ ; BU 1403/19-1//Deutsche Forschungsgemeinschaft/ ; 466680522//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.},
}
@article {pmid37905072,
year = {2023},
author = {Cheng, X and Steinrücken, M},
title = {diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.12.562101},
pmid = {37905072},
abstract = {SUMMARY: Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA (aDNA) sequences and data from evolve-and-resequence (E&amp;R) experiments are generated at a rapid pace. Such data presents unprecedented opportunities to elucidate the dynamics of adaptative genetic variation. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications. Here, we present diplo-locus , an open-source Python package that provides functionality to simulate and perform inference from time-series under the Wright-Fisher diffusion with general diploid selection. The package includes Python modules as well as command-line tools.<br><br>AVAILABILITY: Python package and command-line tool avilable at: https://github.com/steinrue/diplo_locus or https://pypi.org/project/diplo-locus/ .},
}
@article {pmid37904954,
year = {2023},
author = {Poyraz, L and Colbran, LL and Mathieson, I},
title = {Predicting functional consequences of recent natural selection in Britain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.16.562549},
pmid = {37904954},
abstract = {Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation ; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.},
}
@article {pmid37900966,
year = {2023},
author = {Papa, V and Galassi, FM and Varotto, E and Gori, A and Vaccarezza, M},
title = {The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review.},
journal = {Pathogens &amp; immunity},
volume = {8},
number = {1},
pages = {93-116},
pmid = {37900966},
issn = {2469-2964},
abstract = {Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.},
}
@article {pmid37895202,
year = {2023},
author = {Uricoechea Patiño, D and Collins, A and García, OJR and Santos Vecino, G and Cuenca, JVR and Bernal, JE and Benavides Benítez, E and Vergara Muñoz, S and Briceño Balcázar, I},
title = {High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia.},
journal = {Genes},
volume = {14},
number = {10},
pages = {},
pmid = {37895202},
issn = {2073-4425},
support = {Convocatoria interna de 2013 (Internal Call of 2013) as per acta 809 de la comisi&#xf3;n de asuntos generales, proyecto MED-168-2013.//Universidad de La Sabana/ ; },
mesh = {Humans ; Colombia ; *DNA, Mitochondrial/genetics/analysis ; *Genetic Variation/genetics ; Haplotypes/genetics ; Indians, South American ; Genetics, Population ; },
abstract = {The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.},
}
@article {pmid37894136,
year = {2023},
author = {Pusadkar, V and Azad, RK},
title = {Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.},
journal = {Microorganisms},
volume = {11},
number = {10},
pages = {},
pmid = {37894136},
issn = {2076-2607},
abstract = {Taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. Although a number of methods for metagenome profiling have been developed, most of them have been assessed on modern metagenomes or simulated metagenomes mimicking modern metagenomes. Further, a comparative assessment of metagenome profilers on simulated metagenomes representing a spectrum of degradation depth, from the extremity of ancient (most degraded) to current or modern (not degraded) metagenomes, has not yet been performed. To understand the strengths and weaknesses of different metagenome profilers, we performed their comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes. All classes of profilers, namely, DNA-to-DNA, DNA-to-protein, and DNA-to-marker comparison-based profilers were evaluated on metagenomes with varying levels of damage simulating deamination, fragmentation, and contamination. Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. Further, the DNA-to-DNA (e.g., Kraken2, Bracken) and DNA-to-marker (e.g., MetaPhlAn4) based profiling approaches showed complementary strengths, which can be leveraged to elevate the state-of-the-art of ancient metagenome profiling.},
}
@article {pmid37884848,
year = {2023},
author = {},
title = {Ancient DNA reveals traces of elusive first humans in Europe.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37884848},
issn = {1476-4687},
}
@article {pmid37876815,
year = {2023},
author = {Duitama González, C and Rangavittal, S and Vicedomini, R and Chikhi, R and Richard, H},
title = {aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.},
journal = {iScience},
volume = {26},
number = {11},
pages = {108057},
pmid = {37876815},
issn = {2589-0042},
abstract = {Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.},
}
@article {pmid37873879,
year = {2023},
author = {Kim, AS and Kreiner, JM and Hernández, F and Bock, DG and Hodgins, KA and Rieseberg, LH},
title = {Temporal collections to study invasion biology.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17176},
pmid = {37873879},
issn = {1365-294X},
abstract = {Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.},
}
@article {pmid37872569,
year = {2023},
author = {Pochon, Z and Bergfeldt, N and Kırdök, E and Vicente, M and Naidoo, T and van der Valk, T and Altınışık, NE and Krzewińska, M and Dalén, L and Götherström, A and Mirabello, C and Unneberg, P and Oskolkov, N},
title = {aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {242},
pmid = {37872569},
issn = {1474-760X},
abstract = {Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.},
}
@article {pmid37868041,
year = {2023},
author = {Skantharajah, N and Baichoo, S and Boughtwood, TF and Casas-Silva, E and Chandrasekharan, S and Dave, SM and Fakhro, KA and Falcon de Vargas, AB and Gayle, SS and Gupta, VK and Hendricks-Sturrup, R and Hobb, AE and Li, S and Llamas, B and Lopez-Correa, C and Machirori, M and Melendez-Zajgla, J and Millner, MA and Page, AJH and Paglione, LD and Raven-Adams, MC and Smith, L and Thomas, EM and Kumuthini, J and Corpas, M},
title = {Equity, diversity, and inclusion at the Global Alliance for Genomics and Health.},
journal = {Cell genomics},
volume = {3},
number = {10},
pages = {100386},
pmid = {37868041},
issn = {2666-979X},
abstract = {A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.},
}
@article {pmid37767965,
year = {2023},
author = {Grathwol, F and Roos, C and Zinner, D and Hume, B and Porcier, SM and Berthet, D and Cuisin, J and Merker, S and Ottoni, C and Van Neer, W and Dominy, NJ and Kopp, GH},
title = {Adulis and the transshipment of baboons during classical antiquity.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.87513},
pmid = {37767965},
issn = {2050-084X},
support = {Young Scholar Fund//Universit&#xe4;t Konstanz/ ; Centre of Excellence 2117 Centre for the Advanced Study of Collective Behaviour" ID: 422037984"//Deutsche Forschungsgemeinschaft/ ; Zukunftskolleg//Universit&#xe4;t Konstanz/ ; Open Access Fund//Max-Planck-Gesellschaft/ ; Hector Pioneer Fellowship//Hector Stiftung II/ ; Die Junge Akademie//Deutsche Akademie der Naturforscher Leopoldina - Nationale Akademie der Wissenschaften/ ; Excellence Strategy of the German Federal and State Governments//Bundesministerium f&#xfc;r Bildung und Forschung/ ; bwHPC//Ministerium f&#xfc;r Wissenschaft, Forschung und Kunst Baden-W&#xfc;rttemberg/ ; INST 37/935- 1 FUGG//Deutsche Forschungsgemeinschaft/ ; ANR-11-LABX-0032-01//Agence Nationale de la Recherche/ ; Centre of Excellence 2117 "Centre for the Advanced Study of Collective Behaviour" ID: 422037984//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers-Agatharchides of Cnidus, Pliny the Elder, Strabo-noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud ('Valley of the Monkeys'), Egypt. Dated to ca. 800-540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five centuries. Previously, Dominy et al. (2020) used stable isotope analysis to show that two New Kingdom specimens of Papio hamadryas originate from the Horn of Africa. Here, we report the complete mitochondrial genomes from a mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of P. hamadryas in Eritrea, Ethiopia, and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, corroborates Greco-Roman historiographies by pointing toward present-day Eritrea, and by extension Adulis, as a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history.},
}
@article {pmid37852263,
year = {2023},
author = {Tao, L and Yuan, H and Zhu, K and Liu, X and Guo, J and Min, R and He, H and Cao, D and Yang, X and Zhou, Z and Wang, R and Zhao, D and Ma, H and Chen, J and Zhao, J and Li, Y and He, Y and Suo, D and Zhang, R and Li, S and Li, L and Yang, F and Li, H and Zhang, L and Jin, L and Wang, CC},
title = {Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.09.055},
pmid = {37852263},
issn = {1879-0445},
abstract = {The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.[1][,][2] However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.},
}
@article {pmid37844237,
year = {2023},
author = {Lucquin, A and Robson, HK and Oras, E and Lundy, J and Moretti, G and González Carretero, L and Dekker, J and Demirci, &#xd6; and Dolbunova, E and McLaughlin, TR and Piezonka, H and Talbot, HM and Adamczak, K and Czekaj-Zastawny, A and Groß, D and Gumiński, W and Hartz, S and Kabaciński, J and Koivisto, S and Linge, TE and Meyer, AK and Mökkönen, T and Philippsen, B and Piličiauskas, G and Visocka, V and Kriiska, A and Raemaekers, D and Meadows, J and Heron, C and Craig, OE},
title = {The impact of farming on prehistoric culinary practices throughout Northern Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {43},
pages = {e2310138120},
doi = {10.1073/pnas.2310138120},
pmid = {37844237},
issn = {1091-6490},
support = {695539//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; R1850601//British Academy (The British Academy)/ ; NA//Riksbankens Jubileumsfond (RJ)/ ; PSG492//Eesti Teadusagentuur (ETAg)/ ; 22-1518//Augustinus Fonden (Augustinus Foundation)/ ; 956351//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; 322331//Academy of Finland (AKA)/ ; 2017/27/B/HS3/00478//Narodowe Centrum Nauki (NCN)/ ; 101079396//EC | Horizon Europe | Coordination and support action (CSA)/ ; 10063975//UKRI | Innovate UK/ ; 856488//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {Animals ; Humans ; *Archaeology ; *Agriculture ; Europe ; Farms ; Farmers ; },
abstract = {To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.},
}
@article {pmid37066254,
year = {2023},
author = {Vilgalys, TP and Klunk, J and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB},
title = {Reply to Barton et al: signatures of natural selection during the Black Death.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37066254},
abstract = {Barton et al.[1] raise several statistical concerns regarding our original analyses[2] that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10[-5]), falling below the Bonferroni-corrected significance threshold recommended by Barton et al. Importantly, the evidence for selection on ERAP2 is further supported by functional data demonstrating the impact of the ERAP2 genotype on the immune response to Y. pestis and by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.},
}
@article {pmid37836192,
year = {2023},
author = {Papalini, S and Di Vittori, V and Pieri, A and Allegrezza, M and Frascarelli, G and Nanni, L and Bitocchi, E and Bellucci, E and Gioia, T and Pereira, LG and Susek, K and Tenaillon, M and Neumann, K and Papa, R},
title = {Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {19},
pages = {},
pmid = {37836192},
issn = {2223-7747},
support = {862862//European Union's Horizon 2020 research and innovation programme/ ; 20177RL4KL//Italian Government (MIUR)/ ; },
abstract = {Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.},
}
@article {pmid37830773,
year = {2023},
author = {Muschick, M and Jemmi, E and Lengacher, N and Hänsch, S and Wales, N and Kishe, MA and Mwaiko, S and Dieleman, J and Lever, MA and Salzburger, W and Verschuren, D and Seehausen, O},
title = {Ancient DNA is preserved in fish fossils from tropical lake sediments.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17159},
pmid = {37830773},
issn = {1365-294X},
support = {CRSII5_183566//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 324249//FP7 Ideas: European Research Council/ ; //Strategy pool of the Faculty of Natural Sciences of the University of Bern/ ; 11-97251-000-INP//MacArthur Foundation/ ; },
abstract = {Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.},
}
@article {pmid37829208,
year = {2022},
author = {Atağ, G and Vural, KB and Kaptan, D and Özkan, M and Koptekin, D and Sağlıcan, E and Doğramacı, S and Köz, M and Yılmaz, A and Söylev, A and Togan, &#x130; and Somel, M and Özer, F},
title = {MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes.},
journal = {Open research Europe},
volume = {2},
number = {},
pages = {100},
pmid = {37829208},
issn = {2732-5121},
abstract = {A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.},
}
@article {pmid37828091,
year = {2023},
author = {Breglia, F and Bouby, L and Wales, N and Ivorra, S and Fiorentino, G},
title = {Disentangling the origins of viticulture in the western Mediterranean.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {17284},
pmid = {37828091},
issn = {2045-2322},
support = {ANR-22-CE27-0026//ANR MICA project/ ; 842577//European Union's Horizon 2020/ ; },
abstract = {We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.},
}
@article {pmid37821799,
year = {2023},
author = {Reeves, IM and Totterdell, JA and Betty, EL and Donnelly, DM and George, A and Holmes, S and Moller, L and Stockin, KA and Wellard, R and White, C and Foote, AD},
title = {Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esad058},
pmid = {37821799},
issn = {1465-7333},
support = {ERC-COG-101045346/ERC_/European Research Council/International ; },
abstract = {Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom," washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.},
}
@article {pmid37819893,
year = {2023},
author = {Reynoso-García, J and Santiago-Rodriguez, TM and Narganes-Storde, Y and Cano, RJ and Toranzos, GA},
title = {Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292077},
pmid = {37819893},
issn = {1932-6203},
abstract = {Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.},
}
@article {pmid37819677,
year = {2023},
author = {Marchi, N and Kapopoulou, A and Excoffier, L},
title = {Demogenomic inference from spatially and temporally heterogeneous samples.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13877},
pmid = {37819677},
issn = {1755-0998},
support = {310030_188883/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.},
}
@article {pmid37810237,
year = {2023},
author = {Gînguță, A and Kovács, B and Schütz, O and Tihanyi, B and Nyerki, E and Maár, K and Maróti, Z and Varga, GIB and Băcueț-Crișan, D and Keresztes, T and Török, T and Neparáczki, E},
title = {Genetic identification of members of the prominent Báthory aristocratic family.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107911},
pmid = {37810237},
issn = {2589-0042},
abstract = {The Báthory family was one of the most powerful noble families in the medieval Hungarian Kingdom. Their influence peaked during the Ottoman occupation of Hungary, when the only partially autonomous region of the country was Transylvania, under Turkish protectorate. Several members of the family became Princes of Transylvania, and one of them, István Báthory, was also the elected King of Poland. We hereby present the first genetic data about this extinct family. Archaeological excavations in Pericei, a settlement now part of Romania, revealed the former family chapel of the Báthory family. Through this work, two Báthory family members were successfully identified among the 13 skeletons found at the site. The presence of Y chromosome haplogroup R-S498 fits the historical account describing the family's German (Swabian) origins. Their genomic composition also indicates a family of Germanic origin that intermixed with medieval Hungarians.},
}
@article {pmid37810206,
year = {2023},
author = {Menéndez, LP and Barbieri, C and López Cruz, IG and Schmelzle, T and Breidenstein, A and Barquera, R and Borzi, G and Schuenemann, VJ and Sánchez-Villagra, MR},
title = {On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis.},
journal = {Swiss journal of palaeontology},
volume = {142},
number = {1},
pages = {26},
pmid = {37810206},
issn = {1664-2384},
abstract = {The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.},
}
@article {pmid37809321,
year = {2023},
author = {Dillon, EM and Dunne, EM and Womack, TM and Kouvari, M and Larina, E and Claytor, JR and Ivkić, A and Juhn, M and Carmona, PSM and Robson, SV and Saha, A and Villafaña, JA and Zill, ME},
title = {Challenges and directions in analytical paleobiology.},
journal = {Paleobiology},
volume = {49},
number = {3},
pages = {377-393},
pmid = {37809321},
issn = {0094-8373},
abstract = {Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.},
}
@article {pmid37808674,
year = {2023},
author = {Tretmanis, JM and Jay, F and Ávila-Arcos, MC and Huerta-Sanchez, E},
title = {Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.09.28.560049},
pmid = {37808674},
abstract = {UNLABELLED: Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (∼ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.<br><br>AVAILABILITY: All software used for simulation and analysis is available at github.com/Jazpy/Paleogenomic-Datasim.},
}
@article {pmid37797036,
year = {2023},
author = {Dalén, L and Heintzman, PD and Kapp, JD and Shapiro, B},
title = {Deep-time paleogenomics and the limits of DNA survival.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6666},
pages = {48-53},
doi = {10.1126/science.adh7943},
pmid = {37797036},
issn = {1095-9203},
abstract = {Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.},
}
@article {pmid37797028,
year = {2023},
author = {Burbano, HA and Gutaker, RM},
title = {Ancient DNA genomics and the renaissance of herbaria.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6666},
pages = {59-63},
doi = {10.1126/science.adi1180},
pmid = {37797028},
issn = {1095-9203},
mesh = {*DNA, Ancient ; *Genomics ; Plants/genetics ; },
abstract = {Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.},
}
@article {pmid37797024,
year = {2023},
author = {Ávila-Arcos, MC and Raghavan, M and Schlebusch, C},
title = {Going local with ancient DNA: A review of human histories from regional perspectives.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6666},
pages = {53-58},
doi = {10.1126/science.adh8140},
pmid = {37797024},
issn = {1095-9203},
abstract = {Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.},
}
@article {pmid37797011,
year = {2023},
author = {Curry, A},
title = {Family ties.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6666},
pages = {24-27},
doi = {10.1126/science.adl1577},
pmid = {37797011},
issn = {1095-9203},
abstract = {Giant family trees based on ancient DNA from thousands of people are revealing prehistoric politics and social structure.},
}
@article {pmid37771087,
year = {2023},
author = {Moaz, I and Fouad, FA and Elmasry, H and Tarek, G and Elzoheiry, A and Elgamal, M and Ibrahim, R and Hisham, Y and Safwat, G and Kamel, MM and El-Batal, HM and Fouda, M},
title = {Associations Between Serum Soluble Toll-like Receptors 4 and 9 and Breast Cancer in Egyptian Patients.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {30},
number = {},
pages = {10732748231204755},
pmid = {37771087},
issn = {1526-2359},
abstract = {BACKGROUND: Toll-like receptors (TLRs) play an important role in regulation of immune cells and are vital in tumorigenesis due to its crucial role in inflammatory microenvironment regulation, as they promote the synthesis and release of inflammatory cytokines and chemokines. Toll-like receptors 4 and TLRs 9 were found to be highly expressed in breast cancer. The aim of this study is to investigate the soluble toll-like receptors 4 and 9 (sTLR4 and sTLR9) as potential biomarkers for diagnosis and prognosis of breast cancer and their association with the clinicopathological parameters of breast cancer.<br><br>PATIENTS AND METHOD: In this retrospective case-control study, 186 female subjects were recruited and divided into three groups, Group I: 62 healthy control, Group II: 62 subjects diagnosed with non-metastatic breast cancer, and Group III: 62 subjects diagnosed with metastatic breast cancer. Enzyme-linked immunosorbent assay (ELISA) technique was used to quantify the levels of sTLR4 and sTLR9 in serum.<br><br>RESULTS: Both non-metastatic and metastatic groups showed significant higher levels of both serum sTLR4 and sTLR9 expression compared to healthy controls. Only sTLR9 was significantly increased among metastatic patients compared to non-metastatic group. Serum levels of sTLR9 and sTLR4 were still significantly associated with breast cancer in a multiple logistic regression model (P = <.001). ROC curves showed that both sTLR4 and sTLR9 can be a significant parameter to discriminate between normal females and breast cancer patients.<br><br>CONCLUSION: Soluble toll-like receptors 4 and sTLR9 are over-expressed in patients with metastatic and non-metastatic BC than in benign cases. The expression levels of sTLR4 and TLR9 have clinical interest as indicators of tumor aggressiveness suggested to be prognostic biomarkers. Toll-like receptors may represent therapeutic targets in breast cancer.},
}
@article {pmid37752842,
year = {2023},
author = {Ruiz-Puerta, EJ and Keighley, X and Desjardins, SPA and Gotfredsen, AB and Pan, SE and Star, B and Boessenkool, S and Barrett, JH and McCarthy, ML and Andersen, LW and Born, EW and Howse, LR and Szpak, P and Pálsson, S and Malmquist, HJ and Rufolo, S and Jordan, PD and Olsen, MT},
title = {Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2007},
pages = {20231349},
pmid = {37752842},
issn = {1471-2954},
abstract = {Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.},
}
@article {pmid37752477,
year = {2023},
author = {Kroes, R and Winkel, Y and Breeuwer, JAJ and van Loon, EE and Loader, SP and Maclaine, JS and Verdonschot, PFM and van der Geest, HG},
title = {Phylogenetic analysis of museum specimens of houting Coregonus oxyrinchus shows the need for a revision of its extinct status.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {57},
pmid = {37752477},
issn = {2730-7182},
abstract = {According to the IUCN Red List the anadromous houting Coregonus oxyrinchus is categorized as 'extinct'. However, this extinct status might be incorrect because taxonomic difference between C. oxyrinchus and the closely related C. lavaretus is based on a disputable morphological comparison. Also, phylogenetic studies on mtDNA only focused on recent obtained coregonids. We are the first to perform a mtDNA analysis on both historic and recent specimens, including the syntype specimen which was used for species description by Linnaeus originally. Two primer pairs for mitochondrial CytB and ND3 were used to extract sequences for phylogenetic analysis. Sequences from 14 out of 21 C. oxyrinchus museum specimens were successfully obtained and compared with sequences from recent obtained C. lavaretus. The sequences were combined with GenBank data from a previous phylogenetic study on houting to create a phylogenetic tree and two minimum spanning haplotype networks. Results show that C. oxyrinchus and C. lavaretus form a clade with limited genetic variation. Low bootstrap values also show weak support for geographical patterns in distribution of mitochondrial haplotypes. Statistical analysis of the haplotype networks also shows that historic and recent specimens are similar species. Our results suggest that C. oxyrinchus is a junior synonym of C. lavaretus. A definitive taxonomic revision could not be made because only CytB sequencing was successful for the syntype specimen. We discuss taxonomic consequences and the species-specific focus in nature conservation. We propose a shift in nature conservation to a more functional approach based on traits rather than species.},
}
@article {pmid37268008,
year = {2023},
author = {Guzmán-Solís, AA and Navarro, MA and Ávila-Arcos, MC and Blanco-Melo, D},
title = {A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History.},
journal = {Annual review of virology},
volume = {10},
number = {1},
pages = {49-75},
doi = {10.1146/annurev-virology-111821-123859},
pmid = {37268008},
issn = {2327-0578},
abstract = {Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.},
}
@article {pmid37744037,
year = {2023},
author = {Singh, PP and Kumar, S and Pasupuleti, N and Weerasooriya, PR and van Driem, G and Tennekoon, KH and Rai, N and Chaubey, G and Ranasinghe, R},
title = {Reconstructing the population history of the Sinhalese, the major ethnic group in Śrī Laṅkā.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107797},
pmid = {37744037},
issn = {2589-0042},
abstract = {The Sinhalese are the major ethnic group in Śrī Laṅkā, inhabiting nearly the whole length and breadth of the island. They speak an Indo-European language of the Indo-Iranian branch, which is held to originate in northwestern India, going back to at least the fifth century BC. Previous genetic studies on low-resolution markers failed to infer the genomic history of the Sinhalese population. Therefore, we have performed a high-resolution fine-grained genetic study of the Sinhalese population and, in the broader context, we attempted to reconstruct the genetic history of Śrī Laṅkā. Our allele-frequency-based analysis showed a tight cluster of Sinhalese and Tamil populations, suggesting strong gene flow beyond the boundary of ethnicity and language. Interestingly, the haplotype-based analysis preserved a trace of the North Indian affiliation to the Sinhalese population. Overall, in the South Asian context, Śrī Laṅkān ethnic groups are genetically more homogeneous than others.},
}
@article {pmid37738339,
year = {2023},
author = {Oliveira, S and Fehn, AM and Amorim, B and Stoneking, M and Rocha, J},
title = {Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.},
journal = {Science advances},
volume = {9},
number = {38},
pages = {eadh3822},
pmid = {37738339},
issn = {2375-2548},
mesh = {Humans ; *Black People/genetics ; *DNA, Ancient ; Namibia ; },
abstract = {Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.},
}
@article {pmid37719142,
year = {2023},
author = {Wang, K and Prüfer, K and Krause-Kyora, B and Childebayeva, A and Schuenemann, VJ and Coia, V and Maixner, F and Zink, A and Schiffels, S and Krause, J},
title = {High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry.},
journal = {Cell genomics},
volume = {3},
number = {9},
pages = {100377},
pmid = {37719142},
issn = {2666-979X},
abstract = {The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.},
}
@article {pmid37718006,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Austin, JJ},
title = {From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates.},
journal = {Science &amp; justice : journal of the Forensic Science Society},
volume = {63},
number = {5},
pages = {588-597},
doi = {10.1016/j.scijus.2023.07.003},
pmid = {37718006},
issn = {1876-4452},
mesh = {Humans ; *Touch ; *Coloring Agents ; Crime ; DNA ; },
abstract = {Titanium dioxide (titania, TiO2) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO2 causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO2-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated. DNA in saliva and touch samples deposited on self-cleaning glass slides exposed to indoor fluorescent light for up to seven days was more degraded than control samples indicating some degree of fluorescent light-induced photocatalytic activity of the self-cleaning surfaces. When exposed to sunlight, DNA yields from saliva and touch samples deposited on the titania-coated substrates decreased rapidly, with a corresponding increase in DNA degradation. After three days no DNA samples applied to self-cleaning glass and exposed to natural sunlight yielded STR profiles. These results suggest that the photocatalytic activation of TiO2 is the likely mechanism of action underlying the extreme DNA degradation on the Bioclean® and SaniTise™ glasses. Consequently, rapid sample collection and use may be warranted in casework scenarios involving TiO2-coated materials.},
}
@article {pmid37717498,
year = {2023},
author = {Díaz-Navarro, S and Haber Uriarte, M and García-González, R},
title = {Holes in the Head. Double cranial surgery on an individual from the Chalcolithic burial site of Camino del Molino (SE Spain).},
journal = {International journal of paleopathology},
volume = {43},
number = {},
pages = {22-30},
doi = {10.1016/j.ijpp.2023.09.003},
pmid = {37717498},
issn = {1879-9825},
abstract = {OBJECTIVE: This article analyses new prehistoric evidence of trepanation from a collective burial site in the south-eastern Iberian Peninsula.<br><br>MATERIALS: The trepanned individual was documented in the Chalcolithic burial site of Camino del Molino, where 1348 individuals (30.7 % non-adults and 69.3 % adults) were deposited in two contiguous funerary phases, making it a reference site for the knowledge of Recent Prehistoric populations.<br><br>METHODS: The individual has been sexed using traditional anthropological methods and ancient DNA. C14 dating has also been obtained. The lesion has been analysed macroscopically and microscopically using SEM.<br><br>RESULTS: The skull under study belonged to an adult female deposited in the second burial phase (2566-2239 years cal BCE). It exhibits in the anterior region of the right temporal fossa two contiguous and partially overlapping holes that correspond to two trepanations performed using the scraping technique.<br><br>CONCLUSIONS: It is a double cranial trepanation with signs of bone remodelling suggesting survival from surgery. No pathological signs were identified potentially associated with the intervention.<br><br>SIGNIFICANCE: This is the second case of surgical interventions in the geographical area of study and one of the few evidences of this practice in women during prehistoric times.<br><br>LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed.<br><br>Further intensive review of skull collection is advised to learn more about these surgical interventions in Copper Age and to go deeper into the causes that motivated their execution.},
}
@article {pmid37712846,
year = {2023},
author = {Davidson, R and Williams, MP and Roca-Rada, X and Kassadjikova, K and Tobler, R and Fehren-Schmitz, L and Llamas, B},
title = {Allelic bias when performing in-solution enrichment of ancient human DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13869},
pmid = {37712846},
issn = {1755-0998},
support = {DE190101069//Australian Research Council/ ; FT170100448//Australian Research Council/ ; 1515138//National Science Foundation/ ; },
abstract = {In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.},
}
@article {pmid37704050,
year = {2023},
author = {Bruno, F and Abondio, P and Bruno, R and Ceraudo, L and Pararazzo, E and Citrigno, L and Luiselli, D and Bruni, AC and Passarino, G and Colao, R and Maletta, R and Montesanto, A},
title = {Alzheimer's Disease as A Viral Infectious Disease: Revisiting the Infectious Hypothesis.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102068},
doi = {10.1016/j.arr.2023.102068},
pmid = {37704050},
issn = {1872-9649},
abstract = {Alzheimer's disease (AD) represents the most frequent type of dementia in elderly people. Two major forms of the disease exist: sporadic - the causes of which have not yet been fully understood - and familial - inherited within families from generation to generation, with a clear autosomal dominant transmission of mutations in Presenilin 1 (PSEN1), 2 (PSEN2) or Amyloid Precursors Protein (APP) genes. The main hallmark of AD consists of extracellular deposits of amyloid-beta (Aβ) peptide and intracellular deposits of the hyperphosphorylated form of the tau protein (p-tau). An ever-growing body of research supports the viral infectious hypothesis of sporadic forms of AD. In particular, it has been shown that several herpes viruses (i.e., HHV-1, HHV-2, HHV-3 or varicella zoster virus, HHV-4 or Epstein Barr virus, HHV-5 or cytomegalovirus, HHV-6A and B, HHV-7), flaviviruses (i.e., Zika virus, Dengue fever virus, Japanese encephalitis virus) as well as Human Immunodeficiency Virus (HIV), the hepatitis viruses (HAV, HBV, HCV, HDV, HEV), SARS-CoV2, Ljungan virus (LV), Influenza A virus and Borna disease virus, could increase the risk of AD. Here, we summarized and discussed these results. Based on these findings, significant issues for future studies are also put forward.},
}
@article {pmid37701515,
year = {2022},
author = {Jaramillo-Valverde, L and Vásquez-Domínguez, A and Levano, KS and Castrejon-Cabanillas, R and Novoa-Bellota, P and Machacuay-Romero, M and Garcia-de-la-Guarda, R and Cano, RJ and Shady Solis, R and Guio, H},
title = {A mobile lab for ancient DNA extraction in Perug.},
journal = {Bioinformation},
volume = {18},
number = {12},
pages = {1114-1118},
pmid = {37701515},
issn = {0973-2063},
abstract = {We report the use of a mobile laboratory set up to extract ancient DNA (aDNA) from 34 human coprolites (fossilized faeces) samples. Our approach enabled the rapid genetic characterization of 5,000 years old archeological samples. It is useful for the on-site screening of museums and freshly excavated samples for DNA. This approach is accessible to other investigators as the mobile laboratory was set up using commercially available instruments.},
}
@article {pmid37230884,
year = {2023},
author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , },
title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {10},
pages = {946-960},
doi = {10.1016/j.tree.2023.04.016},
pmid = {37230884},
issn = {1872-8383},
mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; },
abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.},
}
@article {pmid37561011,
year = {2023},
author = {Sánchez-Barreiro, F and De Cahsan, B and Westbury, MV and Sun, X and Margaryan, A and Fontsere, C and Bruford, MW and Russo, IM and Kalthoff, DC and Sicheritz-Pontén, T and Petersen, B and Dalén, L and Zhang, G and Marquès-Bonet, T and Gilbert, MTP and Moodley, Y},
title = {Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.},
journal = {Molecular biology and evolution},
volume = {40},
number = {9},
pages = {},
doi = {10.1093/molbev/msad180},
pmid = {37561011},
issn = {1537-1719},
support = {681396//ERC Consolidator/ ; 7578//EMBO Short-Term Fellowship/ ; //National Research Foundation/ ; },
abstract = {The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.},
}
@article {pmid37699853,
year = {2023},
author = {Chocholova, E and Roudnicky, P and Potesil, D and Fialova, D and Krystofova, K and Drozdova, E and Zdrahal, Z},
title = {Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.3c00370},
pmid = {37699853},
issn = {1535-3907},
abstract = {Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.},
}
@article {pmid37683613,
year = {2023},
author = {Sandoval-Velasco, M and Jagadeesan, A and Ramos-Madrigal, J and Ávila-Arcos, MC and Fortes-Lima, CA and Watson, J and Johannesdóttir, E and Cruz-Dávalos, DI and Gopalakrishnan, S and Moreno-Mayar, JV and Niemann, J and Renaud, G and Robson Brown, KA and Bennett, H and Pearson, A and Helgason, A and Gilbert, MTP and Schroeder, H},
title = {The ancestry and geographical origins of St Helena's liberated Africans.},
journal = {American journal of human genetics},
volume = {110},
number = {9},
pages = {1590-1599},
doi = {10.1016/j.ajhg.2023.08.001},
pmid = {37683613},
issn = {1537-6605},
mesh = {Humans ; Female ; Male ; *African People ; DNA, Ancient ; Black People/genetics ; *Enslaved Persons ; Genotype ; },
abstract = {The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.},
}
@article {pmid37673908,
year = {2023},
author = {Hodgins, HP and Chen, P and Lobb, B and Wei, X and Tremblay, BJM and Mansfield, MJ and Lee, VCY and Lee, PG and Coffin, J and Duggan, AT and Dolphin, AE and Renaud, G and Dong, M and Doxey, AC},
title = {Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5475},
pmid = {37673908},
issn = {2041-1723},
support = {R01 NS080833/NS/NINDS NIH HHS/United States ; R01 NS117626/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *DNA, Ancient ; Neurotoxins ; *Tetanus ; Phylogeny ; Clostridium ; Chile ; Mammals ; },
abstract = {The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.},
}
@article {pmid37666338,
year = {2023},
author = {Han, W and Zhang, E and Sun, W and Lin, Q and Meng, X and Ni, Z and Ning, D and Shen, J},
title = {Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau.},
journal = {The Science of the total environment},
volume = {904},
number = {},
pages = {166715},
doi = {10.1016/j.scitotenv.2023.166715},
pmid = {37666338},
issn = {1879-1026},
abstract = {Lakes on the Qinghai-Tibet Plateau (QTP) have been subject to multiple environmental pressures from rapid climate change and intensified human activity in recent decades. However, their ecological effects on the lake ecosystem remain largely unclear due to the lack of long-term monitoring data. This study presented the environmental and ecological changes of the lake Yamzhog Yumco (Southern QTP) over the past three decades based on multi-proxy analysis (geochemistry and sedaDNA) on a high-time resolution sediment core. The result showed that the lake exhibited a continuous eutrophication process from 2004 CE, which has accelerated since 2014 CE. The nutrient enrichment was mainly attributed to anthropogenic emissions from the catchment. The sedimentary ancient DNA (sedaDNA) metabarcoding data registered a sensitive response of aquatic communities to the additional nutrient supply. Eukaryotic algae and aquatic invertebrate communities exhibited similar temporal dynamics, characterized by the increase in eutrophic taxa and the decrease in oligotrophic taxa. Change points analysis suggested that lake ecosystems underwent a slight ecological shift in 2003 CE and an abrupt shift in 2012 CE driven by nutrient enrichment. Quantitative analysis revealed that nutrients and human activity accounted for 27.9 % and 21.7 % of the temporal variation in aquatic communities, whereas climate change only explained 6.9 % of the total variation. From a paleolimnological view, our study supported that regional human activity could distinctly alter the nutrient level and aquatic community structure of lake ecosystems in the QTP. Considering that anthropogenic disturbance will continuously increase, it is crucial to strengthen the field monitoring of the lakes on the plateau and make effective management measures to avoid irreversible ecological consequences.},
}
@article {pmid37592021,
year = {2023},
author = {Moots, HM and Antonio, M and Sawyer, S and Spence, JP and Oberreiter, V and Weiß, CL and Lucci, M and Cherifi, YMS and La Pastina, F and Genchi, F and Praxmeier, E and Zagorc, B and Cheronet, O and Özdoğan, KT and Demetz, L and Amrani, S and Candilio, F and De Angelis, D and Gasperetti, G and Fernandes, D and Gao, Z and Fantar, M and Coppa, A and Pritchard, JK and Pinhasi, R},
title = {A genetic history of continuity and mobility in the Iron Age central Mediterranean.},
journal = {Nature ecology &amp; evolution},
volume = {7},
number = {9},
pages = {1515-1524},
pmid = {37592021},
issn = {2397-334X},
mesh = {Mediterranean Region ; Archaeology ; *Human Migration/history ; Humans ; Principal Component Analysis ; Human Genetics ; *DNA, Ancient/analysis ; Sequence Analysis, DNA ; Burial ; Anthropology ; History, Ancient ; },
abstract = {The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. Here, to investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbours together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.},
}
@article {pmid37652999,
year = {2023},
author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ},
title = {Ancient DNA reveals genetic admixture in China during tiger evolution.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {37652999},
issn = {2397-334X},
support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; },
abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.},
}
@article {pmid37652634,
year = {2023},
author = {Beltrame, MO and Moviglia, GS and De Tommaso, D and Quintana, S},
title = {Gastrointestinal parasites of domestic sheep from Patagonia throughout historical times: A paleoparasitological approach.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {44},
number = {},
pages = {100915},
doi = {10.1016/j.vprsr.2023.100915},
pmid = {37652634},
issn = {2405-9390},
mesh = {Animals ; Sheep ; *Parasites ; Sheep, Domestic ; *Intestinal Diseases, Parasitic/veterinary ; *Fascioliasis/veterinary ; Argentina/epidemiology ; *Eimeria ; *Nematodirus ; *Sheep Diseases ; },
abstract = {Sheep husbandry in Patagonia, Argentina, started at the beginning of the 20th century from European settlers. Sanitary management is minimal, which has serious implications for the sheep health. Sheep can be infested by diverse parasites, with well over 150 species of internal and external parasites reported worldwide. Gastrointestinal parasitism is one of the most common and important infections in sheep concerning the health status, and is the cause of significant morbidity and mortality, which generates considerable production losses. The present work is the first paleoparasitological study of sheep coprolites from Patagonia throughout historical times. Fifty-seven coprolites from the 'Cueva Peligro' archaeological site (Patagonia, Argentina) were analyzed using the Lutz spontaneous sedimentation technique and the modified Faust flotation technique. Ancient DNA (aDNA) study was carried out in order to identify the zoological origin of coprolites. The results obtained from Cytb analysis confirmed the identity of the host as Ovis aries (domestic sheep). A total of 39 coprolites examined were positive for parasites by at least one of the studied methods. Thirty eight samples were positive by spontaneous sedimentation and 10 samples were positive by the modified Faust technique. The parasitic fauna found was Trichuris sp. (Trichinellida: Trichuridae), Nematodirus sp., Nematodirus spathiger (Strongylida, Trichostrongyloidea), two unidentified Strongylida-type egg morphotypes, Fasciola hepatica (Trematoda: Digenea) and coccidia oocysts of Eimeria spp. (Apicomplexa: Eimeriidae). The modified Faust technique provided satisfactory results in terms of sensitivity for the detection of Eimeria spp. The use of this methodology as a routine procedure enables the processing of ancient samples, in order to increase recoveries. These results show the importance of integrating different diagnostic approaches in order to optimize parasitic findings. The recorded parasite diversity appears to have not changed over the last 120 years. The study displayed the presence of different parasitic species which suggests potential exposure to parasitic diseases through the historical times, both for sheep and for other domestic and wild mammals from Patagonia. Also, suggests the presence of fasciolosis, a zoonotic disease that implies a potential risk for Patagonian populations in the past.},
}
@article {pmid37644833,
year = {2023},
author = {Aoki, K and Takahata, N and Oota, H and Wakano, JY and Feldman, MW},
title = {Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2005},
pages = {20231262},
doi = {10.1098/rspb.2023.1262},
pmid = {37644833},
issn = {1471-2954},
mesh = {Humans ; *Archaeology ; Asia, Eastern ; *Communicable Diseases ; DNA, Ancient ; East Asian People ; },
abstract = {An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.},
}
@article {pmid37638716,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Simon, C and Henry, JM and Austin, JJ},
title = {Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis.},
journal = {Electrophoresis},
volume = {},
number = {},
pages = {},
doi = {10.1002/elps.202300070},
pmid = {37638716},
issn = {1522-2683},
abstract = {Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.},
}
@article {pmid37631973,
year = {2023},
author = {Burk, RD and Mirabello, L and DeSalle, R},
title = {Distinguishing Genetic Drift from Selection in Papillomavirus Evolution.},
journal = {Viruses},
volume = {15},
number = {8},
pages = {},
pmid = {37631973},
issn = {1999-4915},
support = {CA238592/NH/NIH HHS/United States ; P30CA013330/NH/NIH HHS/United States ; },
mesh = {Phylogeny ; *Papillomaviridae/genetics ; *Alphapapillomavirus ; Genetic Drift ; Codon Usage ; },
abstract = {Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.},
}
@article {pmid37628575,
year = {2023},
author = {Kusliy, MA and Yurlova, AA and Neumestova, AI and Vorobieva, NV and Gutorova, NV and Molodtseva, AS and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Semibratov, VP and Iderkhangai, TO and Kovalev, AA and Erdenebaatar, D and Graphodatsky, AS and Tishkin, AA},
title = {Genetic History of the Altai Breed Horses: From Ancient Times to Modernity.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628575},
issn = {2073-4425},
mesh = {Animals ; Horses/genetics ; Phylogeny ; *Hybridization, Genetic ; *DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes/genetics ; },
abstract = {This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.},
}
@article {pmid37611212,
year = {2023},
author = {van Waaij, J and Li, S and Garcia-Erill, G and Albrechtsen, A and Wiuf, C},
title = {Evaluation of population structure inferred by principal component analysis or the admixture model.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyad157},
pmid = {37611212},
issn = {1943-2631},
abstract = {Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.},
}
@article {pmid37608001,
year = {2023},
author = {Arbøll, TP and Rasmussen, SL and de Jonge, N and Hansen, AH and Pertoldi, C and Nielsen, JL},
title = {Revealing the secrets of a 2900-year-old clay brick, discovering a time capsule of ancient DNA.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13092},
pmid = {37608001},
issn = {2045-2322},
support = {CF19_0669//Carlsbergfondet/ ; 2020-3//Aalborg Zoos Naturbevaringsfond/ ; },
mesh = {Humans ; *DNA, Ancient ; Clay ; Drug Contamination ; *Fractures, Bone ; Iraq ; },
abstract = {The recent development of techniques to sequence ancient DNA has provided valuable insights into the civilisations that came before us. However, the full potential of these methods has yet to be realised. We extracted ancient DNA from a recently exposed fracture surface of a clay brick deriving from the palace of king Ashurnasirpal II (883-859 BCE) in Nimrud, Iraq. We detected 34 unique taxonomic groups of plants. With this research we have made the pioneering discovery that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2900-year-old clay brick. We encourage future research into this subject, as the scientific prospects for this approach are substantial, potentially leading to a deeper understanding of ancient and lost civilisations.},
}
@article {pmid37604894,
year = {2023},
author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L},
title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13635},
pmid = {37604894},
issn = {2045-2322},
support = {RFO//University of Bologna/ ; RFO//University of Bologna/ ; RFO//University of Bologna/ ; COST Action RGB-Net//European Union/ ; },
mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; },
abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.},
}
@article {pmid37589132,
year = {2023},
author = {Essel, E},
title = {Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel.},
journal = {BioTechniques},
volume = {75},
number = {2},
pages = {42-46},
doi = {10.2144/btn-2023-0067},
pmid = {37589132},
issn = {1940-9818},
mesh = {Humans ; Female ; *DNA, Ancient ; *Anthropology ; Body Remains ; Sequence Analysis, DNA ; Universities ; },
abstract = {Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow.},
}
@article {pmid37588383,
year = {2020},
author = {Wang, CC and Robbeets, M},
title = {The homeland of Proto-Tungusic inferred from contemporary words and ancient genomes.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e8},
pmid = {37588383},
issn = {2513-843X},
abstract = {The Tungusic languages form a language family spoken in Xinjiang, Siberia, Manchuria and the Russian Far East. There is a general consensus that these languages are genealogically related and descend from a common ancestral language, conventionally called 'Proto-Tungusic'. However, the exact geographical location where the ancestral speakers of Proto-Tungusic originated from is subject to debate. Here we take an unprecedented approach to this problem, by integrating linguistic, archaeological and genetic evidence in a single study. Our analysis of ancient DNA suggests genetic continuity between an ancient Amur genetic lineage and the contemporary speakers of the Tungusic languages. Adding an archaeolinguistic perspective, we infer that the most plausible homeland for the speakers of Proto-Tungusic is the region around Lake Khanka in the Russian Far East. Our study pushes the field forward in answering the tantalizing question about the location of the Tungusic homeland and in illustrating how these three disciplines can converge into a holistic approach to the human past.},
}
@article {pmid37580949,
year = {2023},
author = {Bretschneider, A and Mazanec, J and Wittmeier, P and Flux, AL and Schmidt, D and Hummel, S},
title = {X-chromosomal STRs in aDNA kinship analysis.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {},
number = {},
pages = {},
doi = {10.1127/anthranz/2023/1714},
pmid = {37580949},
issn = {0003-5548},
abstract = {The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.},
}
@article {pmid37567955,
year = {2023},
author = {Kim, J and Rosenberg, NA},
title = {Record-matching of STR profiles with fragmentary genomic SNP data.},
journal = {European journal of human genetics : EJHG},
volume = {},
number = {},
pages = {},
pmid = {37567955},
issn = {1476-5438},
support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; },
abstract = {In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.},
}
@article {pmid37588356,
year = {2020},
author = {Cui, Y and Zhang, F and Ma, P and Fan, L and Ning, C and Zhang, Q and Zhang, W and Wang, L and Robbeets, M},
title = {Bioarchaeological perspective on the expansion of Transeurasian languages in Neolithic Amur River basin.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e15},
pmid = {37588356},
issn = {2513-843X},
abstract = {Owing to the development of sequencing technology, paleogenomics has become an important source of information on human migration and admixture, complementing findings from archaeology and linguistics. In this study, we retrieved the whole genome and Y chromosome lineage from late Neolithic Honghe individuals in the Middle Amur region in order to provide a bioarchaeological perspective on the origin and expansion of Transeurasian languages in the Amur River basin. Our genetic analysis reveals that the population of the Amur River basin has a stable and continuous genetic structure from the Mesolithic Age up to date. Integrating linguistic and archaeological evidence, we support the hypothesis that the expansion of the Transeurasian language system in the Amur River basin is related to the agricultural development and expansion of the southern Hongshan culture. The spread of agricultural technology resulted in the addition of millet cultivation to the original subsistence mode of fishing and hunting. It played a vital role in the expansion of the population of the region, which in its turn has contributed to the spread of language.},
}
@article {pmid37588379,
year = {2020},
author = {Hudson, MJ and Nakagome, S and Whitman, JB},
title = {The evolving Japanese: the dual structure hypothesis at 30.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e6},
pmid = {37588379},
issn = {2513-843X},
abstract = {The population history of Japan has been one of the most intensively studied anthropological questions anywhere in the world, with a huge literature dating back to the nineteenth century and before. A growing consensus over the 1980s that the modern Japanese comprise an admixture of a Neolithic population with Bronze Age migrants from the Korean peninsula was crystallised in Kazurō Hanihara's influential 'dual structure hypothesis' published in 1991. Here, we use recent research in biological anthropology, historical linguistics and archaeology to evaluate this hypothesis after three decades. Although the major assumptions of Hanihara's model have been supported by recent work, we discuss areas where new findings have led to a re-evaluation of aspects of the hypothesis and emphasise the need for further research in key areas including ancient DNA and archaeology.},
}
@article {pmid37562011,
year = {2023},
author = {Gerber, D and Szeifert, B and Székely, O and Egyed, B and Gyuris, B and Giblin, JI and Horváth, A and Köhler, K and Kulcsár, G and Kustár, &#xc1; and Major, I and Molnár, M and Palcsu, L and Szeverényi, V and Fábián, S and Mende, BG and Bondár, M and Ari, E and Kiss, V and Szécsényi-Nagy, A},
title = {AInterdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad182},
pmid = {37562011},
issn = {1537-1719},
abstract = {In this study we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures (3530-1620 cal BCE). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture related population and one from a previously unrecognised source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe, but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analysing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.},
}
@article {pmid37559969,
year = {2023},
author = {Ozga, AT and Ottoni, C},
title = {Dental calculus as a proxy for animal microbiomes.},
journal = {Quaternary international : the journal of the International Union for Quaternary Research},
volume = {653-654},
number = {},
pages = {47-52},
pmid = {37559969},
issn = {1040-6182},
abstract = {The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.},
}
@article {pmid37559898,
year = {2023},
author = {Ciucani, MM and Ramos-Madrigal, J and Hernández-Alonso, G and Carmagnini, A and Aninta, SG and Sun, X and Scharff-Olsen, CH and Lanigan, LT and Fracasso, I and Clausen, CG and Aspi, J and Kojola, I and Baltrūnaitė, L and Balčiauskas, L and Moore, J and Åkesson, M and Saarma, U and Hindrikson, M and Hulva, P and Bolfíková, B&#x10c; and Nowak, C and Godinho, R and Smith, S and Paule, L and Nowak, S and Mysłajek, RW and Lo Brutto, S and Ciucci, P and Boitani, L and Vernesi, C and Stenøien, HK and Smith, O and Frantz, L and Rossi, L and Angelici, FM and Cilli, E and Sinding, MS and Gilbert, MTP and Gopalakrishnan, S},
title = {The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs.},
journal = {iScience},
volume = {26},
number = {8},
pages = {107307},
pmid = {37559898},
issn = {2589-0042},
abstract = {The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.},
}
@article {pmid37548135,
year = {2023},
author = {Arencibia, V and Muñoz, M and Crespo, CM and Russo, MG and Vera, P and Lia, VV and García Guraieb, S and Goñi, RA and Avena, S and Puebla, A and Dejean, CB},
title = {Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24822},
pmid = {37548135},
issn = {2692-7691},
support = {PICT 2014-3012//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; //Fundaci&#xf3;n Cient&#xed;fica Felipe Fiorellino/ ; //Fundaci&#xf3;n de Historia Natural F&#xe9;lix Azara/ ; UBACyT 20020150200233BA//Universidad de Buenos Aires/ ; UBACyT 20020170200363BA//Universidad de Buenos Aires/ ; //CONICET/ ; },
abstract = {OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia.<br><br>MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network.<br><br>RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (&#x2265;1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established.<br><br>DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.},
}
@article {pmid37541241,
year = {2023},
author = {Harney, &#xc9; and Sirak, K and Sedig, J and Micheletti, S and Curry, R and Ancona Esselmann, S and Reich, D},
title = {Ethical considerations when co-analyzing ancient DNA and data from private genetic databases.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2023.06.011},
pmid = {37541241},
issn = {1537-6605},
abstract = {Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.},
}
@article {pmid37537290,
year = {2023},
author = {Callaway, E},
title = {Ancient DNA reveals the living descendants of enslaved people through 23andMe.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37537290},
issn = {1476-4687},
}
@article {pmid37535713,
year = {2023},
author = {Jackson, FLC},
title = {Community-initiated genomics.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6657},
pages = {482-483},
doi = {10.1126/science.adj2380},
pmid = {37535713},
issn = {1095-9203},
abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.},
}
@article {pmid37529780,
year = {2023},
author = {Zhao, C and Han, B and Yi, G and Jin, S and Zhang, Z and Li, S},
title = {Editorial: Epigenomics implication for economic traits in domestic animals.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1252640},
doi = {10.3389/fgene.2023.1252640},
pmid = {37529780},
issn = {1664-8021},
}
@article {pmid37528780,
year = {2023},
author = {Fesenko, DO and Aramova, OY and Vdovchenkov, EV and Ivanovsky, ID and Fesenko, OE and Polyakov, SA and Faleeva, TG and Filippova, MA and Florinskaya, VS and Kornienko, IV},
title = {[DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia].},
journal = {Molekuliarnaia biologiia},
volume = {57},
number = {4},
pages = {597-608},
pmid = {37528780},
issn = {0026-8984},
abstract = {Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate.},
}
@article {pmid37528222,
year = {2023},
author = {Delsol, N and Stucky, BJ and Oswald, JA and Cobb, CR and Emery, KF and Guralnick, R},
title = {Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12444},
pmid = {37528222},
issn = {2045-2322},
support = {1930628//National Science Foundation/ ; },
abstract = {Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.},
}
@article {pmid37525572,
year = {2023},
author = {Tamburrini, C and Dahinten, SL and Saihueque, RRR and Ávila-Arcos, MC and Parolin, ML},
title = {Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24821},
pmid = {37525572},
issn = {2692-7691},
abstract = {Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.},
}
@article {pmid37523413,
year = {2023},
author = {Long, GS and Hider, J and Duggan, AT and Klunk, J and Eaton, K and Karpinski, E and Giuffra, V and Ventura, L and Prowse, TL and Fornaciari, A and Fornaciari, G and Holmes, EC and Golding, GB and Poinar, HN},
title = {A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade.},
journal = {PLoS pathogens},
volume = {19},
number = {7},
pages = {e1011538},
doi = {10.1371/journal.ppat.1011538},
pmid = {37523413},
issn = {1553-7374},
abstract = {Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.},
}
@article {pmid37510218,
year = {2023},
author = {Zhang, N and Shao, X and Guo, Y and Zhang, X and Zhou, Y and Yuan, J and Tang, Z and Hu, S and Minyaev, SS and Cai, D},
title = {Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China.},
journal = {Genes},
volume = {14},
number = {7},
pages = {},
pmid = {37510218},
issn = {2073-4425},
mesh = {Animals ; Cattle/genetics ; *Genome, Mitochondrial ; Phylogeny ; Genetic Variation ; DNA, Ancient ; DNA, Mitochondrial/genetics ; China ; },
abstract = {Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle.},
}
@article {pmid37503227,
year = {2023},
author = {Simon, A and Coop, G},
title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.07.11.548607},
pmid = {37503227},
abstract = {Genomic time-series from experimental evolution studies and ancient DNA datasets offer us a chance to more directly observe the interplay of various evolutionary forces. Here we show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide allele frequency change is due to gene flow. In both cases, after correcting for known major gene flow events in those populations, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.},
}
@article {pmid37499002,
year = {2023},
author = {Heggarty, P and Anderson, C and Scarborough, M and King, B and Bouckaert, R and Jocz, L and Kümmel, MJ and Jügel, T and Irslinger, B and Pooth, R and Liljegren, H and Strand, RF and Haig, G and Macák, M and Kim, RI and Anonby, E and Pronk, T and Belyaev, O and Dewey-Findell, TK and Boutilier, M and Freiberg, C and Tegethoff, R and Serangeli, M and Liosis, N and Stroński, K and Schulte, K and Gupta, GK and Haak, W and Krause, J and Atkinson, QD and Greenhill, SJ and Kühnert, D and Gray, RD},
title = {Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6656},
pages = {eabg0818},
doi = {10.1126/science.abg0818},
pmid = {37499002},
issn = {1095-9203},
abstract = {The origins of the Indo-European language family are hotly disputed. Bayesian phylogenetic analyses of core vocabulary have produced conflicting results, with some supporting a farming expansion out of Anatolia ~9000 years before present (yr B.P.), while others support a spread with horse-based pastoralism out of the Pontic-Caspian Steppe ~6000 yr B.P. Here we present an extensive database of Indo-European core vocabulary that eliminates past inconsistencies in cognate coding. Ancestry-enabled phylogenetic analysis of this dataset indicates that few ancient languages are direct ancestors of modern clades and produces a root age of ~8120 yr B.P. for the family. Although this date is not consistent with the Steppe hypothesis, it does not rule out an initial homeland south of the Caucasus, with a subsequent branch northward onto the steppe and then across Europe. We reconcile this hybrid hypothesis with recently published ancient DNA evidence from the steppe and the northern Fertile Crescent.},
}
@article {pmid37495791,
year = {2023},
author = {Callaway, E},
title = {Seven generations of a prehistoric family mapped with ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37495791},
issn = {1476-4687},
}
@article {pmid37495780,
year = {2023},
author = {},
title = {Family trees of a Neolithic community uncovered by ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37495780},
issn = {1476-4687},
}
@article {pmid37495691,
year = {2023},
author = {Rivollat, M and Rohrlach, AB and Ringbauer, H and Childebayeva, A and Mendisco, F and Barquera, R and Szolek, A and Le Roy, M and Colleran, H and Tuke, J and Aron, F and Pemonge, MH and Späth, E and Télouk, P and Rey, L and Goude, G and Balter, V and Krause, J and Rottier, S and Deguilloux, MF and Haak, W},
title = {Extensive pedigrees reveal the social organization of a Neolithic community.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37495691},
issn = {1476-4687},
abstract = {Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations[1-4]. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality[5]. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.},
}
@article {pmid37494435,
year = {2023},
author = {Salazar, L and Burger, R and Forst, J and Barquera, R and Nesbitt, J and Calero, J and Washburn, E and Verano, J and Zhu, K and Sop, K and Kassadjikova, K and Ibarra Asencios, B and Davidson, R and Bradley, B and Krause, J and Fehren-Schmitz, L},
title = {Insights into the genetic histories and lifeways of Machu Picchu's occupants.},
journal = {Science advances},
volume = {9},
number = {30},
pages = {eadg3377},
doi = {10.1126/sciadv.adg3377},
pmid = {37494435},
issn = {2375-2548},
abstract = {Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.},
}
@article {pmid37494366,
year = {2023},
author = {Romboni, M and Arienzo, I and Di Vito, MA and Lubritto, C and Piochi, M and Di Cicco, MR and Rickards, O and Rolfo, MF and Sevink, J and De Angelis, F and Alessandri, L},
title = {La Sassa cave: Isotopic evidence for Copper Age and Bronze Age population dynamics in Central Italy.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288637},
doi = {10.1371/journal.pone.0288637},
pmid = {37494366},
issn = {1932-6203},
abstract = {This study focuses on the changes in diet and mobility of people buried in the La Sassa cave (Latium, Central Italy) during the Copper and Bronze Ages to contribute to the understanding of the complex contemporary population dynamics in Central Italy. To that purpose, carbon and nitrogen stable isotope analyses, strontium isotope analyses, and FT-IR evaluations were performed on human and faunal remains from this cave. The stable isotope analyses evidence a slight shift in diet between Copper and Bronze Age individuals, which becomes prominent in an individual, dating from a late phase, when the cave was mainly used as a cultic shelter. This diachronic study documents an increased dietary variability due to the introduction of novel resources in these protohistoric societies, possibly related to the southward spread of northern human groups into Central Italy. This contact between different cultures is also testified by the pottery typology found in the cave. The latter shows an increase in cultural intermingling starting during the beginning of the middle Bronze Age. The local mobility during this phase likely involved multiple communities scattered throughout an area of a few kilometers around the cave, which used the latter as a burial site both in the Copper and Bronze ages.},
}
@article {pmid37491505,
year = {2023},
author = {Barsch, E and Kowarik, K and Rodler, K and Hörweg, C and Reschreiter, H and Sattmann, H and Walochnik, J},
title = {First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12055},
pmid = {37491505},
issn = {2045-2322},
abstract = {Palaeoparasitological studies can provide valuable information on the emergence, distribution, and elimination of parasites during a particular time in the past. In the prehistoric salt mines of Hallstatt, located in the Austrian Alps, human faeces have been conserved in salt. The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. Altogether, 35 coprolites from the Hallstatt salt mines, dating back to the Bronze Age mining phase (1158-1063 BCE) and the Iron Age mining phase (750-662 BCE), respectively, were analysed by microscopy and molecular methods. In 91% of the coprolite samples, eggs of soil-transmitted helminths (STH), namely of Trichuris and/or Ascaris were detected by light microscopy. The Ascaris eggs were exceptionally well preserved. For further analysis, DNA was extracted from the palaeofaecal samples and species-specific primers targeting different genes were designed. While amplification of Trichuris DNA remained unsuccessful, sequence data of A. lumbricoides species complex were successfully obtained from 16 coprolites from three different genes, the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), the mitochondrial cytochrome B gene (cytB) and the mitochondrial NADH dehydrogenase subunit 1 gene (nadh1). Importantly, these included two Ascaris sequences from a coprolite from the Bronze Age, which to the best of our knowledge are the first molecular data of this genus from this period.},
}
@article {pmid37485357,
year = {2023},
author = {Ginja, C and Guimarães, S and da Fonseca, RR and Rasteiro, R and Rodríguez-Varela, R and Simões, LG and Sarmento, C and Belarte, MC and Kallala, N and Torres, JR and Sanmartí, J and Arruda, AM and Detry, C and Davis, S and Matos, J and Götherström, A and Pires, AE and Valenzuela-Lamas, S},
title = {Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.},
journal = {iScience},
volume = {26},
number = {7},
pages = {107196},
pmid = {37485357},
issn = {2589-0042},
abstract = {The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.},
}
@article {pmid37474518,
year = {2023},
author = {Campos, PE and Pruvost, O and Boyer, K and Chiroleu, F and Cao, TT and Gaudeul, M and Baider, C and Utteridge, TMA and Becker, N and Rieux, A and Gagnevin, L},
title = {Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4306},
pmid = {37474518},
issn = {2041-1723},
mesh = {Humans ; Phylogeny ; *Xanthomonas/genetics ; Genomics ; *Citrus/microbiology ; Plant Diseases/microbiology ; },
abstract = {Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).},
}
@article {pmid37463654,
year = {2023},
author = {Lin, H and Hu, J and Baleka, S and Yuan, J and Chen, X and Xiao, B and Song, S and Du, Z and Lai, X and Hofreiter, M and Sheng, G},
title = {A genetic glimpse of the Chinese straight-tusked elephants.},
journal = {Biology letters},
volume = {19},
number = {7},
pages = {20230078},
pmid = {37463654},
issn = {1744-957X},
mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Elephants/genetics ; Fossils ; Phylogeny ; Phylogeography ; },
abstract = {Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.},
}
@article {pmid37450551,
year = {2023},
author = {Pryor, Y and Lindo, J},
title = {Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21993},
pmid = {37450551},
issn = {1520-6505},
support = {1926075//Division of Behavioral and Cognitive Sciences/ ; 1945046//Division of Behavioral and Cognitive Sciences/ ; //Ford Foundation Predoctoral Fellowship/ ; 21602//National Science Foundation Graduate Research Fellowship/ ; },
abstract = {The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.},
}
@article {pmid37438988,
year = {2023},
author = {Lewis, DA and Simpson, R and Hermes, A and Brown, A and Llamas, B},
title = {More than dirt: Sedimentary ancient DNA and Indigenous Australia.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13835},
pmid = {37438988},
issn = {1755-0998},
support = {2011277//National Health and Medical Research Council/ ; 1137563//National Health and Medical Research Council/ ; },
abstract = {The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.},
}
@article {pmid37438588,
year = {2023},
author = {Dance, A},
title = {Germs, genes and soil: tales of pathogens past.},
journal = {Nature},
volume = {619},
number = {7969},
pages = {424-426},
pmid = {37438588},
issn = {1476-4687},
mesh = {*Soil ; *Soil Microbiology ; *Bacteria/genetics/isolation &amp; purification ; *DNA, Ancient/analysis/isolation &amp; purification ; History, Ancient ; },
}
@article {pmid37438447,
year = {2023},
author = {Tran, HL and Mai, HP and Le Thi, D and Thi, ND and Le Tung, L and Thanh, TP and Manh, HT and Mau, HN and Chu, HH and Hoang, H},
title = {The first maternal genetic study of hunter-gatherers from Vietnam.},
journal = {Molecular genetics and genomics : MGG},
volume = {},
number = {},
pages = {},
pmid = {37438447},
issn = {1617-4623},
support = {DL0000.08/20-23//Vietnam Academy of Science and Technology/ ; },
abstract = {The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.},
}
@article {pmid37433640,
year = {2023},
author = {Weissensteiner, MH and Cremona, MA and Guiblet, WM and Stoler, N and Harris, RS and Cechova, M and Eckert, KA and Chiaromonte, F and Huang, YF and Makova, KD},
title = {Accurate sequencing of DNA motifs able to form alternative (non-B) structures.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277490.122},
pmid = {37433640},
issn = {1549-5469},
abstract = {Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.},
}
@article {pmid37431939,
year = {2023},
author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S},
title = {Diversity in matrilineages among the Jomon individuals of Japan.},
journal = {Annals of human biology},
volume = {50},
number = {1},
pages = {324-331},
doi = {10.1080/03014460.2023.2224060},
pmid = {37431939},
issn = {1464-5033},
mesh = {Humans ; Japan ; *Body Remains ; *Archaeology ; High-Throughput Nucleotide Sequencing ; Knowledge ; },
abstract = {BACKGROUND: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited.<br><br>AIM: We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.<br><br>SUBJECTS AND METHODS: For human remains dated to 8200-8600&#x2009;cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing.<br><br>RESULTS: We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period.<br><br>CONCLUSION: The genetic diversity within the population was not found to be low even in the Initial Jomon period.},
}
@article {pmid37423869,
year = {2023},
author = {Bailey, E},
title = {Ancient DNA reveals an early adoption of horse culture by Native Americans.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.06.010},
pmid = {37423869},
issn = {0168-9525},
abstract = {Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.},
}
@article {pmid37422275,
year = {2023},
author = {Ibrahim, J and Rechav, K and Boaretto, E and Weiner, S},
title = {Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation.},
journal = {Journal of structural biology},
volume = {215},
number = {3},
pages = {107998},
doi = {10.1016/j.jsb.2023.107998},
pmid = {37422275},
issn = {1095-8657},
abstract = {We report on the 3D ultrastructure of the mineralized petrous bone of mature pig using focused ion beam - scanning electron microscopy (FIB-SEM). We divide the petrous bone into two zones based on the degree of mineralization; one zone close to the otic chamber has higher mineral density than the second zone further away from the otic chamber. The hypermineralization of the petrous bone results in the collagen D-banding being poorly revealed in the lower mineral density zone (LMD), and absent in the high mineral density zone (HMD). We therefore could not use D-banding to decipher the 3D structure of the collagen assembly. Instead we exploited the anisotropy option in the Dragonfly image processing software to visualize the less mineralized collagen fibrils and/or nanopores that surround the more mineralized zones known as tesselles. This approach therefore indirectly tracks the orientations of the collagen fibrils in the matrix itself. We show that the HMD bone has a structure similar to that of woven bone, and the LMD is composed of lamellar bone with a plywood-like structural motif. This agrees with the fact that the bone close to the otic chamber is fetal bone and is not remodeled. The lamellar structure of the bone further away from the otic chamber is consistent with modeling/remodeling. The absence of the less mineralized collagen fibrils and nanopores resulting from the confluence of the mineral tesselles may contribute to shielding DNA during diagenesis. We show that anisotropy evaluation of the less mineralized collagen fibrils could be a useful tool to analyze bone ultrastructures and in particular the directionality of collagen fibril bundles that make up the bone matrix.},
}
@article {pmid37380840,
year = {2023},
author = {Lewis, D},
title = {Ancient-DNA researcher fired for 'serious misconduct' lands new role.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-023-02147-x},
pmid = {37380840},
issn = {1476-4687},
}
@article {pmid37374141,
year = {2023},
author = {Abondio, P and Cilli, E and Luiselli, D},
title = {Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {37374141},
issn = {2075-1729},
abstract = {A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.},
}
@article {pmid37372418,
year = {2023},
author = {Bonfigli, A and Cesare, P and Volpe, AR and Colafarina, S and Forgione, A and Aloisi, M and Zarivi, O and Poma, AMG},
title = {Estimation of DNA Degradation in Archaeological Human Remains.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/genes14061238},
pmid = {37372418},
issn = {2073-4425},
abstract = {The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.},
}
@article {pmid37372367,
year = {2023},
author = {Song, S and Xiao, B and Hu, J and Lin, H and Du, Z and Xiang, K and Pan, D and Hou, X and Yuan, J and Lai, X and Sheng, G},
title = {Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/genes14061187},
pmid = {37372367},
issn = {2073-4425},
support = {No. 42172027//National Natural Science Foundation of China/ ; },
abstract = {As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.},
}
@article {pmid37341062,
year = {2023},
author = {Silva, V and Pérez, V and Gillanders, BM},
title = {Short-term plastisphere colonization dynamics across six plastic types.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16445},
pmid = {37341062},
issn = {1462-2920},
support = {//Australian Government Research Training Program Scholarship/ ; },
abstract = {Marine plastic pollution is a major concern worldwide, but the understanding of plastisphere dynamics remains limited in the southern hemisphere. To address this knowledge gap, we conducted a study in South Australia to investigate the prokaryotic community of the plastisphere and its temporal changes over 4 weeks. We submerged six plastic types (i.e., High-Density Polyethylene [HDPE], Polyvinyl chloride [PVC], Low-Density Polyethylene [LDPE], Polypropylene [PP], Polystyrene [PS] and the understudied textile, polyester [PET]) and wood in seawater and sampled them weekly to characterize the prokaryotic community using 16S rRNA gene metabarcoding. Our results showed that the plastisphere composition shifted significantly over short time scales (i.e., 4 weeks), and each plastic type had distinct groups of unique genera. In particular, the PVC plastisphere was dominated by Cellvibrionaceae taxa, distinguishing it from other plastics. Additionally, the textile polyester, which is rarely studied in plastisphere research, supported the growth of a unique group of 25 prokaryotic genera (which included the potential pathogenic Legionella genus). Overall, this study provides valuable insights into the colonization dynamics of the plastisphere over short time scales and contributes to narrowing the research gap on the southern hemisphere plastisphere.},
}
@article {pmid37339987,
year = {2023},
author = {Sousa da Mota, B and Rubinacci, S and Cruz Dávalos, DI and G Amorim, CE and Sikora, M and Johannsen, NN and Szmyt, MH and Włodarczak, P and Szczepanek, A and Przybyła, MM and Schroeder, H and Allentoft, ME and Willerslev, E and Malaspinas, AS and Delaneau, O},
title = {Imputation of ancient human genomes.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3660},
pmid = {37339987},
issn = {2041-1723},
support = {PP00P3_176977//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.},
}
@article {pmid37259901,
year = {2023},
author = {Signore, AV and Morrison, PR and Brauner, CJ and Fago, A and Weber, RE and Campbell, KL},
title = {Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller's sea cows.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.85414},
pmid = {37259901},
issn = {2050-084X},
support = {RGPIN/238838-2011//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/412336-2011//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/06562-2016//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/261924-2013//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/446005-2013//Natural Sciences and Engineering Research Council of Canada/ ; DFF-4181-00094//Danmarks Frie Forskningsfond/ ; },
abstract = {The extinct Steller's sea cow (Hydrodamalis gigas; †1768) was a whale-sized marine mammal that manifested profound morphological specializations to exploit the harsh coastal climate of the North Pacific. Yet despite first-hand accounts of their biology, little is known regarding the physiological adjustments underlying their evolution to this environment. Here, the adult-expressed hemoglobin (Hb; α2β/δ2) of this sirenian is shown to harbor a fixed amino acid replacement at an otherwise invariant position (β/δ82Lys→Asn) that alters multiple aspects of Hb function. First, our functional characterization of recombinant sirenian Hb proteins demonstrates that the Hb-O2 affinity of this sub-Arctic species was less affected by temperature than those of living (sub)tropical sea cows. This phenotype presumably safeguarded O2 delivery to cool peripheral tissues and largely arises from a reduced intrinsic temperature sensitivity of the H. gigas protein. Additional experiments on H. gigas β/δ82Asn→Lys mutant Hb further reveal this exchange renders Steller's sea cow Hb unresponsive to the potent intraerythrocytic allosteric effector 2,3-diphosphoglycerate, a radical modification that is the first documented example of this phenotype among mammals. Notably, β/δ82Lys→Asn moreover underlies the secondary evolution of a reduced blood-O2 affinity phenotype that would have promoted heightened tissue and maternal/fetal O2 delivery. This conclusion is bolstered by analyses of two Steller's sea cow prenatal Hb proteins (Hb Gower I; ζ2ε2 and HbF; α2γ2) that suggest an exclusive embryonic stage expression pattern, and reveal uncommon replacements in H. gigas HbF (γ38Thr→Ile and γ101Glu→Asp) that increased Hb-O2 affinity relative to dugong HbF. Finally, the β/δ82Lys→Asn replacement of the adult/fetal protein is shown to increase protein solubility, which may have elevated red blood cell Hb content within both the adult and fetal circulations and contributed to meeting the elevated metabolic (thermoregulatory) requirements and fetal growth rates associated with this species cold adaptation.},
}
@article {pmid37337956,
year = {2023},
author = {Doan, K and Schnitzler, A and Preston, F and Griggo, C and Lang, G and Belhaoues, F and Blaise, E and Crégut-Bonnoure, E and Frère, S and Foucras, S and Gardeisen, A and Laurent, A and Müller, W and Picavet, R and Puissant, S and Yvinec, JH and Pilot, M},
title = {Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17054},
pmid = {37337956},
issn = {1365-294X},
abstract = {Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.},
}
@article {pmid37332506,
year = {2022},
author = {Fagernäs, Z and Salazar-García, DC and Haber Uriarte, M and Avilés Fernández, A and Henry, AG and Lomba Maurandi, J and Ozga, AT and Velsko, IM and Warinner, C},
title = {Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.},
journal = {FEMS microbes},
volume = {3},
number = {},
pages = {xtac006},
pmid = {37332506},
issn = {2633-6685},
abstract = {The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.},
}
@article {pmid37330109,
year = {2023},
author = {Yang, L and Zhang, X and Hu, Y and Zhu, P and Li, H and Peng, Z and Xiang, H and Zhou, X and Zhao, X},
title = {Ancient mitochondrial genome depicts sheep maternal dispersal and migration in eastern Asia.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2023.06.002},
pmid = {37330109},
issn = {1673-8527},
abstract = {Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 years old) found in Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region might have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429-2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in eastern Asia.},
}
@article {pmid37326229,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Simon, C and Goodwin, CS and Henry, JM and Austin, JJ},
title = {Quantitative PCR overestimation of DNA in samples contaminated with tin.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.15312},
pmid = {37326229},
issn = {1556-4029},
abstract = {Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an "inhibition study" and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.},
}
@article {pmid37323114,
year = {2023},
author = {Russo, MG and Arencibia, V and Emery, M and Bettera Marcat, G and Seldes, V and Mercolli, P and Soria, S and Maldonado, L and Kamenetzky, L and Avena, S and Dejean, C and Stone, AC},
title = {Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24795},
pmid = {37323114},
issn = {2692-7691},
abstract = {OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina).<br><br>MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970&#x2009;&#xb1;&#x2009;60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina&#xae; MiSeq&#x2122; platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset.<br><br>RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669&#x2009;ya.<br><br>DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.},
}
@article {pmid37311857,
year = {2023},
author = {de Sousa, AA and Beaudet, A and Calvey, T and Bardo, A and Benoit, J and Charvet, CJ and Dehay, C and Gómez-Robles, A and Gunz, P and Heuer, K and van den Heuvel, MP and Hurst, S and Lauters, P and Reed, D and Salagnon, M and Sherwood, CC and Ströckens, F and Tawane, M and Todorov, OS and Toro, R and Wei, Y},
title = {From fossils to mind.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {636},
pmid = {37311857},
issn = {2399-3642},
mesh = {*Fossils ; Phylogeny ; *Brain ; Archaeology ; Artifacts ; },
abstract = {Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.},
}
@article {pmid37291482,
year = {2023},
author = {Chen, N and Nedoluzhko, A},
title = {Ancient DNA: the past for the future.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {309},
pmid = {37291482},
issn = {1471-2164},
mesh = {Animals ; *DNA, Ancient ; Sequence Analysis, DNA/methods ; *Plants/genetics ; Laboratories ; },
abstract = {The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.},
}
@article {pmid37138083,
year = {2023},
author = {Essel, E and Zavala, EI and Schulz-Kornas, E and Kozlikin, MB and Fewlass, H and Vernot, B and Shunkov, MV and Derevianko, AP and Douka, K and Barnes, I and Soulier, MC and Schmidt, A and Szymanski, M and Tsanova, T and Sirakov, N and Endarova, E and McPherron, SP and Hublin, JJ and Kelso, J and Pääbo, S and Hajdinjak, M and Soressi, M and Meyer, M},
title = {Ancient human DNA recovered from a Palaeolithic pendant.},
journal = {Nature},
volume = {618},
number = {7964},
pages = {328-332},
pmid = {37138083},
issn = {1476-4687},
mesh = {Humans ; Animals ; Female ; History, Ancient ; *DNA, Ancient ; *Deer/genetics ; DNA/genetics ; Bone and Bones ; Siberia ; Archaeology ; DNA, Mitochondrial/genetics ; },
abstract = {Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals[1] who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited[2-5]. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.},
}
@article {pmid37286670,
year = {2023},
author = {Humphrey, L and Bouzouggar, A},
title = {Ancient DNA reveals how farming spread into northwest Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37286670},
issn = {1476-4687},
}
@article {pmid37284851,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M},
title = {Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {37284851},
issn = {1437-1596},
abstract = {Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.},
}
@article {pmid37265549,
year = {2022},
author = {Elalouf, JM and Palacio, P and Bon, C and Berthonaud, V and Maksud, F and Stafford, TW and Hitte, C},
title = {The genome and diet of a 35,000-year-old Canis lupus specimen from the Paleolithic painted cave, Chauvet-Pont d'Arc, France.},
journal = {Ecology and evolution},
volume = {12},
number = {8},
pages = {e9238},
pmid = {37265549},
issn = {2045-7758},
abstract = {The Chauvet-Pont-d'Arc Cave (Ardèche, France) contains some of the oldest Paleolithic paintings recorded to date, as well as thousands of bones of the extinct cave bear, and some remains and footprints of other animals. As part of the interdisciplinary research project devoted to this reference cave site, we analyzed a coprolite collected within the deep cave. AMS radiocarbon dating of bone fragments from the coprolite yielded an age of 30,450 ± 550 RC yr. BP (AAR-19656; 36,150-34,000 cal BP), similar to ages assigned to Paleolithic artwork and cave bear remains from the same cave sector. Using high-throughput shotgun DNA sequencing, we demonstrated a high abundance of canid DNA and lesser amounts of DNA from the extinct cave bear. We interpret the sample as feces from a canid that had consumed cave bear tissue. The high amount of canid DNA allowed us to reconstruct a complete canid mitochondrial genome sequence (average coverage: 83×) belonging to a deeply divergent clade of extinct mitochondrial wolf lineages that are most closely related to coeval (~35 ka) Belgian wolves. Analysis of the nuclear genome yielded a similar coverage for the X chromosome (2.4×) and the autosomes (range: 2.3-3.2×), indicating that the Chauvet canid was a female. Comparing the relationship of the nuclear genome of this specimen with that of a variety of canids, we found it more closely related to gray wolves' genomes than to other wild canid or dog genomes, especially wolf genomes from Europe and the Middle East. We conclude that the coprolite is feces from an animal within an extinct wolf lineage. The consumption of cave bear by this wolf likely explains its intrusion into the dark cave sectors and sheds new light on the paleoecology of a major cave site.},
}
@article {pmid37252429,
year = {2023},
author = {Furtwängler, A and Baumann, C and Majander, K and Wilkin, S and Tomoum, N and Rühli, F and Jaeggi, AV and Eppenberger, P and Bender, N and Schuenemann, VJ},
title = {The Mummy Explorer-a self-regulated open-access online teaching tool.},
journal = {Evolution, medicine, and public health},
volume = {11},
number = {1},
pages = {129-138},
pmid = {37252429},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Virtual teaching tools have gained increasing importance in recent years. In particular, the COVID-19 pandemic has reinforced the need for media-based and self-regulated tools. What is missing are tools that allow us to interlink highly interdisciplinary fields such as evolutionary medicine and, at the same time, allow us to adapt content to different lectures.<br><br>METHODOLOGY: We designed an interactive online teaching tool, namely, the Mummy Explorer, using open-access software (Google Web Designer), and we provided a freely downloadable template. We tested the tool on students and lecturers of evolutionary medicine using questionnaires and improved the tool according to their feedback.<br><br>RESULTS: The tool has a modular design and provides an overview of a virtual mummy excavation, including the subfields of palaeopathology, paleoradiology, cultural and ethnographic context, provenance studies, paleogenetics, and physiological analyses. The template allows lecturers to generate their own versions of the tool for any topic of interest by simply changing the text and pictures. Tests undertaken with students of evolutionary medicine showed that the tool was helpful during their studies. Lecturers commented that they appreciated having a similar tool in other fields.<br><br>CONCLUSIONS AND IMPLICATIONS: Mummy Explorer fills a gap in the virtual teaching landscape of highly interdisciplinary fields such as evolutionary medicine. It will be offered for free download and can be adapted to any educational topic. Translations into German and possibly other languages are in progress.},
}
@article {pmid37250315,
year = {2023},
author = {Clavel, P and Louis, L and Sarkissian, C and Thèves, C and Gillet, C and Chauvey, L and Tressières, G and Schiavinato, S and Calvière-Tonasso, L and Telmon, N and Clavel, B and Jonvel, R and Tzortzis, S and Bouniol, L and Fémolant, JM and Klunk, J and Poinar, H and Signoli, M and Costedoat, C and Spyrou, MA and Seguin-Orlando, A and Orlando, L},
title = {Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.},
journal = {iScience},
volume = {26},
number = {5},
pages = {106787},
pmid = {37250315},
issn = {2589-0042},
abstract = {Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17[th] and 18[th] centuries Common Era.},
}
@article {pmid37239398,
year = {2023},
author = {Buss, DL and Atmore, LM and Zicos, MH and Goodall-Copestake, WP and Brace, S and Archer, FI and Baker, CS and Barnes, I and Carroll, EL and Hart, T and Kitchener, AC and Sabin, R and Sremba, AL and Weir, CR and Jackson, JA},
title = {Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239398},
issn = {2073-4425},
mesh = {Animals ; *Fin Whale/genetics ; Whales/genetics ; Population Density ; Antarctic Regions ; },
abstract = {Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.},
}
@article {pmid37239354,
year = {2023},
author = {Thomas, JT and Cavagnino, C and Kjelland, K and Anderson, E and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Amory, C and Spatola, B and Moran, K and Parson, W and Marshall, C},
title = {Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/genes14050994},
pmid = {37239354},
issn = {2073-4425},
abstract = {This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.},
}
@article {pmid37224187,
year = {2023},
author = {Gibbon, VE and Feris, L and Gretzinger, J and Smith, K and Hall, S and Penn, N and Mutsvangwa, TEM and Heale, M and Finaughty, DA and Karanja, YW and Esterhuyse, J and Kotze, D and Barnes, N and Gunston, G and May, J and Krause, J and Wilkinson, CM and Schiffels, S and Februarie, D and Alves, S and Sealy, JC},
title = {Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0284785},
pmid = {37224187},
issn = {1932-6203},
mesh = {Humans ; South Africa ; *Anthropology ; *Archaeology ; Cemeteries ; DNA, Ancient ; },
abstract = {We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.},
}
@article {pmid37141357,
year = {2023},
author = {Gibbons, A},
title = {The woman with the deer pendant.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6644},
pages = {446},
doi = {10.1126/science.adi5371},
pmid = {37141357},
issn = {1095-9203},
mesh = {Animals ; Female ; Humans ; Deer ; *DNA, Ancient/isolation &amp; purification ; },
abstract = {Pioneering technique gleans DNA from a Stone Age ornament, revealing its last wearer.},
}
@article {pmid37220274,
year = {2023},
author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A},
title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {22},
pages = {e2213061120},
doi = {10.1073/pnas.2213061120},
pmid = {37220274},
issn = {1091-6490},
abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.},
}
@article {pmid37216609,
year = {2023},
author = {Ciecierski, L and Stolarek, I and Figlerowicz, M},
title = {Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad428},
pmid = {37216609},
issn = {1362-4962},
abstract = {Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.},
}
@article {pmid37215481,
year = {2023},
author = {Mármol-Sánchez, E and Heidemann, PL and Gredal, H and Cirera, S},
title = {MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1144084},
doi = {10.3389/fvets.2023.1144084},
pmid = {37215481},
issn = {2297-1769},
abstract = {INTRODUCTION: Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment.<br><br>METHODS: By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group.<br><br>RESULTS: Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO.<br><br>DISCUSSION: Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.},
}
@article {pmid37212188,
year = {2023},
author = {Bunce, M},
title = {It is time for ancient DNA to sweat the small stuff.},
journal = {Molecular ecology},
volume = {32},
number = {11},
pages = {2689-2691},
doi = {10.1111/mec.16970},
pmid = {37212188},
issn = {1365-294X},
abstract = {When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs - despite the pervasive idea of 'dino DNA' from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected 'small stuff' - lizards, frogs, and other herpetofauna. But here's the rub - extracting DNA from the bones of this 'small stuff' is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.},
}
@article {pmid37207647,
year = {2023},
author = {Fleskes, RE and Owsley, DW and Bruwelheide, KS and Barca, KG and Griffith, DR and Cabana, GS and Schurr, TG},
title = {Historical genomes elucidate European settlement and the African diaspora in Delaware.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.04.069},
pmid = {37207647},
issn = {1879-0445},
abstract = {The 17[th]-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.[1] The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.[2] European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.[3][,][4] To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.[5] Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17[th] and early 18[th] century North America.},
}
@article {pmid37187366,
year = {2023},
author = {Wilke, T and Kehlmaier, C and Stelbrink, B and Albrecht, C and Bouchet, P},
title = {Historical DNA solves century-old mystery on sessility in freshwater gastropods.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {107813},
doi = {10.1016/j.ympev.2023.107813},
pmid = {37187366},
issn = {1095-9513},
abstract = {Extinction rates are increasing unabatedly but resources available for conservation action are limited. Therefore, some conservationists are pushing for ecology- and evolution-based conservation choices, prioritizing taxa with phylogenetic and trait-based originality. Extinction of original taxa may result in a disproportionate loss of evolutionary innovations and potentially prevent transformative changes in living systems. Here, we generated historical DNA data from an almost 120-year-old syntype of the enigmatic sessile snail Helicostoa sinensis from the Three Gorges region of the Yangtze River (PR China), using a next-generation sequencing protocol developed for ancient DNA. In a broader phylogenetic context, we assessed the phylogenetic and trait-based originality of this enigmatic taxon to solve the century-old puzzle of sessility in freshwater gastropods. Our multi-locus data confirm the phylogenetic and trait-based originality of H. sinensis. It is an ultra-rare, subfamily-level taxon (Helicostoinae stat. nov.) within the family Bithyniidae, which exhibits the evolutionary innovation of sessility. While we conservatively classify H. sinensis as "Critically Endangered", there is mounting evidence of the biological annihilation of this endemic species. Although rapidly rising extinction rates in invertebrates are increasingly recognized, the potential loss of originality in these "little things that run the world" has received little attention. We therefore call for comprehensive surveys of originality in invertebrates, particularly from extreme environments such as rapids of large rivers, as a basis for urgently needed ecology- and evolution-based conservation decisions.},
}
@article {pmid37185708,
year = {2023},
author = {Abondio, P and Bruno, F and Luiselli, D},
title = {Apolipoprotein E (APOE) Haplotypes in Healthy Subjects from Worldwide Macroareas: A Population Genetics Perspective for Cardiovascular Disease, Neurodegeneration, and Dementia.},
journal = {Current issues in molecular biology},
volume = {45},
number = {4},
pages = {2817-2831},
doi = {10.3390/cimb45040184},
pmid = {37185708},
issn = {1467-3045},
abstract = {Human APOE is a 299-amino acid long protein expressed and secreted in several tissues and body districts, where it exerts different functions mainly related to lipid metabolism, with specific activities around cholesterol transport and absorption/elimination. It has three main isoforms, determined by the pair of mutations rs7412-C/T and rs429358-C/T, which gives rise to the functionally different APOE variants ε2, ε3, and ε4. These have a distinct impact on lipid metabolism and are differentially implicated in Alzheimer's disease and neurodegeneration, cardiovascular disease, and dyslipidemia. A plethora of other single nucleotide variants along the sequence of the APOE gene have been studied in cohorts of affected individuals, where they also modulate the influence of the three main isoforms to determine the risk of developing the disease. However, no contextual analysis of gene-long haplotypes has been carried out so far, and never extensively in cohorts of healthy individuals from different worldwide populations. Leveraging a rich population genomics dataset, this study elucidates the distribution of APOE variants and haplotypes that are shared across populations and to specific macroareas, revealing a variety of risk-allele associations that distinguish specific ancestral backgrounds and can be leveraged for specific ancestry-informed screenings in medicine and public health.},
}
@article {pmid37167404,
year = {2023},
author = {Llamas, B and Roca-Rada, X},
title = {Paleogenomic study of the Mexican past.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6645},
pages = {578-579},
doi = {10.1126/science.adh7902},
pmid = {37167404},
issn = {1095-9203},
mesh = {Humans ; *DNA, Ancient ; Mexico ; },
abstract = {Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.},
}
@article {pmid37163039,
year = {2023},
author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM},
title = {Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.24.538113},
pmid = {37163039},
abstract = {Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G12 ancient , on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.},
}
@article {pmid37157914,
year = {2023},
author = {Whitehouse, LS and Schrider, DR},
title = {Timesweeper: Accurately Identifying Selective Sweeps Using Population Genomic Time Series.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyad084},
pmid = {37157914},
issn = {1943-2631},
abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional Convolutional Neural Network on said simulations, and inferring which polymorphisms in this serialized dataset were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.},
}
@article {pmid37153511,
year = {2023},
author = {Sharko, FS and Zhur, KV and Trifonov, VA and Prokhortchouk, EB},
title = {Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.},
journal = {Acta naturae},
volume = {15},
number = {1},
pages = {87-96},
pmid = {37153511},
issn = {2075-8251},
abstract = {Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.},
}
@article {pmid37141673,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Zupanc, T and Podovšovnik, E},
title = {A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples.},
journal = {Forensic science international. Genetics},
volume = {65},
number = {},
pages = {102882},
doi = {10.1016/j.fsigen.2023.102882},
pmid = {37141673},
issn = {1878-0326},
abstract = {An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.},
}
@article {pmid37095409,
year = {2023},
author = {Callaway, E},
title = {'Truly gobsmacked': Ancient-human genome count surpasses 10,000.},
journal = {Nature},
volume = {617},
number = {7959},
pages = {20},
pmid = {37095409},
issn = {1476-4687},
mesh = {Humans ; *Anthropology/trends ; *Archaeology/trends ; *Genome, Human/genetics ; *DNA, Ancient ; },
}
@article {pmid37141315,
year = {2023},
author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P},
title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadf5300},
doi = {10.1126/science.adf5300},
pmid = {37141315},
issn = {1095-9203},
abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.},
}
@article {pmid37137206,
year = {2023},
author = {Zupanič Pajnič, I and Geršak, &#x17d;M and Leskovar, T and Črešnar, M},
title = {Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site.},
journal = {Forensic science international. Genetics},
volume = {65},
number = {},
pages = {102886},
doi = {10.1016/j.fsigen.2023.102886},
pmid = {37137206},
issn = {1878-0326},
abstract = {The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.},
}
@article {pmid37127762,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M},
title = {Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {37127762},
issn = {1437-1596},
abstract = {In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10[7] (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.},
}
@article {pmid37117261,
year = {2023},
author = {Ferrando-Bernal, M},
title = {Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6968},
pmid = {37117261},
issn = {2045-2322},
mesh = {Humans ; Skull ; DNA, Ancient ; Paleopathology ; *Anemia/complications ; *Hyperostosis/genetics ; *Bone Diseases, Metabolic/complications ; },
abstract = {Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.},
}
@article {pmid37101579,
year = {2023},
author = {Kowal, E and Weyrich, LS and Argüelles, JM and Bader, AC and Colwell, C and Cortez, AD and Davis, JL and Figueiro, G and Fox, K and Malhi, RS and Matisoo-Smith, E and Nayak, A and Nelson, EA and Nicholas, G and Nieves-Colón, MA and Russell, L and Ulm, S and Vergara-Silva, F and Villanea, FA and Wagner, JK and Yracheta, JM and Tsosie, KS},
title = {Community partnerships are fundamental to ethical ancient DNA research.},
journal = {HGG advances},
volume = {4},
number = {2},
pages = {100161},
pmid = {37101579},
issn = {2666-2477},
mesh = {Humans ; *DNA, Ancient ; *Ethics, Research ; Population Groups ; Family ; Research Personnel ; },
abstract = {The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.},
}
@article {pmid37097268,
year = {2023},
author = {Rogers, NM and Zammit, N and Nguyen-Ngo, D and Souilmi, Y and Minhas, N and Meijles, DN and Self, E and Walters, SN and Warren, J and Cultrone, D and El-Rashid, M and Li, J and Chtanova, T and O'Connell, PJ and Grey, ST},
title = {The impact of the cytoplasmic ubiquitin ligase TNFAIP3 gene variation on transcription factor NF-κB activation in acute kidney injury.},
journal = {Kidney international},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.kint.2023.02.030},
pmid = {37097268},
issn = {1523-1755},
abstract = {Nuclear factor κB (NF-κB) activation is a deleterious molecular mechanism that drives acute kidney injury (AKI) and manifests in transplanted kidneys as delayed graft function. The TNFAIP3 gene encodes A20, a cytoplasmic ubiquitin ligase and a master negative regulator of the NF- κB signaling pathway. Common population-specific TNFAIP3 coding variants that reduce A20's enzyme function and increase NF- κB activation have been linked to heightened protective immunity and autoimmune disease, but have not been investigated in AKI. Here, we functionally identified a series of unique human TNFAIP3 coding variants linked to the autoimmune genome-wide association studies single nucleotide polymorphisms of F127C; namely F127C;R22Q, F127C;G281E, F127C;W448C and F127C;N449K that reduce A20's anti-inflammatory function in an NF- κB reporter assay. To investigate the impact of TNFAIP3 hypomorphic coding variants in AKI we tested a mouse Tnfaip3 hypomorph in a model of ischemia reperfusion injury (IRI). The mouse Tnfaip3 coding variant I325N increases NF- κB activation without overt inflammatory disease, providing an immune boost as I325N mice exhibit enhanced innate immunity to a bacterial challenge. Surprisingly, despite exhibiting increased intra-kidney NF- κB activation with inflammation in IRI, the kidney of I325N mice was protected. The I325N variant influenced the outcome of IRI by changing the dynamic expression of multiple cytoprotective mechanisms, particularly by increasing NF- κB-dependent anti-apoptotic factors BCL-2, BCL-XL, c-FLIP and A20, altering the active redox state of the kidney with a reduction of superoxide levels and the enzyme super oxide dismutase-1, and enhancing cellular protective mechanisms including increased Foxp3[+] T cells. Thus, TNFAIP3 gene variants represent a kidney and population-specific molecular factor that can dictate the course of IRI.},
}
@article {pmid37096383,
year = {2023},
author = {da Silva Coelho, FA and Gill, S and Tomlin, CM and Papavassiliou, M and Farley, SD and Cook, JA and Sonsthagen, SA and Sage, GK and Heaton, TH and Talbot, SL and Lindqvist, C},
title = {Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16960},
pmid = {37096383},
issn = {1365-294X},
abstract = {During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.},
}
@article {pmid37094265,
year = {2023},
author = {Demeure, CE and Poinar, H and Barreiro, L and Pizarro-Cerdá, J},
title = {[The Black Death, natural selection and susceptibility to auto-immune disorders].},
journal = {Medecine sciences : M/S},
volume = {39},
number = {4},
pages = {331-333},
doi = {10.1051/medsci/2023050},
pmid = {37094265},
issn = {1958-5381},
support = {R01-GM134376/NH/NIH HHS/United States ; },
}
@article {pmid37072186,
year = {2023},
author = {Fernandes, DM and Sirak, KA and Cheronet, O and Novak, M and Brück, F and Zelger, E and Llanos-Lizcano, A and Wagner, A and Zettl, A and Mandl, K and Duffett Carlson, KS and Oberreiter, V and Özdoğan, KT and Sawyer, S and La Pastina, F and Borgia, E and Coppa, A and Dobeš, M and Velemínský, P and Reich, DE and Bell, LS and Pinhasi, R},
title = {Density separation of petrous bone powders for optimized ancient DNA yields.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277714.123},
pmid = {37072186},
issn = {1549-5469},
abstract = {Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders prior to DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into 8 density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30-2.35 and 2.35-2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm3 intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA lab equipment and fewer than 30 minutes of extra lab work, the implementation of density separation prior to DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.},
}
@article {pmid37071008,
year = {2023},
author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L},
title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0437422},
doi = {10.1128/spectrum.04374-22},
pmid = {37071008},
issn = {2165-0497},
abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.},
}
@article {pmid37068234,
year = {2023},
author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M},
title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {17},
pages = {e2213563120},
doi = {10.1073/pnas.2213563120},
pmid = {37068234},
issn = {1091-6490},
abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.},
}
@article {pmid37066305,
year = {2023},
author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D},
title = {The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.06.535797},
pmid = {37066305},
abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.},
}
@article {pmid37065506,
year = {2023},
author = {Gancz, AS and Weyrich, LS},
title = {Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {109},
pmid = {37065506},
issn = {2046-1402},
abstract = {Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.},
}
@article {pmid37059363,
year = {2023},
author = {Kattner, AA},
title = {When it doesn't run in the blood(vessels) - events involved in vascular disorders.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2023.03.004},
pmid = {37059363},
issn = {2320-2890},
abstract = {In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.},
}
@article {pmid37057308,
year = {2023},
author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R},
title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13157},
pmid = {37057308},
issn = {1758-2229},
abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.},
}
@article {pmid37043523,
year = {2023},
author = {Rümpler, F and Tessari, C and Gramzow, L and Gafert, C and Blohs, M and Theißen, G},
title = {The origin of floral quartet formation - Ancient exon duplications shaped the evolution of MIKC-type MADS-domain transcription factor interactions.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad088},
pmid = {37043523},
issn = {1537-1719},
abstract = {During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute "floral quartets"or related "floral quartet-like complexes"(FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerisation of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerisation and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that FQC formation likely originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus, generating the tetramerisation interface found in extant MIKCC type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other K-domain exons occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerisation between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.},
}
@article {pmid37040705,
year = {2023},
author = {Wegmann, D and Eckel, R},
title = {Human evolution: When admixture met selection.},
journal = {Current biology : CB},
volume = {33},
number = {7},
pages = {R259-R261},
doi = {10.1016/j.cub.2023.02.077},
pmid = {37040705},
issn = {1879-0445},
abstract = {Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.},
}
@article {pmid37002784,
year = {2023},
author = {Honap, TP and Monroe, CR and Johnson, SJ and Jacobson, DK and Abin, CA and Austin, RM and Sandberg, P and Levine, M and Sankaranarayanan, K and Lewis, CM},
title = {Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24735},
pmid = {37002784},
issn = {2692-7691},
abstract = {OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.<br><br>MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450&#x2009;CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.<br><br>RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.<br><br>DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.},
}
@article {pmid37002389,
year = {2023},
author = {Callaway, E},
title = {Ancient DNA illuminates Swahili culture's origins.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37002389},
issn = {1476-4687},
}
@article {pmid36996223,
year = {2023},
author = {Curry, A},
title = {'Persian princes' helped found early African trade power.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6639},
pages = {1284-1285},
doi = {10.1126/science.adi0093},
pmid = {36996223},
issn = {1095-9203},
abstract = {Ancient DNA reflects foreign influx to Swahili coast, but its culture is largely local.},
}
@article {pmid36994803,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13790},
pmid = {36994803},
issn = {1755-0998},
abstract = {Innovations in ancient DNA (aDNA) preparation and sequencing technologies have exponentially increased the quality and quantity of aDNA data extracted from ancient biological materials. The additional temporal component from the incoming aDNA data can provide improved power to address fundamental evolutionary questions like characterising selection processes that shape the phenotypes and genotypes of contemporary populations or species. However, utilising aDNA to study past selection processes still involves considerable hurdles like how to eliminate the confounding factor of genetic interactions in the inference of selection. To address this issue, we extend the approach of He et al. (2022) to infer temporally variable selection from the aDNA data in the form of genotype likelihoods with the flexibility of modelling linkage and epistasis in this work. Our posterior computation is carried out by a robust adaptive version of the particle marginal Metropolis-Hastings algorithm with a coerced acceptance rate. Our extension inherits the desirable features of He et al. (2022) such as modelling sample uncertainty resulting from the damage and fragmentation of aDNA molecules and reconstructing underlying gamete frequency trajectories of the population. We evaluate its performance through extensive simulations and show its utility with an application to the aDNA data from pigmentation loci in horses.},
}
@article {pmid36993413,
year = {2023},
author = {Barton, AR and Santander, CG and Skoglund, P and Moltke, I and Reich, D and Mathieson, I},
title = {Insufficient evidence for natural selection associated with the Black Death.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.14.532615},
pmid = {36993413},
abstract = {Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2 , for which they estimate a selection coefficient of 0.39â€"several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis , we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.},
}
@article {pmid36991187,
year = {2023},
author = {Brielle, ES and Fleisher, J and Wynne-Jones, S and Sirak, K and Broomandkhoshbacht, N and Callan, K and Curtis, E and Iliev, L and Lawson, AM and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Zalzala, F and Ayodo, G and Gidna, AO and Kabiru, A and Kwekason, A and Mabulla, AZP and Manthi, FK and Ndiema, E and Ogola, C and Sawchuk, E and Al-Gazali, L and Ali, BR and Ben-Salem, S and Letellier, T and Pierron, D and Radimilahy, C and Rakotoarisoa, JA and Raaum, RL and Culleton, BJ and Mallick, S and Rohland, N and Patterson, N and Mwenje, MA and Ahmed, KB and Mohamed, MM and Williams, SR and Monge, J and Kusimba, S and Prendergast, ME and Reich, D and Kusimba, CM},
title = {Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.},
journal = {Nature},
volume = {615},
number = {7954},
pages = {866-873},
pmid = {36991187},
issn = {1476-4687},
abstract = {The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people[1,2]. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast[3]. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia[4]. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.},
}
@article {pmid36980999,
year = {2023},
author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D},
title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030727},
pmid = {36980999},
issn = {2073-4425},
abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.},
}
@article {pmid36980972,
year = {2023},
author = {Sharko, F and Slobodova, N and Boulygina, E and Cheprasov, M and Gladysheva-Azgari, M and Tsygankova, S and Rastorguev, S and Novgorodov, G and Boeskorov, G and Grigorieva, L and Hwang, WS and Tikhonov, A and Nedoluzhko, A},
title = {Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030700},
pmid = {36980972},
issn = {2073-4425},
abstract = {Paleoclimatic changes during the Pleistocene-Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller's sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene-Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the "young" specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.},
}
@article {pmid36968599,
year = {2023},
author = {Yu, HX and Ao, C and Wang, XP and Zhang, XP and Sun, J and Li, H and Liu, KJ and Wei, LH},
title = {The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1139722},
pmid = {36968599},
issn = {1664-8021},
abstract = {Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis. Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch. Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China. Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.},
}
@article {pmid36967935,
year = {2023},
author = {Sen, A and Andersen, LW and Kjeldsen, KU and Michel, LN and Hong, WL and Choquet, M and Rasmussen, TL},
title = {The phylogeography and ecology of Oligobrachia frenulate species suggest a generalist chemosynthesis-based fauna in the arctic.},
journal = {Heliyon},
volume = {9},
number = {3},
pages = {e14232},
pmid = {36967935},
issn = {2405-8440},
abstract = {We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments). Due to its similarity with O. webbi, the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known.},
}
@article {pmid36966434,
year = {2023},
author = {Hixson, KK and Fajardo, DA and Devitt, NP and Sena, JA and Costa, MA and Meng, Q and Boschiero, C and Zhao, PX and Baack, E and Paurus, VL and Davin, LB and Lewis, NG and Bell, CJ},
title = {Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkad060},
pmid = {36966434},
issn = {2160-1836},
abstract = {Red alder (Alnus rubra Bong.) is an ecologically significant and important, fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen fixing symbiosis, and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation and wood quality traits. We established that this clone is most likely diploid, and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales, and established some similarities with previous reports in this clade suggesting biased retention of certain gene functions in the vestiges of an ancient genome duplication as compared to more recent tandem duplications.},
}
@article {pmid36964154,
year = {2023},
author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U},
title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1650},
pmid = {36964154},
issn = {2041-1723},
abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.},
}
@article {pmid36963383,
year = {2023},
author = {Davy, T and Ju, D and Mathieson, I and Skoglund, P},
title = {Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.02.049},
pmid = {36963383},
issn = {1879-0445},
abstract = {Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.[1][,][2][,][3][,][4] Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10[-56]). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.},
}
@article {pmid36958333,
year = {2023},
author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J},
title = {Genomic analyses of hair from Ludwig van Beethoven.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.02.041},
pmid = {36958333},
issn = {1879-0445},
abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.},
}
@article {pmid36951219,
year = {2023},
author = {Kolbe, D and da Silva, NA and Dose, J and Torres, GG and Caliebe, A and Krause-Kyora, B and Nebel, A},
title = {Current allele distribution of the human longevity gene APOE in Europe can mainly be explained by ancient admixture.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e13819},
doi = {10.1111/acel.13819},
pmid = {36951219},
issn = {1474-9726},
abstract = {Variation in apolipoprotein E (APOE) has been shown to have the strongest genetic effect on human longevity. The aim of this study was to unravel the evolutionary history of the three major APOE alleles in Europe by analysing ancient samples up to 12,000 years old. We detected significant allele frequency shifts between populations and over time. Our analyses indicated that selection led to large frequency differences between the earliest European populations (i.e., hunter-gatherers vs. first farmers), possibly due to changes in diet/lifestyle. In contrast, the allele distributions in populations from ~4000 BCE onward can mainly be explained by admixture, suggesting that it also played an important role in shaping current APOE variation. In any case, the resulting allele frequencies strongly influence the predisposition for longevity today, likely as a consequence of past adaptations and demographic processes.},
}
@article {pmid36945531,
year = {2023},
author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Patterson, N and Reich, D},
title = {ancIBD - Screening for identity by descent segments in human ancient DNA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.08.531671},
pmid = {36945531},
abstract = {Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.},
}
@article {pmid36933795,
year = {2023},
author = {Zhang, G and Cui, C and Wangdue, S and Lu, H and Chen, H and Xi, L and He, W and Yuan, H and Tsring, T and Chen, Z and Yang, F and Tsering, T and Li, S and Tashi, N and Yang, T and Tong, Y and Wu, X and Li, L and He, Y and Cao, P and Dai, Q and Liu, F and Feng, X and Wang, T and Yang, R and Ping, W and Zhang, M and Gao, X and Liu, Y and Wang, W and Fu, Q},
title = {Maternal genetic history of ancient Tibetans over the past 4000 years.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2023.03.007},
pmid = {36933795},
issn = {1673-8527},
abstract = {The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstructed a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show ancient Tibetans shared the most recent common ancestor (TMRCA) with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians varied over the past 4000 years, with a stronger matrilineal connection between the two during 4000-3000 BP, and a weakened connection after 3000 BP, that coincident with climate change, followed by a reinforced connection after the Tubo period (1400-1100 BP). Besides, an over 4000-year matrilineal continuity was observed in some of the maternal lineages. We also found the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that were dynamically shaped by geography, climate changes, as well as historical events.},
}
@article {pmid36930997,
year = {2023},
author = {Schats, R},
title = {Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {32-42},
doi = {10.1016/j.ijpp.2023.03.002},
pmid = {36930997},
issn = {1879-9825},
abstract = {OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.<br><br>MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.<br><br>METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.<br><br>RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.<br><br>CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.<br><br>SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.<br><br>LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.<br><br>More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.},
}
@article {pmid36930529,
year = {2023},
author = {de-Dios, T and Scheib, CL and Houldcroft, CJ},
title = {An adagio for viruses, played out on ancient DNA.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad047},
pmid = {36930529},
issn = {1759-6653},
abstract = {Studies of ancient DNA have transformed our understanding of human evolution. Palaeogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic and pandemic pathogens. Viruses - and in particular those with single or double-stranded DNA genomes - are an important part of the palaeogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly-evolving viruses which cause disease. In this review, we will revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We will look at how palaeogenomics works for viral pathogens, such as the need for careful precautions against modern contamination, and robust computational pipelines to identify and analyse authenticated viral sequences. We will discuss the insights into virus evolution which have been gained through palaeogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.},
}
@article {pmid36922577,
year = {2023},
author = {Kerner, G and Choin, J and Quintana-Murci, L},
title = {Ancient DNA as a tool for medical research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {36922577},
issn = {1546-170X},
}
@article {pmid36919783,
year = {2023},
author = {Motti, JMB and Pauro, M and Scabuzzo, C and García, A and Aldazábal, V and Vecchi, R and Bayón, C and Pastor, N and Demarchi, DA and Bravi, CM and Reich, D and Cabana, GS and Nores, R},
title = {Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24727},
pmid = {36919783},
issn = {2692-7691},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.<br><br>MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723&#x2009;cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.<br><br>RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000&#x2009;years BP.<br><br>DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.},
}
@article {pmid36918761,
year = {2023},
author = {Marsh, WA and Brace, S and Barnes, I},
title = {Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {111},
pmid = {36918761},
issn = {1471-2164},
abstract = {BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material.<br><br>RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors).<br><br>CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (<&#x2009;0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.},
}
@article {pmid36859677,
year = {2023},
author = {Callaway, E},
title = {Ancient genomes show how humans escaped Europe's deep freeze.},
journal = {Nature},
volume = {615},
number = {7951},
pages = {197-198},
pmid = {36859677},
issn = {1476-4687},
mesh = {Humans ; Europe ; *Genome, Human ; *DNA, Ancient/analysis ; *Human Migration/history ; Freezing ; *Cold Temperature ; History, Ancient ; },
}
@article {pmid36890036,
year = {2023},
author = {Johnson, OL and Tobler, R and Schmidt, JM and Huber, CD},
title = {Fluctuating selection and the determinants of genetic variation.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.02.004},
pmid = {36890036},
issn = {0168-9525},
abstract = {Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.},
}
@article {pmid36869137,
year = {2023},
author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M},
title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {240},
pmid = {36869137},
issn = {2399-3642},
abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.},
}
@article {pmid36862777,
year = {2023},
author = {Curry, A},
title = {Ancient DNA upends European prehistory.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6635},
pages = {865-866},
doi = {10.1126/science.adh3912},
pmid = {36862777},
issn = {1095-9203},
abstract = {Genes reveal striking diversity within similar ice age cultures.},
}
@article {pmid36855115,
year = {2023},
author = {Nyerki, E and Kalmár, T and Schütz, O and Lima, RM and Neparáczki, E and Török, T and Maróti, Z},
title = {correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {38},
pmid = {36855115},
issn = {1474-760X},
abstract = {Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.},
}
@article {pmid36458990,
year = {2023},
author = {Flohr, S},
title = {Canine dimensions for estimation of sex in adult and non-adult individuals with external validation by aDNA.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {80},
number = {2},
pages = {225-231},
doi = {10.1127/anthranz/2022/1653},
pmid = {36458990},
issn = {0003-5548},
mesh = {Humans ; Female ; *Tooth ; DNA, Ancient ; Discriminant Analysis ; Germany ; *Sex Determination by Skeleton/methods ; },
abstract = {Using discriminant functions obtained from canine dimensions for sex estimation in human skeletons has frequently been proposed as a promising approach within assemblages, even when used in non-adult individuals. However, applicability of this method to adult and non-adult individuals from other assemblages was rarely investigated, probably due to frequently observed inter-population differences in tooth dimensions. In the present study, discriminant functions obtained for permanent canine dimensions at the cemento-enamel junction in a previous study of the early medieval assemblage from Greding, were applied to individuals from a late medieval Jewish cemetery at Erfurt, Germany. The results were validated by aDNA analyses. Prior to the application of the functions, canine dimensions of the assemblages were compared. The comparison showed largely corresponding canine dimensions between the two assemblages. The application of the formulae obtained on the early medieval assemblage to the late medieval assemblage at Erfurt revealed a 100 % correct classification rate in the adult individuals. In non-adults, the correct classification rate was poorer, with 7 of 9 (77.8 %) individuals correctly classified. The study showed that the application of discriminant functions for sex estimation from canine measurements to assemblages other than those for which the functions were developed can lead to high correct classification rates in adults if the average canine dimensions are similar in the respective assemblages. An application to non-adult individuals should only be made with caution as canine dimensions in the "non-survivors" can lead to an over-estimation of the proportion of female non-adults.},
}
@article {pmid33267568,
year = {2023},
author = {Gerussi, A and Halliday, N and Carbone, M and Invernizzi, P and Thorburn, D},
title = {Open challenges in the management of autoimmune hepatitis.},
journal = {Minerva gastroenterology},
volume = {69},
number = {1},
pages = {61-83},
doi = {10.23736/S2724-5895.20.02805-6},
pmid = {33267568},
issn = {2724-5365},
abstract = {Autoimmune hepatitis (AIH) is a rare autoimmune disease of the liver with many open questions as regards its etiopathogenesis, natural history and clinical management. The classical picture of AIH is chronic hepatitis with fluctuating elevation of serum transaminases and Immunoglobulin G levels, the presence of circulating autoantibodies and typical histological features. However, atypical presentations do occur and are not well captured by current diagnostic scores, with important consequences in terms of missed diagnoses and delayed treatments. AIH is treated with corticosteroids and immunosuppressive drugs but up to 40% of patients do not achieve full biochemical response and are at risk of progressing to cirrhosis and liver failure. Moreover, standard therapies are associated by significant side-effects which may impair the quality of life of patients living with AIH. However, advances in the understanding of the underlying immunology of AIH is raising the prospect of novel therapies and optimization of existing therapeutic approaches to reduce side-effect burdens and potentially restore immunological tolerance. In this review we outlined the clinical characteristics, etiopathogenesis and management of AIH and current challenges in the diagnosis and management of AIH and provided evidence underlying the evolution of diagnostic and clinical management protocols.},
}
@article {pmid36853456,
year = {2023},
author = {Ayling, C},
title = {TA Cloning Approaches to Cloning DNA with Damaged Ends DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {55-64},
pmid = {36853456},
issn = {1940-6029},
abstract = {DNA ends can become damaged for various reasons making them unsuitable for TA cloning techniques, the easiest and most common of the DNA cloning technologies. Examples of end-damaged DNA include ancient DNA and those produced by laboratory methods such as sonication. In this chapter, we discuss how to deal with end-damaged DNA prior to cloning with either the popular pGEM[®]-T Easy Vector Systems Kit and TOPO™ TA Cloning™ Kits.},
}
@article {pmid36853452,
year = {2023},
author = {Mikić, A and Alomari, A and Gowers, DM},
title = {Classical Recombinant DNA Cloning.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {1-24},
pmid = {36853452},
issn = {1940-6029},
abstract = {Traditional molecular cloning involves a series of linked experimental steps performed with the overall goal of isolating ("cloning") a specific DNA sequence-often a gene. The main purpose of cloning is to study either that DNA sequence or the RNA or protein product it encodes. Building on key enzymatic discoveries in the late 1960s, gene cloning was pioneered in the early 1970s. Since then, DNA cloning and manipulation have been used in every area of biological and biomedical research, from molecular genetics, structural biology, and developmental biology to neurobiology, ancient DNA studies, and immunology. It is a versatile technique that can be applied to a variety of starting DNA types and lengths, including cDNAs, genes, gene fragments, chromosomal regions, or shorter fragments such as PCR products and functional control regions such as enhancers or promoters. The starting DNA can originate from any cell, tissue, or organism. In this chapter we will cover traditional ("classic") molecular cloning strategy. This comprises six linked stages in which (1) PCR is used to amplify a DNA region of interest that is then (2) digested with restriction enzymes, alongside a selected vector, to produce complementary ends crucial for the two molecules to be (3) ligated by an ATP-dependent DNA ligase, creating a recombinant DNA molecule. The recombinant DNA is then (4) introduced into competent bacterial cells by transformation and (5) grown on a selective agar media, followed by (6) colony-PCR for screening purposes. We provide a worked example to demonstrate the cloning of an average-size gene (in this case the 2 kb DNA ligase A gene) from E. coli into a common plasmid expression vector. We have included six color figures and two tables to depict the key stages of a classical molecular cloning protocol. If you are cloning a segment of DNA or a gene, remember that each DNA cloning experiment is unique in terms of sequence, length, and experimental purpose. However, the principles of traditional cloning covered in this chapter are the same for any DNA sequence; we have included a detailed notes section, so you should easily be able to transfer them to your own work. Some of the following chapters in this volume will cover other, more recently developed, cloning protocols.},
}
@article {pmid36847465,
year = {2022},
author = {Hublin, JJ and Changeux, JP},
title = {Paleoanthropology of cognition: an overview on Hominins brain evolution.},
journal = {Comptes rendus biologies},
volume = {345},
number = {2},
pages = {57-75},
doi = {10.5802/crbiol.92},
pmid = {36847465},
issn = {1768-3238},
abstract = {Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.},
}
@article {pmid36821583,
year = {2023},
author = {Schmid, C and Schiffels, S},
title = {Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {9},
pages = {e2218375120},
doi = {10.1073/pnas.2218375120},
pmid = {36821583},
issn = {1091-6490},
mesh = {Humans ; History, Ancient ; *Genomics ; *DNA, Ancient/analysis ; Europe ; },
abstract = {The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility.},
}
@article {pmid36841239,
year = {2023},
author = {Eaton, K and Sidhu, RK and Klunk, J and Gamble, JA and Boldsen, JL and Carmichael, AG and Varlık, N and Duchene, S and Featherstone, L and Grimes, V and Golding, GB and DeWitte, SN and Holmes, EC and Poinar, HN},
title = {Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.01.064},
pmid = {36841239},
issn = {1879-0445},
abstract = {The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.[1][,][2] A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.[3] Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.[4][,][5] To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.},
}
@article {pmid36834612,
year = {2023},
author = {Bruno, F and Abondio, P and Montesanto, A and Luiselli, D and Bruni, AC and Maletta, R},
title = {The Nerve Growth Factor Receptor (NGFR/p75[NTR]): A Major Player in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
doi = {10.3390/ijms24043200},
pmid = {36834612},
issn = {1422-0067},
abstract = {Alzheimer's disease (AD) represents the most prevalent type of dementia in elderly people, primarily characterized by brain accumulation of beta-amyloid (Aβ) peptides, derived from Amyloid Precursor Protein (APP), in the extracellular space (amyloid plaques) and intracellular deposits of the hyperphosphorylated form of the protein tau (p-tau; tangles or neurofibrillary aggregates). The Nerve growth factor receptor (NGFR/p75[NTR]) represents a low-affinity receptor for all known mammalians neurotrophins (i.e., proNGF, NGF, BDNF, NT-3 e NT-4/5) and it is involved in pathways that determine both survival and death of neurons. Interestingly, also Aβ peptides can blind to NGFR/p75[NTR] making it the "ideal" candidate in mediating Aβ-induced neuropathology. In addition to pathogenesis and neuropathology, several data indicated that NGFR/p75[NTR] could play a key role in AD also from a genetic perspective. Other studies suggested that NGFR/p75[NTR] could represent a good diagnostic tool, as well as a promising therapeutic target for AD. Here, we comprehensively summarize and review the current experimental evidence on this topic.},
}
@article {pmid36833406,
year = {2023},
author = {Dalal, V and Pasupuleti, N and Chaubey, G and Rai, N and Shinde, V},
title = {Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020479},
pmid = {36833406},
issn = {2073-4425},
abstract = {Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.},
}
@article {pmid36833230,
year = {2023},
author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA},
title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020303},
pmid = {36833230},
issn = {2073-4425},
abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.},
}
@article {pmid36819665,
year = {2023},
author = {Kerner, G and Neehus, AL and Philippot, Q and Bohlen, J and Rinchai, D and Kerrouche, N and Puel, A and Zhang, SY and Boisson-Dupuis, S and Abel, L and Casanova, JL and Patin, E and Laval, G and Quintana-Murci, L},
title = {Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe.},
journal = {Cell genomics},
volume = {3},
number = {2},
pages = {100248},
pmid = {36819665},
issn = {2666-979X},
abstract = {Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.},
}
@article {pmid36812666,
year = {2023},
author = {Bľandová, G and Patlevičová, A and Palkovičová, J and Pavlíková, &#x160; and Beňuš, R and Repiská, V and Baldovič, M},
title = {Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {1-7},
doi = {10.1016/j.ijpp.2023.02.001},
pmid = {36812666},
issn = {1879-9825},
abstract = {OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains.<br><br>MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Dev&#xed;n (11th-12th century AD) and C&#xed;fer-P&#xe1;c (8th-9th century AD).<br><br>METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917&#xa0;+&#xa0;326&#xa0;C>T (rs4988235) associated with lactose intolerance.<br><br>RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917&#xa0;+&#xa0;326&#xa0;C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion.<br><br>SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance.<br><br>LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out.<br><br>Genetic research based on larger sample sizes and in more diverse geographical regions.},
}
@article {pmid36812179,
year = {2023},
author = {Kalisher, R and Cradic, MS and Adams, MJ and Martin, MAS and Finkelstein, I},
title = {Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0281020},
doi = {10.1371/journal.pone.0281020},
pmid = {36812179},
issn = {1932-6203},
abstract = {Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death.},
}
@article {pmid36799477,
year = {2023},
author = {Cortez, AD and Lippert, D and Davis, JL and Nicholas, G and Malhi, RS and Weyrich, LS and Claw, KG and Bader, AC and Colwell, C},
title = {Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24714},
pmid = {36799477},
issn = {2692-7691},
abstract = {OBJECTIVES: The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process.<br><br>MATERIALS AND METHODS: We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews.<br><br>RESULTS: Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities.<br><br>DISCUSSION: This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.},
}
@article {pmid36796758,
year = {2023},
author = {Min-Shan Ko, A},
title = {The 2022 Nobel Prize in Physiology or Medicine awarded for the decoding of the complete ancient human genome.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2023.02.004},
pmid = {36796758},
issn = {2320-2890},
abstract = {Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.},
}
@article {pmid36790695,
year = {2022},
author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ},
title = {Metagenomic analysis of Ancient Egyptian canopic jars.},
journal = {American journal of biological anthropology},
volume = {179},
number = {2},
pages = {307-313},
doi = {10.1002/ajpa.24600},
pmid = {36790695},
issn = {2692-7691},
abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.<br><br>OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.<br><br>METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).<br><br>RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.<br><br>DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.},
}
@article {pmid36790664,
year = {2022},
author = {Vigeant, J and Ribot, I and Hélie, JF},
title = {Investigating individual migration life histories: An isotopic case study from 17th to 18th century Nouvelle France.},
journal = {American journal of biological anthropology},
volume = {177},
number = {2},
pages = {232-248},
doi = {10.1002/ajpa.24455},
pmid = {36790664},
issn = {2692-7691},
abstract = {OBJECTIVES: This isotopic study explores the mobility patterns of a growing urban population from Notre Dame's Catholic cemetery (1691-1796), located in Montreal (Canada). The site offers a unique opportunity to investigate early colonial settlement in Nouvelle France through individual life patterns.<br><br>MATERIALS AND METHODS: Stable oxygen isotopic compositions (&#x3b4;[18]O) were measured on the enamel of 32 individuals from the Notre Dame collection. Premolars and third molars were selected, as they reflected the &#x3b4;[18]O of the drinking water during childhood (2.5-5.5&#x2009;years) and pre-adulthood (9.5-15.5&#x2009;years). Firstly, premolars from three children (4-8&#x2009;years of age) allowed us to provide a mean &#x3b4;[18]O for the water consumed locally (22.7&#x2009;&#xb1;&#x2009;&#x2009;1.0 &#x2030; vs. VSMOW). Then, our &#x3b4;[18]O were compared with published data from various geographical regions in North America (Eastern Canada and the United States) and Europe (France and the British Isles) to highlight mobility patterns of each individual.<br><br>RESULTS: Forty-eight percent of our sample (14 out of 29 individuals) did not reflect any long-distance mobility, as all their &#x3b4;[18]O reflected Montreal's variation during their lifetime. The remaining (15 out of 29 individuals) experienced mobility within (n&#xa0;=&#xa0;8) and outside (n&#xa0;=&#xa0;7) North America and at different phases of their life (five at pre-adulthood, six at adulthood and four during both phases). Their migration patterns were analyzed according to age, sex, diet and possible ancestry in order to propose some "biographies."<br><br>DISCUSSION: This study highlights high population diversity in early colonial Montreal. Historians wrote that the city was growing, not only with the arrival of Europeans (e.g., young male workers, sailors), but also other groups (e.g., Indigenous people, slaves from North America). Additional analyses (e.g., ancient DNA) will be needed to explore further this phenomenon.},
}
@article {pmid36790637,
year = {2023},
author = {Balentine, CM and Alfonso-Durruty, M and Reynolds, AW and Vilar, M and Morello, F and Román, MS and Springs, LC and Smith, RWA and Archer, SM and Mata-Míguez, J and Wing, N and Bolnick, DA},
title = {Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.},
journal = {American journal of biological anthropology},
volume = {180},
number = {1},
pages = {144-161},
doi = {10.1002/ajpa.24638},
pmid = {36790637},
issn = {2692-7691},
abstract = {OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.<br><br>METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895&#x2009;cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.<br><br>RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p&#x2009;<&#x2009;0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000&#x2009;cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.<br><br>DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.},
}
@article {pmid36787794,
year = {2023},
author = {Baca, M and Popović, D and Agadzhanyan, AK and Baca, K and Conard, NJ and Fewlass, H and Filek, T and Golubiński, M and Horáček, I and Knul, MV and Krajcarz, M and Krokhaleva, M and Lebreton, L and Lemanik, A and Maul, LC and Nagel, D and Noiret, P and Primault, J and Rekovets, L and Rhodes, SE and Royer, A and Serdyuk, NV and Soressi, M and Stewart, JR and Strukova, T and Talamo, S and Wilczyński, J and Nadachowski, A},
title = {Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1993},
pages = {20222238},
doi = {10.1098/rspb.2022.2238},
pmid = {36787794},
issn = {1471-2954},
abstract = {The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.},
}
@article {pmid36787792,
year = {2022},
author = {Broccard, N and Silva, NM and Currat, M},
title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.},
journal = {American journal of biological anthropology},
volume = {177},
number = {1},
pages = {134-146},
doi = {10.1002/ajpa.24431},
pmid = {36787792},
issn = {2692-7691},
abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.<br><br>MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.<br><br>RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.<br><br>DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.},
}
@article {pmid36762361,
year = {2022},
author = {Riedel, A},
title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.},
journal = {ZooKeys},
volume = {1124},
number = {},
pages = {109-130},
pmid = {36762361},
issn = {1313-2989},
abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka &amp; Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo &amp; Riedel is chosen to prevail over T.tounaensis Narakusumo &amp; Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.},
}
@article {pmid36760997,
year = {2023},
author = {Chang, X and Pamjav, H and Zhabagin, M and Wen, S},
title = {Editorial: The genetic history of human populations along the ancient silk road.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1130104},
pmid = {36760997},
issn = {1664-8021},
}
@article {pmid36755065,
year = {2021},
author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C},
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {66},
pmid = {36755065},
issn = {2730-6151},
abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.},
}
@article {pmid36750197,
year = {2023},
author = {Tiwari, J and Sur, S and Yadav, A and Kumar, R and Rai, N and Rani, S and Malik, S},
title = {Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1992},
pages = {20222374},
doi = {10.1098/rspb.2022.2374},
pmid = {36750197},
issn = {1471-2954},
abstract = {The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca[2+]/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca[2+] signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.},
}
@article {pmid36748324,
year = {2023},
author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L},
title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16859},
pmid = {36748324},
issn = {1365-294X},
abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.},
}
@article {pmid36747166,
year = {2023},
author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F},
title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {9},
pmid = {36747166},
issn = {1741-7007},
abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.<br><br>RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.<br><br>CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.},
}
@article {pmid36721228,
year = {2023},
author = {Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M and He, G},
title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.},
journal = {Human genomics},
volume = {17},
number = {1},
pages = {3},
doi = {10.1186/s40246-023-00452-0},
pmid = {36721228},
issn = {1479-7364},
abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.<br><br>OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.<br><br>RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.<br><br>CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.},
}
@article {pmid36714834,
year = {2022},
author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C},
title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac148},
pmid = {36714834},
issn = {2752-6542},
abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.},
}
@article {pmid36712342,
year = {2022},
author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG},
title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac209},
pmid = {36712342},
issn = {2752-6542},
abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.},
}
@article {pmid36691623,
year = {2023},
author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC},
title = {Genetic and functional odorant receptor variation in the Homo lineage.},
journal = {iScience},
volume = {26},
number = {1},
pages = {105908},
pmid = {36691623},
issn = {2589-0042},
abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.},
}
@article {pmid36672975,
year = {2023},
author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K},
title = {Methodological Changes in the Field of Paleogenetics.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010234},
pmid = {36672975},
issn = {2073-4425},
abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.},
}
@article {pmid36672874,
year = {2023},
author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A},
title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010133},
pmid = {36672874},
issn = {2073-4425},
abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.},
}
@article {pmid36672816,
year = {2022},
author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA},
title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010075},
pmid = {36672816},
issn = {2073-4425},
abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.},
}
@article {pmid36669262,
year = {2023},
author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J},
title = {Kinship analysis of skeletal remains from the Middle Ages.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102829},
doi = {10.1016/j.fsigen.2023.102829},
pmid = {36669262},
issn = {1878-0326},
abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.},
}
@article {pmid36661852,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA Data.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad008},
pmid = {36661852},
issn = {1537-1719},
abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies, and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat colouration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.},
}
@article {pmid36661298,
year = {2023},
author = {Henriksen, RA and Zhao, L and Korneliussen, TS},
title = {NGSNGS: Next generation simulator for next generation sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad041},
pmid = {36661298},
issn = {1367-4811},
abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data has become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here we present a multithreaded next-generation simulation tool for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform specific characteristics based on nucleotide quality score profiles, as well as including a post-mortem damage model which is relevant for simulating ancient DNA (aDNA). The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies, or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.<br><br>AVAILABILITY: The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36658311,
year = {2023},
author = {Eaton, K and Featherstone, L and Duchene, S and Carmichael, AG and Varlık, N and Golding, GB and Holmes, EC and Poinar, HN},
title = {Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {23},
pmid = {36658311},
issn = {2399-3642},
abstract = {Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.},
}
@article {pmid36656838,
year = {2023},
author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE},
title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.},
journal = {PLoS genetics},
volume = {19},
number = {1},
pages = {e1010551},
doi = {10.1371/journal.pgen.1010551},
pmid = {36656838},
issn = {1553-7404},
abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.},
}
@article {pmid36653523,
year = {2023},
author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S},
title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {72},
pmid = {36653523},
issn = {2399-3642},
abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.},
}
@article {pmid36654346,
year = {2021},
author = {Liu, J and Zeng, W and Sun, B and Mao, X and Zhao, Y and Wang, F and Li, Z and Luan, F and Guo, J and Zhu, C and Wang, Z and Wei, C and Zhang, M and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Hou, W and Ping, W and Wu, X and Andrew Bennett, E and Liu, Y and Fu, Q},
title = {Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago.},
journal = {Science bulletin},
volume = {66},
number = {11},
pages = {1129-1135},
doi = {10.1016/j.scib.2021.01.029},
pmid = {36654346},
issn = {2095-9281},
abstract = {Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.},
}
@article {pmid36650598,
year = {2023},
author = {Popli, D and Peyrégne, S and Peter, BM},
title = {KIN: a method to infer relatedness from low-coverage ancient DNA.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {10},
pmid = {36650598},
issn = {1474-760X},
abstract = {Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.},
}
@article {pmid36649412,
year = {2023},
author = {Wang, X and Skourtanioti, E and Benz, M and Gresky, J and Ilgner, J and Lucas, M and Morsch, M and Peters, J and Pöllath, N and Ringbauer, H and le Roux, P and Schultz, M and Krause, J and Roberts, P and Stockhammer, PW},
title = {Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2210611120},
doi = {10.1073/pnas.2210611120},
pmid = {36649412},
issn = {1091-6490},
abstract = {Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ([87]Sr/[86]Sr), carbon, and oxygen (δ[18]O and δ[13]Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. [87]Sr/[86]Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.},
}
@article {pmid36649410,
year = {2023},
author = {Lewis, CM and Akinyi, MY and DeWitte, SN and Stone, AC},
title = {Ancient pathogens provide a window into health and well-being.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2209476119},
doi = {10.1073/pnas.2209476119},
pmid = {36649410},
issn = {1091-6490},
abstract = {This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.},
}
@article {pmid36646948,
year = {2023},
author = {Skourtanioti, E and Ringbauer, H and Gnecchi Ruscone, GA and Bianco, RA and Burri, M and Freund, C and Furtwängler, A and Gomes Martins, NF and Knolle, F and Neumann, GU and Tiliakou, A and Agelarakis, A and Andreadaki-Vlazaki, M and Betancourt, P and Hallager, BP and Jones, OA and Kakavogianni, O and Kanta, A and Karkanas, P and Kataki, E and Kissas, K and Koehl, R and Kvapil, L and Maran, J and McGeorge, PJP and Papadimitriou, A and Papathanasiou, A and Papazoglou-Manioudaki, L and Paschalidis, K and Polychronakou-Sgouritsa, N and Preve, S and Prevedorou, EA and Price, G and Protopapadaki, E and Schmidt-Schultz, T and Schultz, M and Shelton, K and Wiener, MH and Krause, J and Jeong, C and Stockhammer, PW},
title = {Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {36646948},
issn = {2397-334X},
abstract = {The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.},
}
@article {pmid36641836,
year = {2023},
author = {Barrenechea Angeles, I and Romero-Martínez, ML and Cavaliere, M and Varrella, S and Francescangeli, F and Piredda, R and Mazzocchi, MG and Montresor, M and Schirone, A and Delbono, I and Margiotta, F and Corinaldesi, C and Chiavarini, S and Montereali, MR and Rimauro, J and Parrella, L and Musco, L and Dell'Anno, A and Tangherlini, M and Pawlowski, J and Frontalini, F},
title = {Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.},
journal = {Environment international},
volume = {172},
number = {},
pages = {107738},
doi = {10.1016/j.envint.2023.107738},
pmid = {36641836},
issn = {1873-6750},
abstract = {The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.},
}
@article {pmid36638796,
year = {2022},
author = {Wang, K and Yu, H and Radzevičiūtė, R and Kiryushin, YF and Tishkin, AA and Frolov, YV and Stepanova, NF and Kiryushin, KY and Kungurov, AL and Shnaider, SV and Tur, SS and Tiunov, MP and Zubova, AV and Pevzner, M and Karimov, T and Buzhilova, A and Slon, V and Jeong, C and Krause, J and Posth, C},
title = {Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.062},
pmid = {36638796},
issn = {1879-0445},
abstract = {The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.},
}
@article {pmid36637197,
year = {2023},
author = {Neuenschwander, S and Cruz Dávalos, DI and Anchieri, L and Sousa da Mota, B and Bozzi, D and Rubinacci, S and Delaneau, O and Rasmussen, S and Malaspinas, AS},
title = {Mapache: a flexible pipeline to map ancient DNA.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad028},
pmid = {36637197},
issn = {1367-4811},
abstract = {SUMMARY: We introduce mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets-such as reference panels and multiple extracts and libraries per sample-to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.<br><br>AVAILABILITY: Mapache is freely available on GitHub (https://github.com/sneuensc/mapache).<br><br>SUPPLEMENTARY INFORMATION: The list of software (and their references) used in the pipeline and the benchmark results can be found in the Supplementary files. An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.},
}
@article {pmid36630487,
year = {2023},
author = {Kehlmaier, C and Graciá, E and Ali, JR and Campbell, PD and Chapman, SD and Deepak, V and Ihlow, F and Jalil, NE and Pierre-Huyet, L and Samonds, KE and Vences, M and Fritz, U},
title = {Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar.},
journal = {Science advances},
volume = {9},
number = {2},
pages = {eabq2574},
doi = {10.1126/sciadv.abq2574},
pmid = {36630487},
issn = {2375-2548},
abstract = {Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.},
}
@article {pmid36625884,
year = {2023},
author = {Xu, Y and Wang, N and Gao, S and Li, C and Ma, P and Yang, S and Jiang, H and Shi, S and Wu, Y and Zhang, Q and Cui, Y},
title = {Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {36625884},
issn = {1437-1596},
abstract = {Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.},
}
@article {pmid36625391,
year = {2023},
author = {Straiton, J},
title = {Ancient DNA sequencing: telling the tale of human history and evolution.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2022-0121},
pmid = {36625391},
issn = {1940-9818},
abstract = {Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].},
}
@article {pmid36623185,
year = {2023},
author = {Fleskes, RE and Cabana, GS and Gilmore, JK and Juarez, C and Karcher, E and Oubré, L and Mishoe, G and Ofunniyin, AA and Schurr, TG},
title = {Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {3},
pages = {e2201620120},
doi = {10.1073/pnas.2201620120},
pmid = {36623185},
issn = {1091-6490},
abstract = {In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.},
}
@article {pmid36620416,
year = {2023},
author = {Alfieri, JM and Johnson, T and Linderholm, A and Blackmon, H and Athrey, GN},
title = {Genomic investigation refutes record of most diverged avian hybrid.},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9689},
pmid = {36620416},
issn = {2045-7758},
abstract = {The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.},
}
@article {pmid36618122,
year = {2021},
author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP},
title = {The genomic origin of Zana of Abkhazia.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {2},
number = {2},
pages = {e10051},
pmid = {36618122},
issn = {2641-6573},
abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.},
}
@article {pmid36610858,
year = {2022},
author = {Miao, B and Liu, Y and Yang, R and Feng, X and Liu, F and Cao, P and Dai, Q and Ping, W and Liu, Y and Fu, Q},
title = {Assessment of contaminants associated with gold-standard ancient DNA protocols.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2022.12.027},
pmid = {36610858},
issn = {2095-9281},
}
@article {pmid36593352,
year = {2023},
author = {Montag, A},
title = {[The history of skin color is the history of mankind!].},
journal = {Dermatologie (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {36593352},
issn = {2731-7013},
abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.},
}
@article {pmid36582485,
year = {2022},
author = {Zhu, K and Du, P and Li, J and Zhang, J and Hu, X and Meng, H and Chen, L and Zhou, B and Yang, X and Xiong, J and Allen, E and Ren, X and Ding, Y and Xu, Y and Chang, X and Yu, Y and Han, S and Dong, G and Wang, CC and Wen, S},
title = {Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105636},
pmid = {36582485},
issn = {2589-0042},
abstract = {A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.},
}
@article {pmid36581666,
year = {2022},
author = {Changmai, P and Pinhasi, R and Pietrusewsky, M and Stark, MT and Ikehara-Quebral, RM and Reich, D and Flegontov, P},
title = {Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22507},
pmid = {36581666},
issn = {2045-2322},
abstract = {Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.},
}
@article {pmid36576953,
year = {2022},
author = {Nägele, K and Rivollat, M and Yu, H and Wang, K},
title = {Ancient genomic research - From broad strokes to nuanced reconstructions of the past.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10017},
pmid = {36576953},
issn = {2037-0644},
abstract = {Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past.},
}
@article {pmid36565457,
year = {2022},
author = {Vallini, L and Pagani, L},
title = {The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10013},
pmid = {36565457},
issn = {2037-0644},
abstract = {The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years.},
}
@article {pmid36555510,
year = {2022},
author = {Abondio, P and Bruno, F and Bruni, AC and Luiselli, D},
title = {Rare Amyloid Precursor Protein Point Mutations Recapitulate Worldwide Migration and Admixture in Healthy Individuals: Implications for the Study of Neurodegeneration.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
doi = {10.3390/ijms232415871},
pmid = {36555510},
issn = {1422-0067},
abstract = {Genetic discoveries related to Alzheimer's disease and other dementias have been performed using either large cohorts of affected subjects or multiple individuals from the same pedigree, therefore disregarding mutations in the context of healthy groups. Moreover, a large portion of studies so far have been performed on individuals of European ancestry, with a remarkable lack of epidemiological and genomic data from underrepresented populations. In the present study, 70 single-point mutations on the APP gene in a publicly available genetic dataset that included 2504 healthy individuals from 26 populations were scanned, and their distribution was analyzed. Furthermore, after gametic phase reconstruction, a pairwise comparison of the segments surrounding the mutations was performed to reveal patterns of haplotype sharing that could point to specific cross-population and cross-ancestry admixture events. Eight mutations were detected in the worldwide dataset, with several of them being specific for a single individual, population, or macroarea. Patterns of segment sharing reflected recent historical events of migration and admixture possibly linked to colonization campaigns. These observations reveal the population dynamics of the considered APP mutations in worldwide human groups and support the development of ancestry-informed screening practices for the improvement of precision and personalized approaches to neurodegeneration and dementia.},
}
@article {pmid36553640,
year = {2022},
author = {Taufik, L and Teixeira, JC and Llamas, B and Sudoyo, H and Tobler, R and Purnomo, GA},
title = {Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/genes13122373},
pmid = {36553640},
issn = {2073-4425},
abstract = {Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.},
}
@article {pmid36546258,
year = {2022},
author = {Wang, Y},
title = {Ancient environmental DNA reveals Arctic ecosystem dynamics in last 50,000 years.},
journal = {Science bulletin},
volume = {67},
number = {13},
pages = {1304-1306},
doi = {10.1016/j.scib.2022.04.018},
pmid = {36546258},
issn = {2095-9281},
mesh = {*Ecosystem ; DNA, Ancient ; *DNA, Environmental ; Arctic Regions ; },
}
@article {pmid36547255,
year = {2022},
author = {van der Kuyl, AC},
title = {Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {3},
number = {4},
pages = {443-464},
doi = {10.3390/epidemiologia3040034},
pmid = {36547255},
issn = {2673-3986},
abstract = {Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.},
}
@article {pmid36536113,
year = {2022},
author = {D'Agostino, A and Di Marco, G and Marvelli, S and Marchesini, M and Rizzoli, E and Rolfo, MF and Canini, A and Gismondi, A},
title = {Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1384},
pmid = {36536113},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Fruit ; Plants, Edible ; Pollen ; Poaceae ; Forests ; DNA, Ancient ; *Calculi ; },
abstract = {Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.},
}
@article {pmid36539480,
year = {2022},
author = {Young, JM and Liddicoat, C and van Dijk, KJ and Tabernero, P and Caillet, C and White, NJ and Linacre, A and Austin, JJ and Newton, PN},
title = {Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets-a pilot study of the pharmabiome.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {21997},
pmid = {36539480},
issn = {2045-2322},
support = {202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; },
abstract = {Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain diverse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven samples of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the 'pharmabiome' shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.},
}
@article {pmid36537881,
year = {2022},
author = {Muktupavela, RA and Petr, M and Ségurel, L and Korneliussen, T and Novembre, J and Racimo, F},
title = {Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.73767},
pmid = {36537881},
issn = {2050-084X},
support = {R01 GM132383/NH/NIH HHS/United States ; 951385/ERC_/European Research Council/International ; },
abstract = {Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.},
}
@article {pmid36531224,
year = {2022},
author = {Xiang, H and Wang, Z and Yang, L and Zhang, X and Zhao, X},
title = {Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1000123},
pmid = {36531224},
issn = {1664-8021},
abstract = {Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10[-3] ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.},
}
@article {pmid36525814,
year = {2022},
author = {Bardan, F and Higgins, D and Austin, JJ},
title = {A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102822},
doi = {10.1016/j.fsigen.2022.102822},
pmid = {36525814},
issn = {1878-0326},
abstract = {Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.},
}
@article {pmid36525576,
year = {2022},
author = {de Flamingh, A and Rivera-Colón, AG and Gnoske, TP and Kerbis Peterhans, JC and Catchen, J and Malhi, RS and Roca, AL},
title = {Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esac065},
pmid = {36525576},
issn = {1465-7333},
abstract = {Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.},
}
@article {pmid36476770,
year = {2022},
author = {Callaway, E},
title = {Oldest-ever DNA shows mastodons roamed Greenland 2 million years ago.},
journal = {Nature},
volume = {612},
number = {7940},
pages = {384},
pmid = {36476770},
issn = {1476-4687},
mesh = {Animals ; Fossils ; Greenland ; *Mastodons/genetics ; *DNA, Ancient/analysis ; History, Ancient ; },
}
@article {pmid36520391,
year = {2023},
author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T},
title = {Analysis of Ancient Microbial DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {103-131},
pmid = {36520391},
issn = {1940-6029},
abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.},
}
@article {pmid36518622,
year = {2022},
author = {Anderson, LA},
title = {Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.},
journal = {Ecology and evolution},
volume = {12},
number = {12},
pages = {e9518},
doi = {10.1002/ece3.9518},
pmid = {36518622},
issn = {2045-7758},
abstract = {Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.},
}
@article {pmid36517229,
year = {2022},
author = {Rohland, N and Mallick, S and Mah, M and Maier, R and Patterson, N and Reich, D},
title = {Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276728.122},
pmid = {36517229},
issn = {1549-5469},
abstract = {The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.},
}
@article {pmid36516232,
year = {2022},
author = {Söylev, A and Çokoglu, SS and Koptekin, D and Alkan, C and Somel, M},
title = {CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.},
journal = {PLoS computational biology},
volume = {18},
number = {12},
pages = {e1010788},
doi = {10.1371/journal.pcbi.1010788},
pmid = {36516232},
issn = {1553-7358},
abstract = {To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.},
}
@article {pmid36514938,
year = {2022},
author = {Rannamäe, E and Saarma, U and Kantanen, J and Bläuer, A},
title = {Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.},
journal = {Animal genetics},
volume = {},
number = {},
pages = {},
doi = {10.1111/age.13281},
pmid = {36514938},
issn = {1365-2052},
abstract = {Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.},
}
@article {pmid36513080,
year = {2022},
author = {Peltola, S and Majander, K and Makarov, N and Dobrovolskaya, M and Nordqvist, K and Salmela, E and Onkamo, P},
title = {Genetic admixture and language shift in the medieval Volga-Oka interfluve.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.036},
pmid = {36513080},
issn = {1879-0445},
abstract = {The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.[1][,][2][,][3] A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9[th] century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.[4][,][5][,][6] In the 10[th]-11[th] centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.[3] This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.},
}
@article {pmid36510283,
year = {2022},
author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B},
title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {250},
pmid = {36510283},
issn = {1474-760X},
support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.<br><br>RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.<br><br>CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.},
}
@article {pmid36494546,
year = {2022},
author = {Forshaw, R},
title = {Dental calculus - oral health, forensic studies and archaeology: a review.},
journal = {British dental journal},
volume = {233},
number = {11},
pages = {961-967},
doi = {10.1038/s41415-022-5266-7},
pmid = {36494546},
issn = {1476-5373},
abstract = {Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.},
}
@article {pmid36493775,
year = {2022},
author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, &#xd6;D and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, &#xd6; and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, &#xc7; and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M},
title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.034},
pmid = {36493775},
issn = {1879-0445},
abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.},
}
@article {pmid36493597,
year = {2022},
author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J},
title = {Reassessment of the human mandible from Banyoles (Girona, Spain).},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103291},
doi = {10.1016/j.jhevol.2022.103291},
pmid = {36493597},
issn = {1095-8606},
abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.},
}
@article {pmid36481947,
year = {2022},
author = {Bundell, S},
title = {Record-breaking ancient DNA found in frozen soil.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-04398-6},
pmid = {36481947},
issn = {1476-4687},
}
@article {pmid36481704,
year = {2022},
author = {Zhang, J and Shi, K and Paerl, HW and Rühland, KM and Yuan, Y and Wang, R and Chen, J and Ge, M and Zheng, L and Zhang, Z and Qin, B and Liu, J and Smol, JP},
title = {Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change.},
journal = {Water research},
volume = {229},
number = {},
pages = {119435},
doi = {10.1016/j.watres.2022.119435},
pmid = {36481704},
issn = {1879-2448},
abstract = {Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.},
}
@article {pmid36472532,
year = {2022},
author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K},
title = {Ecology, not host phylogeny, shapes the oral microbiome in closely related species.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac263},
pmid = {36472532},
issn = {1537-1719},
abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through dietary differences. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.},
}
@article {pmid36465121,
year = {2022},
author = {Ma, X and Xu, S},
title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105614},
pmid = {36465121},
issn = {2589-0042},
abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.},
}
@article {pmid36463384,
year = {2022},
author = {Wang, K and Bleasdale, M and Le Moyne, C and Freund, C and Krause, J and Boivin, N and Schiffels, S},
title = {4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20939},
pmid = {36463384},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient ; Africa, Eastern ; *Hair ; Sudan ; Body Remains ; },
abstract = {Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.},
}
@article {pmid36455558,
year = {2022},
author = {Waldman, S and Backenroth, D and Harney, &#xc9; and Flohr, S and Neff, NC and Buckley, GM and Fridman, H and Akbari, A and Rohland, N and Mallick, S and Olalde, I and Cooper, L and Lomes, A and Lipson, J and Cano Nistal, J and Yu, J and Barzilai, N and Peter, I and Atzmon, G and Ostrer, H and Lencz, T and Maruvka, YE and Lämmerhirt, M and Beider, A and Rutgers, LV and Renson, V and Prufer, KM and Schiffels, S and Ringbauer, H and Sczech, K and Carmi, S and Reich, D},
title = {Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14[th] century.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2022.11.002},
pmid = {36455558},
issn = {1097-4172},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14[th] century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14[th] century and highlight late medieval genetic heterogeneity no longer present in modern AJ.},
}
@article {pmid36454815,
year = {2022},
author = {Curry, A},
title = {Meeting the ancestors.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6623},
pages = {940-943},
doi = {10.1126/science.adg0308},
pmid = {36454815},
issn = {1095-9203},
mesh = {*Jews/genetics ; Population/genetics ; Germany ; Cemeteries/history ; DNA, Ancient ; Humans ; },
abstract = {DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.},
}
@article {pmid36450657,
year = {2022},
author = {Oh, CS and Kim, MJ and Kim, YS and Min, S and Oh, KT and Lee, SD and Shin, DH},
title = {Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.},
journal = {Anatomy &amp; cell biology},
volume = {},
number = {},
pages = {},
doi = {10.5115/acb.22.178},
pmid = {36450657},
issn = {2093-3665},
abstract = {Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.},
}
@article {pmid36437963,
year = {2022},
author = {Charlier, P and Bourdin, V and Augias, A and Brun, L and Kenmogne, JB and Josue, E},
title = {Are museums the future of evolutionary medicine?.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1043702},
pmid = {36437963},
issn = {1664-8021},
}
@article {pmid36437603,
year = {2022},
author = {Jeunen, GJ and Dowle, E and Edgecombe, J and von Ammon, U and Gemmell, NJ and Cross, H},
title = {CRABS - A software program to generate curated reference databases for metabarcoding sequencing data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13741},
pmid = {36437603},
issn = {1755-0998},
abstract = {The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data has been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present CRABS (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. CRABS includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for the immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness, and taxonomic resolution. CRABS is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. CRABS can be installed via Docker and is available for download as a conda package and via GitHub (https://github.com/gjeunen/reference_database_creator).},
}
@article {pmid36426357,
year = {2022},
author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G},
title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {987655},
pmid = {36426357},
issn = {1664-3224},
mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; },
abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.},
}
@article {pmid36414613,
year = {2022},
author = {Quagliariello, A and Modi, A and Innocenti, G and Zaro, V and Conati Barbaro, C and Ronchitelli, A and Boschin, F and Cavazzuti, C and Dellù, E and Radina, F and Sperduti, A and Bondioli, L and Ricci, S and Lognoli, M and Belcastro, MG and Mariotti, V and Caramelli, D and Mariotti Lippi, M and Cristiani, E and Martino, ME and Muntoni, IM and Lari, M},
title = {Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6927},
pmid = {36414613},
issn = {2041-1723},
mesh = {Humans ; *Agriculture ; *Microbiota ; Diet ; Farmers ; Italy ; },
abstract = {The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.},
}
@article {pmid36410480,
year = {2022},
author = {Paquis, P and Hengst, MB and Florez, JZ and Tapia, J and Molina, V and Pérez, V and Pardo-Esté, C},
title = {Short-term characterisation of climatic-environmental variables and microbial community diversity in a high-altitude Andean wetland (Salar de Huasco, Chile).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160291},
doi = {10.1016/j.scitotenv.2022.160291},
pmid = {36410480},
issn = {1879-1026},
abstract = {Microbial community structures are shaped by geochemical factors and their interactions with the lithosphere, hydrosphere, and atmosphere through the processes of chemical mobilisation and mineralisation. High-altitude wetlands and salt flats in the central Andes are characterised by pronounced physicochemical gradients and extreme climatic conditions, representing hotspots of microbial diversity. We here hypothesise about the existence of direct relationships between the local microbiology and the climate cyclicity variables based on meteorological and biogeochemical patterns that develop over a short time scale (five years). We have here analysed the interactions between hydrometeorological and biogeochemical variables and the microbial communities of the Salar de Huasco. These results were obtained by correlating 16S cDNA and DNA gene Illumina sequences with meteorological/satellite data collected both at monitoring stations and by remote sensing between the years 2015 and 2020. The precipitation levels and flooded areas (i.e., areas covered and/or saturated with permanent water) detected in the Salar de Huasco revealed a marked hydric cyclicity that correlated seasonally with intra-annual wet and dry seasons. Overall, at this site, wet periods occurred from December to April, and dry periods from May to November. Meteorological variables such as solar radiation, air temperature, relative humidity, wind speed, atmospheric pressure, and wind direction were well-defined, showing a potential association with the hydrogeology of the area, which is directly related to the wetlands' flooded areas. Finally, the microbial presence and potentially active microbial communities were determined through the sequencing of the 16S gene (DNA and cDNA, respectively), this were associated with climatic seasonality and spatially distributed physical and chemical heterogeneity. Other non-local inter-annual scale processes, such as El Niño-Southern Oscillation (ENSO) events, modify the physical and chemical context of the wetland, thus forming unique ecological niches in the Andean Mountains.},
}
@article {pmid36405775,
year = {2022},
author = {Arzelier, A and Rivollat, M and De Belvalet, H and Pemonge, MH and Binder, D and Convertini, F and Duday, H and Gandelin, M and Guilaine, J and Haak, W and Deguilloux, MF and Pruvost, M},
title = {Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities.},
journal = {iScience},
volume = {25},
number = {11},
pages = {105387},
pmid = {36405775},
issn = {2589-0042},
abstract = {Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.},
}
@article {pmid36400919,
year = {2022},
author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M},
title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1262},
pmid = {36400919},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; },
abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.},
}
@article {pmid36399972,
year = {2022},
author = {Pilli, E and Morelli, S and Poggiali, B and Alladio, E},
title = {Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology.},
journal = {Forensic science international. Genetics},
volume = {62},
number = {},
pages = {102806},
doi = {10.1016/j.fsigen.2022.102806},
pmid = {36399972},
issn = {1878-0326},
abstract = {As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.},
}
@article {pmid36399550,
year = {2022},
author = {Sugiyama, N and Sugiyama, S and Cagnato, C and France, CAM and Iriki, A and Hughes, KS and Singleton, RR and Thornton, E and Hofman, CA},
title = {Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {47},
pages = {e2212431119},
pmid = {36399550},
issn = {1091-6490},
mesh = {Humans ; Animals ; *Diplomacy ; Ceremonial Behavior ; DNA, Ancient ; *Atelinae ; Mexico ; },
abstract = {A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human-primate interaction include age at capture and transport (before ∼3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey's sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state's eventual ascent to prominence.},
}
@article {pmid36377787,
year = {2022},
author = {Ausmees, K and Nettelblad, C},
title = {Achieving improved accuracy for imputation of ancient DNA.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btac738},
pmid = {36377787},
issn = {1367-4811},
abstract = {MOTIVATION: Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.<br><br>RESULTS: We present an implementation called prophaser, and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.<br><br>AVAILABILITY: The C&#x2009;++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser.<br><br>SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.},
}
@article {pmid36375244,
year = {2022},
author = {Harvati, K and Reyes-Centeno, H},
title = {Evolution of Homo in the Middle and Late Pleistocene.},
journal = {Journal of human evolution},
volume = {173},
number = {},
pages = {103279},
doi = {10.1016/j.jhevol.2022.103279},
pmid = {36375244},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; },
abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.},
}
@article {pmid36373266,
year = {2022},
author = {Gaughran, SJ and vonHoldt, B},
title = {Pleistocene parades of carnivores into North America.},
journal = {Molecular ecology},
volume = {31},
number = {24},
pages = {6387-6389},
doi = {10.1111/mec.16783},
pmid = {36373266},
issn = {1365-294X},
mesh = {Animals ; Humans ; *Carnivora/genetics ; Phylogeography ; *Ursidae/genetics ; Biological Evolution ; *Lions ; North America ; Phylogeny ; },
abstract = {The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.},
}
@article {pmid36371979,
year = {2022},
author = {Howarth, A and Drummond, B and Wasef, S and Matheson, CD},
title = {An assessment of DNA extraction methods from blood-stained soil in forensic science.},
journal = {Forensic science international},
volume = {341},
number = {},
pages = {111502},
doi = {10.1016/j.forsciint.2022.111502},
pmid = {36371979},
issn = {1872-6283},
mesh = {Humans ; *Soil ; Polymerase Chain Reaction/methods ; DNA/analysis ; Chloroform/analysis ; Povidone ; Endopeptidase K ; *Blood Stains ; Silicon Dioxide ; },
abstract = {In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.},
}
@article {pmid36360198,
year = {2022},
author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A},
title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
pmid = {36360198},
issn = {2073-4425},
mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.},
}
@article {pmid36359074,
year = {2022},
author = {Armstrong, AJ and Walker, FM and Sobek, CJ and Sanville, CJ and Martin, SL and Szewczak, JM},
title = {Bat Use of Hollows in California's Old-Growth Redwood Forests: From DNA to Ecology.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {21},
pages = {},
pmid = {36359074},
issn = {2076-2615},
abstract = {The loss of roosting resources, either through disturbance or removal, negatively affects bats. Identifying sensitive species and determining roost requirements are critical components in conserving their habitat. Cavity-roosting bats on the North Coast of California are known to use hollows in large redwood trees. In this study, we examined the factors determining the use of basal tree hollows by different bat species at eight redwood forest sites in Del Norte, Humboldt, and Mendocino Counties, California. Bat guano was collected from 179 basal hollow roosts from 2017 to 2018, and guano mass was used as an index of roosting activity. Nine bat species and one species group were identified by analysis of DNA in guano. We made a total of 253 identifications from 83 hollows into the 10 species categories. The most prevalent species were Myotis californicus (California myotis; 28.5% of all identifications), the Myotis evotis-Myotis thysanodes group (17.4%), Corynorhinus townsendii (17.0%), and Myotis volans (15.0%). We evaluated the extent to which habitat variables at the scales of the hollow, vicinity, and site influenced the level of roost use. The correlations between guano mass and habitat variables were examined using generalized additive mixed models. At the hollow scale, guano mass increased with ceiling height above the opening. At the vicinity scale, guano mass increased with less cover of small trees. At the site scale, there was no association between guano mass and distance to foraging areas, elevation, or the number of nearby hollows. These tree hollow roost preferences can inform land managers when planning the management and conservation of redwood forests.},
}
@article {pmid36348137,
year = {2022},
author = {Kimsis, J and Petersone-Gordina, E and Poksane, A and Vilcāne, A and Moore, J and Gerhards, G and Ranka, R},
title = {Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {36348137},
issn = {1556-2891},
abstract = {Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.},
}
@article {pmid36344562,
year = {2022},
author = {Miszkiewicz, JJ and Buckley, HR and Feldman, M and Kiko, L and Carlhoff, S and Naegele, K and Bertolini, E and Guimarães, NRD and Walker, MM and Powell, A and Posth, C and Kinaston, RL},
title = {Female bone physiology resilience in a past Polynesian Outlier community.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {18857},
pmid = {36344562},
issn = {2045-2322},
mesh = {Male ; Humans ; Female ; *Haversian System ; *Femur ; Bone and Bones ; Bone Remodeling ; Melanesia ; },
abstract = {Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region.},
}
@article {pmid36333301,
year = {2022},
author = {Garcés-Pastor, S and Coissac, E and Lavergne, S and Schwörer, C and Theurillat, JP and Heintzman, PD and Wangensteen, OS and Tinner, W and Rey, F and Heer, M and Rutzer, A and Walsh, K and Lammers, Y and Brown, AG and Goslar, T and Rijal, DP and Karger, DN and Pellissier, L and , and Heiri, O and Alsos, IG},
title = {High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6559},
pmid = {36333301},
issn = {2041-1723},
mesh = {Humans ; *Climate Change ; *DNA, Ancient ; Plants/genetics ; Lakes ; Pollen ; },
abstract = {The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.},
}
@article {pmid36329382,
year = {2022},
author = {Lord, E and Marangoni, A and Baca, M and Popović, D and Goropashnaya, AV and Stewart, JR and Knul, MV and Noiret, P and Germonpré, M and Jimenez, EL and Abramson, NI and Vartanyan, S and Prost, S and Smirnov, NG and Kuzmina, EA and Olsen, RA and Fedorov, VB and Dalén, L},
title = {Population dynamics and demographic history of Eurasian collared lemmings.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {126},
pmid = {36329382},
issn = {2730-7182},
support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; P20 GM130443/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Ecosystem ; *Arvicolinae ; Population Dynamics ; Arctic Regions ; DNA, Ancient ; },
abstract = {BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.<br><br>RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.<br><br>CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.},
}
@article {pmid36322514,
year = {2022},
author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J},
title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1986},
pages = {20221078},
pmid = {36322514},
issn = {1471-2954},
support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; },
abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.},
}
@article {pmid36322483,
year = {2022},
author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV},
title = {Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus).},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac241},
pmid = {36322483},
issn = {1537-1719},
abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (∼200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest palaeogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope's extinction.},
}
@article {pmid36316412,
year = {2022},
author = {Souilmi, Y and Tobler, R and Johar, A and Williams, M and Grey, ST and Schmidt, J and Teixeira, JC and Rohrlach, A and Tuke, J and Johnson, O and Gower, G and Turney, C and Cox, M and Cooper, A and Huber, CD},
title = {Admixture has obscured signals of historical hard sweeps in humans.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {12},
pages = {2003-2015},
pmid = {36316412},
issn = {2397-334X},
mesh = {Animals ; Humans ; *Selection, Genetic ; *Hominidae ; Biological Evolution ; Genome, Human ; Genomics ; },
abstract = {The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.},
}
@article {pmid36316157,
year = {2022},
author = {Mathieson, I and Terhorst, J},
title = {Direct detection of natural selection in Bronze Age Britain.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276862.122},
pmid = {36316157},
issn = {1549-5469},
abstract = {We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories, and is robust to mis-specification of population size. We applied it to a large dataset of ancient and present-day human genomes from Britain, and identified seven loci with genome-wide significant evidence of selection in the past 4500 years. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.},
}
@article {pmid36300941,
year = {2022},
author = {Nino Barreat, JG and Katzourakis, A},
title = {Evolutionary Analysis of Placental Orthologues Reveals Two Ancient DNA Virus Integrations.},
journal = {Journal of virology},
volume = {96},
number = {22},
pages = {e0093322},
pmid = {36300941},
issn = {1098-5514},
mesh = {Animals ; Female ; Humans ; Pregnancy ; *DNA, Ancient ; Eutheria ; *Evolution, Molecular ; Genome, Human ; *Mammals/genetics/virology ; Marsupialia ; Phylogeny ; Virus Integration ; *DNA Viruses/genetics ; },
abstract = {The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.},
}
@article {pmid36292573,
year = {2022},
author = {Melchionda, F and Silvestrini, B and Robino, C and Bini, C and Fattorini, P and Martinez-Labarga, C and De Angelis, F and Tagliabracci, A and Turchi, C},
title = {Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292573},
issn = {2073-4425},
mesh = {Humans ; *Eye Color/genetics ; Genetic Markers ; *Polymorphism, Single Nucleotide ; Hair Color/genetics ; DNA/genetics ; },
abstract = {Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1-5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field.},
}
@article {pmid36292570,
year = {2022},
author = {Hou, X and Zhao, J and Zhang, H and Preick, M and Hu, J and Xiao, B and Wang, L and Deng, M and Liu, S and Chang, F and Sheng, G and Lai, X and Hofreiter, M and Yuan, J},
title = {Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292570},
issn = {2073-4425},
mesh = {Animals ; *Bison/genetics ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Fossils ; Biological Evolution ; },
abstract = {Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.},
}
@article {pmid36289417,
year = {2022},
author = {Thompson, B and Bundell, S},
title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-03460-7},
pmid = {36289417},
issn = {1476-4687},
}
@article {pmid36282902,
year = {2022},
author = {Atmore, LM and Martínez-García, L and Makowiecki, D and André, C and Lõugas, L and Barrett, JH and Star, B},
title = {Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {45},
pages = {e2208703119},
pmid = {36282902},
issn = {1091-6490},
mesh = {Animals ; Humans ; *Fisheries ; *DNA, Ancient ; Conservation of Natural Resources ; Population Dynamics ; Fishes/genetics ; Genomics ; Baltic States ; },
abstract = {The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.},
}
@article {pmid36282813,
year = {2022},
author = {Ibrahim, J and Brumfeld, V and Addadi, Y and Rubin, S and Weiner, S and Boaretto, E},
title = {The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone.},
journal = {PloS one},
volume = {17},
number = {10},
pages = {e0269348},
pmid = {36282813},
issn = {1932-6203},
mesh = {Humans ; Swine ; Animals ; *Osteocytes/pathology ; *DNA, Ancient ; Petrous Bone/diagnostic imaging ; Bone and Bones ; DNA/genetics ; },
abstract = {The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.},
}
@article {pmid36277234,
year = {2022},
author = {Cessford, C and Neil, B},
title = {The people of the Cambridge Austin friars.},
journal = {Archaeological journal},
volume = {179},
number = {2},
pages = {383-444},
pmid = {36277234},
issn = {2373-2288},
abstract = {The Austin friars in Cambridge was an important religious institution between the late thirteenth and mid-sixteenth centuries. Excavations have revealed well-dated and contextualised burials associated with the friary, as well as a range of material culture. The burials have been subject to a wide range of analyses including osteology, palaeopathology, stable isotopes, ancient DNA and geometric morphometrics. Significantly the distinction between clothed and shrouded burials allows members of the Augustinian order and the laity to be identified. This represents the best-understood published group of burials from an Austin friars in the British Isles and emphasises the importance of nuanced interpretation, as burial at friaries was a structured and multi-local phenomenon. These burials and other material can be interpreted in terms of both mendicant ideals and anti-fraternal criticisms.},
}
@article {pmid36276948,
year = {2022},
author = {Xu, B and Yang, G and Jiao, B and Zhu, H},
title = {Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {944933},
pmid = {36276948},
issn = {1664-8021},
abstract = {Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs' potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.},
}
@article {pmid36264804,
year = {2022},
author = {Gibbons, A},
title = {How the Black Death left its mark on immune system genes.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6617},
pages = {237-238},
doi = {10.1126/science.adf3947},
pmid = {36264804},
issn = {1095-9203},
mesh = {Humans ; Immune System ; *Plague/genetics/history/immunology ; *Immunity/genetics ; *Selection, Genetic ; *Pandemics/history ; DNA, Ancient ; },
abstract = {Study of DNA from medieval victims and survivors finds gene that helped protect people from deadly pathogen.},
}
@article {pmid36261712,
year = {2022},
author = {Enard, D},
title = {Ancient DNA reveals rapid natural selection during the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {237-238},
pmid = {36261712},
issn = {1476-4687},
mesh = {Humans ; *DNA, Ancient ; *Plague ; Selection, Genetic ; Evolution, Molecular ; },
}
@article {pmid36261521,
year = {2022},
author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB},
title = {Evolution of immune genes is associated with the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {312-319},
pmid = {36261521},
issn = {1476-4687},
support = {F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; },
abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.},
}
@article {pmid36259206,
year = {2022},
author = {Martínez-García, L and Ferrari, G and Cuevas, A and Atmore, LM and López-Arias, B and Culling, M and Llorente-Rodríguez, L and Morales-Muñiz, A and Roselló-Izquierdo, E and Quirós, JA and Marlasca-Martín, R and Hänfling, B and Hutchinson, WF and Jakobsen, KS and Jentoft, S and Orton, D and Star, B and Barrett, JH},
title = {Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1985},
pages = {20221107},
pmid = {36259206},
issn = {1471-2954},
mesh = {Animals ; *DNA, Ancient ; Europe ; Fisheries ; *Gadus morhua/genetics ; Hunting ; Internationality ; },
abstract = {Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.},
}
@article {pmid36224018,
year = {2022},
author = {Xu, Y and Allen, E and Wang, L and Wen, S},
title = {Identifying Human Remains from 20th Century Warfare: A State of the Field Essay.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {9},
pages = {271},
doi = {10.31083/j.fbl2709271},
pmid = {36224018},
issn = {2768-6698},
mesh = {Body Remains ; *DNA Fingerprinting/methods ; DNA, Ancient ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; *Microsatellite Repeats ; },
abstract = {As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics.},
}
@article {pmid36206720,
year = {2022},
author = {Ter Schure, ATM and Bruch, AA and Kandel, AW and Gasparyan, B and Bussmann, RW and Brysting, AK and de Boer, HJ and Boessenkool, S},
title = {Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia.},
journal = {Journal of human evolution},
volume = {172},
number = {},
pages = {103258},
doi = {10.1016/j.jhevol.2022.103258},
pmid = {36206720},
issn = {1095-8606},
mesh = {Humans ; Animals ; *DNA, Ancient ; Armenia ; DNA Barcoding, Taxonomic ; Charcoal ; Caves ; *Hominidae/genetics ; Archaeology/methods ; Plants/genetics ; },
abstract = {Current knowledge about Paleolithic human plant use is limited by the rare survival of identifiable plant remains as well as the availability of methods for plant detection and identification. By analyzing DNA preserved in cave sediments, we can identify organisms in the absence of any visible remains, opening up new ways to study details of past human behavior, including plant use. Aghitu-3 Cave contains a 15,000-yearlong record (from ∼39,000 to 24,000 cal BP) of Upper Paleolithic human settlement and environmental variability in the Armenian Highlands. Finds from this cave include stone artifacts, faunal remains, bone tools, shell beads, charcoal, and pollen, among others. We applied sedimentary ancient DNA (sedaDNA) metabarcoding to the Aghitu-3 sedimentary sequence and combined this with pollen data to obtain a temporal reconstruction of plant assemblages. Our results reveal a stratification of plant abundance and diversity where sedaDNA reflects periods of human occupation, showing higher diversity in layers with increased human activity. Low pollen concentrations combined with high sedaDNA abundance indicate plant remains may have been brought into the cave by animals or humans during the deposition of the lower two archaeological horizons. Most of the recovered plants are reported to be useful for food, flavor, medicine, and/or technical purposes, demonstrating the potential of the environment around Aghitu-3 Cave to support humans during the Upper Paleolithic. Moreover, we identified several specific plant taxa that strengthen previous findings about Upper Paleolithic plant use in this region (i.e., for medicine and the manufacturing and dyeing of textiles). This study represents the first application of plant sedaDNA analysis of cave sediments for the investigation of potential plant use by prehistoric humans.},
}
@article {pmid36203052,
year = {2022},
author = {Seersholm, FV and Harmsen, H and Gotfredsen, AB and Madsen, CK and Jensen, JF and Hollesen, J and Meldgaard, M and Bunce, M and Hansen, AJ},
title = {Ancient DNA provides insights into 4,000 years of resource economy across Greenland.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {36203052},
issn = {2397-3374},
abstract = {The success and failure of past cultures across the Arctic was tightly coupled to the ability of past peoples to exploit the full range of resources available to them. There is substantial evidence for the hunting of birds, caribou and seals in prehistoric Greenland. However, the extent to which these communities relied on fish and cetaceans is understudied because of taphonomic processes that affect how these taxa are presented in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological middens across Greenland covering the Palaeo-Inuit, Norse and Neo-Inuit culture. We identify an assemblage of 42 species, including nine fish species and five whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we identify a new haplotype in caribou (Rangifer tarandus), suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou in Greenland 3,000 years ago.},
}
@article {pmid36201580,
year = {2022},
author = {Curry, A},
title = {Ancient DNA pioneer Svante Pääbo wins Nobel.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6615},
pages = {12},
doi = {10.1126/science.adf1845},
pmid = {36201580},
issn = {1095-9203},
mesh = {Animals ; *DNA, Ancient ; *Hominidae/genetics ; Humans ; Nobel Prize ; },
abstract = {By sequencing ancient hominins' DNA, Pääbo explored "what makes us uniquely human".},
}
@article {pmid36195712,
year = {2022},
author = {Graham, F},
title = {Daily briefing: Medicine Nobel for ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-03163-z},
pmid = {36195712},
issn = {1476-4687},
}
@article {pmid36192444,
year = {2022},
author = {Callaway, E and Ledford, H},
title = {Geneticist who unmasked lives of ancient humans wins medicine Nobel.},
journal = {Nature},
volume = {610},
number = {7930},
pages = {16-17},
pmid = {36192444},
issn = {1476-4687},
mesh = {*DNA, Ancient ; Humans ; *Medicine/standards ; *Nobel Prize ; },
}
@article {pmid36191217,
year = {2022},
author = {Reitsema, LJ and Mittnik, A and Kyle, B and Catalano, G and Fabbri, PF and Kazmi, ACS and Reinberger, KL and Sineo, L and Vassallo, S and Bernardos, R and Broomandkhoshbacht, N and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Fernandes, D and Lari, M and Lawson, AM and Mah, M and Mallick, S and Mandl, K and Micco, A and Modi, A and Oppenheimer, J and Özdogan, KT and Rohland, N and Stewardson, K and Vai, S and Vergata, C and Workman, JN and Zalzala, F and Zaro, V and Achilli, A and Anagnostopoulos, A and Capelli, C and Constantinou, V and Lancioni, H and Olivieri, A and Papadopoulou, A and Psatha, N and Semino, O and Stamatoyannopoulos, J and Valliannou, I and Yannaki, E and Lazaridis, I and Patterson, N and Ringbauer, H and Caramelli, D and Pinhasi, R and Reich, D},
title = {The diverse genetic origins of a Classical period Greek army.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {41},
pages = {e2205272119},
pmid = {36191217},
issn = {1091-6490},
mesh = {*Archaeology/methods ; Europe ; Greece ; History, Ancient ; Humans ; *Military Personnel ; Warfare ; },
abstract = {Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.},
}
@article {pmid36190761,
year = {2022},
author = {Daly, KG and Arbuckle, BS and Rossi, C and Mattiangeli, V and Lawlor, PA and Mashkour, M and Sauer, E and Lesur, J and Atici, L and Erek, CM and Bradley, DG},
title = {A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36190761},
issn = {2050-084X},
mesh = {Alleles ; Animals ; *Genomics ; *Goats/genetics ; Phylogeny ; Turkey ; },
abstract = {Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten 'Taurasian tur' likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.},
}
@article {pmid36184671,
year = {2022},
author = {Armbrecht, L and Weber, ME and Raymo, ME and Peck, VL and Williams, T and Warnock, J and Kato, Y and Hernández-Almeida, I and Hoem, F and Reilly, B and Hemming, S and Bailey, I and Martos, YM and Gutjahr, M and Percuoco, V and Allen, C and Brachfeld, S and Cardillo, FG and Du, Z and Fauth, G and Fogwill, C and Garcia, M and Glüder, A and Guitard, M and Hwang, JH and Iizuka, M and Kenlee, B and O'Connell, S and Pérez, LF and Ronge, TA and Seki, O and Tauxe, L and Tripathi, S and Zheng, X},
title = {Ancient marine sediment DNA reveals diatom transition in Antarctica.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5787},
pmid = {36184671},
issn = {2041-1723},
mesh = {Antarctic Regions ; DNA, Ancient ; *Diatoms/genetics ; Ecosystem ; Eukaryota ; Geologic Sediments ; },
abstract = {Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.},
}
@article {pmid36182700,
year = {2022},
author = {Gopalakrishnan, S and Ebenesersdóttir, SS and Lundstrøm, IKC and Turner-Walker, G and Moore, KHS and Luisi, P and Margaryan, A and Martin, MD and Ellegaard, MR and Magnússon, &#xd3;&#xde; and Sigurðsson, &#xc1; and Snorradóttir, S and Magnúsdóttir, DN and Laffoon, JE and van Dorp, L and Liu, X and Moltke, I and Ávila-Arcos, MC and Schraiber, JG and Rasmussen, S and Juan, D and Gelabert, P and de-Dios, T and Fotakis, AK and Iraeta-Orbegozo, M and Vågene, &#xc5;J and Denham, SD and Christophersen, A and Stenøien, HK and Vieira, FG and Liu, S and Günther, T and Kivisild, T and Moseng, OG and Skar, B and Cheung, C and Sandoval-Velasco, M and Wales, N and Schroeder, H and Campos, PF and Guðmundsdóttir, VB and Sicheritz-Ponten, T and Petersen, B and Halgunset, J and Gilbert, E and Cavalleri, GL and Hovig, E and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Willerslev, E and Balloux, F and Marques-Bonet, T and Lalueza-Fox, C and Nielsen, R and Stefánsson, K and Helgason, A and Gilbert, MTP},
title = {The population genomic legacy of the second plague pandemic.},
journal = {Current biology : CB},
volume = {32},
number = {21},
pages = {4743-4751.e6},
pmid = {36182700},
issn = {1879-0445},
mesh = {Humans ; *Plague/epidemiology/genetics ; Pandemics/history ; Metagenomics ; Genome, Bacterial ; Phylogeny ; },
abstract = {Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.[1] It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).[2] Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17[th]-19[th] century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.},
}
@article {pmid36178955,
year = {2022},
author = {Dimopoulos, EA and Carmagnini, A and Velsko, IM and Warinner, C and Larson, G and Frantz, LAF and Irving-Pease, EK},
title = {HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010493},
pmid = {36178955},
issn = {1553-7358},
support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Algorithms ; Bayes Theorem ; *DNA, Ancient ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Software ; },
abstract = {Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive read mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC.},
}
@article {pmid36174312,
year = {2022},
author = {Hider, J and Duggan, AT and Klunk, J and Eaton, K and Long, GS and Karpinski, E and Giuffra, V and Ventura, L and Fornaciari, A and Fornaciari, G and Golding, GB and Prowse, TL and Poinar, HN},
title = {Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis.},
journal = {International journal of paleopathology},
volume = {39},
number = {},
pages = {20-34},
doi = {10.1016/j.ijpp.2022.08.002},
pmid = {36174312},
issn = {1879-9825},
mesh = {Humans ; *Brucella melitensis/genetics ; DNA, Ancient ; *Monks ; *Brucellosis ; Italy ; },
abstract = {OBJECTIVE: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 [th] century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.<br><br>METHODS: Shotgun sequencing data from was examined to determine the presence of Brucella DNA.<br><br>RESULTS: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria.<br><br>CONCLUSIONS: We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.<br><br>SIGNIFICANCE: Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.<br><br>LIMITATIONS: Study focuses on pathogen recovery in a single individual.<br><br>Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.},
}
@article {pmid36170372,
year = {2022},
author = {Alsos, IG and Rijal, DP and Ehrich, D and Karger, DN and Yoccoz, NG and Heintzman, PD and Brown, AG and Lammers, Y and Pellissier, L and Alm, T and Bråthen, KA and Coissac, E and Merkel, MKF and Alberti, A and Denoeud, F and Bakke, J and , },
title = {Postglacial species arrival and diversity buildup of northern ecosystems took millennia.},
journal = {Science advances},
volume = {8},
number = {39},
pages = {eabo7434},
pmid = {36170372},
issn = {2375-2548},
abstract = {What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.},
}
@article {pmid36164432,
year = {2022},
author = {Connah, K and Michael, B and Brassey, C},
title = {MiTiSegmenter: Software for high throughput segmentation and meshing of microCT data in microtiter plate arrays.},
journal = {MethodsX},
volume = {9},
number = {},
pages = {101849},
pmid = {36164432},
issn = {2215-0161},
abstract = {Lab-based microCT is a powerful means of visualising the internal structure of physical specimens deployed across the physical sciences, engineering and the arts. As its popularity has grown, demand for bulk digitisation of multiple samples within a single scan has increased. High throughput workflows can increase sample sizes and reduce scan time, yet downstream segmentation and meshing remain a bottleneck. We present MiTiSegmenter as a new tool for the bulk archiving of valuable zooarchaeological and palaeontological remains. We foresee MiTiSegmenter as particularly useful when incorporated into workflows that ultimately require the destructive testing of specimens, including sampling for ancient DNA and proteomics. The software may also play an important role in national museums' ongoing mass digitisation efforts, facilitating the high-speed archiving of specimen 3D morphology across extensive collections with very minimal user intervention or prior training. •We present MiTiSegmenter, a software package for semi-automated image processing and segmentation of array-based batch microCT data.•Implemented in Python, MiTiSegmenter expedites cropping, meshing and exporting samples within stacked microtiter plates, facilitating the rapid digitisation of hundreds-thousands of samples per scan.•We illustrate MiTiSegmenter's capabilities when applied to bulk archiving of valuable zooarchaeological and palaeontological remains.},
}
@article {pmid36161899,
year = {2022},
author = {Alagöz, G and Molz, B and Eising, E and Schijven, D and Francks, C and Stein, JL and Fisher, SE},
title = {Using neuroimaging genomics to investigate the evolution of human brain structure.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {40},
pages = {e2200638119},
pmid = {36161899},
issn = {1091-6490},
support = {R01 DC016977/DC/NIDCD NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Brain/growth &amp; development/ultrastructure ; DNA, Ancient ; *Genomics/methods ; Humans ; *Neuroimaging/methods ; *Polymorphism, Single Nucleotide ; },
abstract = {Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.},
}
@article {pmid36159977,
year = {2022},
author = {Modi, A and Vizzari, MT and Catalano, G and Boscolo Agostini, R and Vai, S and Lari, M and Vergata, C and Zaro, V and Liccioli, L and Fedi, M and Barone, S and Nigro, L and Lancioni, H and Achilli, A and Sineo, L and Caramelli, D and Ghirotto, S},
title = {Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {945227},
pmid = {36159977},
issn = {1664-8021},
abstract = {Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations' interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre-Iron Age populations, that should be further investigated.},
}
@article {pmid36152077,
year = {2022},
author = {Yu, XE and Sun, C and Zou, YT and Li, JY and Ren, X and Li, H},
title = {Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations.},
journal = {Molecular genetics and genomics : MGG},
volume = {297},
number = {6},
pages = {1755-1765},
pmid = {36152077},
issn = {1617-4623},
mesh = {Humans ; *DNA, Ancient ; *Genetics, Population ; Tibet ; Asians/genetics ; Ethnicity ; Genetic Variation/genetics ; },
abstract = {The rise of the Tubo Kingdom is considered as the key period for the formation of modern groups on the Tibetan Plateau. The ethnic origin of the residents of the Tubo Kingdom is quite complex, and their genetic structure remains unclear. The tombs of the Tubo Kingdom period in Dulan County, Qinghai Province, dating back to the seventh century, are considered to be the remains left by Tubo conquerors or the Tuyuhun people dominated by the Tubo Kingdom. The human remains of these tombs are ideal materials for studying the population dynamics in the Tubo Kingdom. In this paper, we analyzed the genome-wide data of eight remains from these tombs by shotgun sequencing and multiplex PCR panels and compared the results with data of available ancient and modern populations across East Asia. Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia. In summary, the genetic diversity of ancient Dulan people and their affiliations with other populations provide an example of the complex origin of the residents in the Tubo Kingdom and their long-distance connection with populations in a vast geographic region across ancient Asia.},
}
@article {pmid36144317,
year = {2022},
author = {Bellanger, N and Dereeper, A and Koebnik, R},
title = {Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri-Witnesses to a Global Expansion of a Bacterial Pathogen over Time.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
pmid = {36144317},
issn = {2076-2607},
abstract = {Xanthomonas citri pv. citri, a Gram-negative bacterium, is the causal agent of citrus canker, a significant threat to citrus production. Understanding of global expansion of the pathogen and monitoring introduction into new regions are of interest for integrated disease management at the local and global level. Genetic diversity can be assessed using genomic approaches or information from partial gene sequences, satellite markers or clustered regularly interspaced short palindromic repeats (CRISPR). Here, we compared CRISPR loci from 355 strains of X. citri pv. citri, including a sample from ancient DNA, and generated the genealogy of the spoligotypes, i.e., the absence/presence patterns of CRISPR spacers. We identified 26 novel spoligotypes and constructed their likely evolutionary trajectory based on the whole-genome information. Moreover, we analyzed ~30 additional pathovars of X. citri and found that the oldest part of the CRISPR array was present in the ancestor of several pathovars of X. citri. This work presents a framework for further analyses of CRISPR loci and allows drawing conclusions about the global spread of the citrus canker pathogen, as exemplified by two introductions in West Africa.},
}
@article {pmid36139328,
year = {2022},
author = {Horsburgh, KA and Gosling, AL and Cochrane, EE and Kirch, PV and Swift, JA and McCoy, MD},
title = {Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {18},
pages = {},
pmid = {36139328},
issn = {2076-2615},
abstract = {Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the "Pacific Clade" that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China's Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800-700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.},
}
@article {pmid36137029,
year = {2022},
author = {Curry, A},
title = {How the Anglo-Saxons settled England.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6613},
pages = {1371},
doi = {10.1126/science.ade9808},
pmid = {36137029},
issn = {1095-9203},
mesh = {Burial ; DNA, Ancient ; *Emigration and Immigration/history ; England ; History, Ancient ; Humans ; Sequence Analysis, DNA ; *Whites/genetics ; },
abstract = {Genetic study of burials suggests whole families migrated to the island in the first millennium C.E.},
}
@article {pmid36131059,
year = {2022},
author = {},
title = {Ancient DNA reveals details about early medieval migration into England.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {36131059},
issn = {1476-4687},
}
@article {pmid36131019,
year = {2022},
author = {Gretzinger, J and Sayer, D and Justeau, P and Altena, E and Pala, M and Dulias, K and Edwards, CJ and Jodoin, S and Lacher, L and Sabin, S and Vågene, &#xc5;J and Haak, W and Ebenesersdóttir, SS and Moore, KHS and Radzeviciute, R and Schmidt, K and Brace, S and Bager, MA and Patterson, N and Papac, L and Broomandkhoshbacht, N and Callan, K and Harney, &#xc9; and Iliev, L and Lawson, AM and Michel, M and Stewardson, K and Zalzala, F and Rohland, N and Kappelhoff-Beckmann, S and Both, F and Winger, D and Neumann, D and Saalow, L and Krabath, S and Beckett, S and Van Twest, M and Faulkner, N and Read, C and Barton, T and Caruth, J and Hines, J and Krause-Kyora, B and Warnke, U and Schuenemann, VJ and Barnes, I and Dahlström, H and Clausen, JJ and Richardson, A and Popescu, E and Dodwell, N and Ladd, S and Phillips, T and Mortimer, R and Sayer, F and Swales, D and Stewart, A and Powlesland, D and Kenyon, R and Ladle, L and Peek, C and Grefen-Peters, S and Ponce, P and Daniels, R and Spall, C and Woolcock, J and Jones, AM and Roberts, AV and Symmons, R and Rawden, AC and Cooper, A and Bos, KI and Booth, T and Schroeder, H and Thomas, MG and Helgason, A and Richards, MB and Reich, D and Krause, J and Schiffels, S},
title = {The Anglo-Saxon migration and the formation of the early English gene pool.},
journal = {Nature},
volume = {610},
number = {7930},
pages = {112-119},
pmid = {36131019},
issn = {1476-4687},
support = {851511/ERC_/European Research Council/International ; 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeology ; DNA, Ancient/analysis ; Denmark ; England ; Female ; France ; *Gene Pool ; Genetics, Population ; Genome, Human/genetics ; Germany ; History, Medieval ; *Human Migration/history ; Humans ; Language ; Male ; Population Dynamics ; Weapons/history ; },
abstract = {The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture[1]. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate[2-4]. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France[5,6].},
}
@article {pmid36124912,
year = {2022},
author = {Wu, MY and Lau, CJ and Ng, EYX and Baveja, P and Gwee, CY and Sadanandan, K and Ferasyi, TR and Haminuddin, and Ramadhan, R and Menner, JK and Rheindt, FE},
title = {Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation.},
journal = {Molecular biology and evolution},
volume = {39},
number = {9},
pages = {},
pmid = {36124912},
issn = {1537-1719},
mesh = {Animals ; DNA/genetics ; Extinction, Biological ; Genome ; Phylogeny ; *Songbirds/genetics ; },
abstract = {Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world's organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.},
}
@article {pmid36114431,
year = {2022},
author = {Cole, G and Taylor, GM and Stewart, GR and Dawson-Hobbis, H},
title = {Ancient DNA confirmation of lepromatous leprosy in a skeleton with concurrent osteosarcoma, excavated from the leprosarium of St. Mary Magdalen in Winchester, Hants., UK.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {41},
number = {11},
pages = {1295-1304},
pmid = {36114431},
issn = {1435-4373},
mesh = {Bone and Bones ; DNA, Ancient ; Humans ; *Leprosy/diagnosis ; *Leprosy, Lepromatous/microbiology ; Male ; Mycobacterium leprae/genetics ; *Osteosarcoma/genetics ; United Kingdom ; },
abstract = {To establish a biological profile and disease aetiologies for one of four burials recovered during a Time Team dig at the St. Mary Magdalen leprosarium, Winchester, UK in AD 2000. Osteological techniques were applied to estimate age at death, biological sex, stature and pathology. Visual assessment of the material was supplemented by radiographic examination. Evidence for leprosy DNA was sought using ancient DNA (aDNA) analysis. The remains are those of a male individual excavated from a west-east aligned grave. The skeleton shows signs of two pathologies. Remodelling of the rhino-maxillary area and degenerative changes to small bones of the feet and reactive bone on the distal lower limbs suggest a multibacillary form of leprosy, whereas the right tibia and fibula show the presence of a primary neoplasm identified as an osteosarcoma. The aDNA study confirmed presence of Mycobacterium leprae in several skeletal elements, and the strain was genotyped to the 3I lineage, one of two main SNP types present in mediaeval Britain and ancestral to extant strains in America. This is a rare documentation of leprosy in association with a primary neoplasm.},
}
@article {pmid36108636,
year = {2022},
author = {Arauna, LR and Bergstedt, J and Choin, J and Mendoza-Revilla, J and Harmant, C and Roux, M and Mas-Sandoval, A and Lémée, L and Colleran, H and François, A and Valentin, F and Cassar, O and Gessain, A and Quintana-Murci, L and Patin, E},
title = {The genomic landscape of contemporary western Remote Oceanians.},
journal = {Current biology : CB},
volume = {32},
number = {21},
pages = {4565-4575.e6},
doi = {10.1016/j.cub.2022.08.055},
pmid = {36108636},
issn = {1879-0445},
mesh = {Humans ; *Human Migration ; *DNA, Ancient ; Genomics ; Genome, Human ; Native Hawaiian or Other Pacific Islander ; Genetics, Population ; },
abstract = {The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands ∼3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report new genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous, sex-biased admixture events that occurred ∼1,700-2,300 years ago, indicating a peopling history common to the whole archipelago. However, East Asian-related ancestry proportions differ markedly across islands, suggesting that the Papuan-related population turnover was geographically uneven. Furthermore, we detect Polynesian ancestry arriving ∼600-1,000 years ago to Central and South Vanuatu in both Polynesian-speaking and non-Polynesian-speaking populations. Last, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide an insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.},
}
@article {pmid36097018,
year = {2022},
author = {Low, YW and Rajaraman, S and Tomlin, CM and Ahmad, JA and Ardi, WH and Armstrong, K and Athen, P and Berhaman, A and Bone, RE and Cheek, M and Cho, NRW and Choo, LM and Cowie, ID and Crayn, D and Fleck, SJ and Ford, AJ and Forster, PI and Girmansyah, D and Goyder, DJ and Gray, B and Heatubun, CD and Ibrahim, A and Ibrahim, B and Jayasinghe, HD and Kalat, MA and Kathriarachchi, HS and Kintamani, E and Koh, SL and Lai, JTK and Lee, SML and Leong, PKF and Lim, WH and Lum, SKY and Mahyuni, R and McDonald, WJF and Metali, F and Mustaqim, WA and Naiki, A and Ngo, KM and Niissalo, M and Ranasinghe, S and Repin, R and Rustiami, H and Simbiak, VI and Sukri, RS and Sunarti, S and Trethowan, LA and Trias-Blasi, A and Vasconcelos, TNC and Wanma, JF and Widodo, P and Wijesundara, DSA and Worboys, S and Yap, JW and Yong, KT and Khew, GSW and Salojärvi, J and Michael, TP and Middleton, DJ and Burslem, DFRP and Lindqvist, C and Lucas, EJ and Albert, VA},
title = {Genomic insights into rapid speciation within the world's largest tree genus Syzygium.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5031},
pmid = {36097018},
issn = {2041-1723},
mesh = {Genetic Speciation ; Genomics ; Phylogeny ; *Syzygium/genetics ; *Trees ; },
abstract = {Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.},
}
@article {pmid36072661,
year = {2022},
author = {Guarino-Vignon, P and Marchi, N and Chimènes, A and Monnereau, A and Kroll, S and Mashkour, M and Lhuillier, J and Bendezu-Sarmiento, J and Heyer, E and Bon, C},
title = {Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan).},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {884612},
pmid = {36072661},
issn = {1664-8021},
abstract = {The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian-speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.},
}
@article {pmid36071150,
year = {2022},
author = {Richards, SM and Li, L and Breen, J and Hovhannisyan, N and Estrada, O and Gasparyan, B and Gilliham, M and Smith, A and Cooper, A and Zhang, H},
title = {Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15164},
pmid = {36071150},
issn = {2045-2322},
mesh = {Armenia ; Edible Grain/genetics ; *Genome, Chloroplast ; Millets ; *Panicum/genetics ; },
abstract = {Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and[14]C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.},
}
@article {pmid36066013,
year = {2022},
author = {Flux, AL and Schultz, M and Hummel, S},
title = {Ancient DNA analysis from epoxy resin Biodur[®]-embedded bones.},
journal = {BioTechniques},
volume = {73},
number = {3},
pages = {113-122},
doi = {10.2144/btn-2022-0056},
pmid = {36066013},
issn = {1940-9818},
mesh = {DNA/analysis/genetics ; *DNA Fingerprinting/methods ; *DNA, Ancient ; Epoxy Resins ; Humans ; Microsatellite Repeats ; },
abstract = {For microscopic investigation, archaeological bone samples are often embedded in Biodur[®] epoxy resin. This study wants to test whether it is possible to extract DNA suitable for PCR amplification from this sample type. For eight individuals a set of samples - each consisting of a Biodur-embedded femur sample, a native femur sample and a control sample of different anatomical origin - were submitted to organic DNA extraction. The extraction success was tested by autosomal short tandem repeat amplification. Seven out of eight Biodur-embedded femur samples revealed successful amplification results. If Biodur-embedded bone material exists from earlier microscopic investigations, our results encourage the use of this sample type as a source for genetic research.},
}
@article {pmid36064759,
year = {2022},
author = {Harvati, K and Ackermann, RR},
title = {Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {10},
pages = {1573-1585},
pmid = {36064759},
issn = {2397-334X},
mesh = {Animals ; DNA, Ancient ; Fossils ; *Hominidae/anatomy &amp; histology/genetics ; Humans ; Hybridization, Genetic ; Mammals/genetics ; *Neanderthals/genetics ; },
abstract = {Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.},
}
@article {pmid36052370,
year = {2022},
author = {Le, MK and Smith, OS and Akbari, A and Harpak, A and Reich, D and Narasimhan, VM},
title = {1,000 ancient genomes uncover 10,000 years of natural selection in Europe.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36052370},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {Ancient DNA has revolutionized our understanding of human population history. However, its potential to examine how rapid cultural evolution to new lifestyles may have driven biological adaptation has not been met, largely due to limited sample sizes. We assembled genome-wide data from 1,291 individuals from Europe over 10,000 years, providing a dataset that is large enough to resolve the timing of selection into the Neolithic, Bronze Age, and Historical periods. We identified 25 genetic loci with rapid changes in frequency during these periods, a majority of which were previously undetected. Signals specific to the Neolithic transition are associated with body weight, diet, and lipid metabolism-related phenotypes. They also include immune phenotypes, most notably a locus that confers immunity to Salmonella infection at a time when ancient Salmonella genomes have been shown to adapt to human hosts, thus providing a possible example of human-pathogen co-evolution. In the Bronze Age, selection signals are enriched near genes involved in pigmentation and immune-related traits, including at a key human protein interactor of SARS-CoV-2. Only in the Historical period do the selection candidates we detect largely mirror previously-reported signals, highlighting how the statistical power of previous studies was limited to the last few millennia. The Historical period also has multiple signals associated with vitamin D binding, providing evidence that lactase persistence may have been part of an oligogenic adaptation for efficient calcium uptake and challenging the theory that its adaptive value lies only in facilitating caloric supplementation during times of scarcity. Finally, we detect selection on complex traits in all three periods, including selection favoring variants that reduce body weight in the Neolithic. In the Historical period, we detect selection favoring variants that increase risk for cardiovascular disease plausibly reflecting selection for a more active inflammatory response that would have been adaptive in the face of increased infectious disease exposure. Our results provide an evolutionary rationale for the high prevalence of these deadly diseases in modern societies today and highlight the unique power of ancient DNA in elucidating biological change that accompanied the profound cultural transformations of recent human history.},
}
@article {pmid36050453,
year = {2022},
author = {Gregory, MD and Berman, KF},
title = {Correction to: Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition.},
journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology},
volume = {47},
number = {12},
pages = {2173},
doi = {10.1038/s41386-022-01439-6},
pmid = {36050453},
issn = {1740-634X},
}
@article {pmid36048257,
year = {2022},
author = {Šuligoj, A and Mesesnel, S and Leskovar, T and Podovšovnik, E and Zupanič Pajnič, I},
title = {Comparison of DNA preservation between adult and non-adult ancient skeletons.},
journal = {International journal of legal medicine},
volume = {136},
number = {6},
pages = {1521-1539},
pmid = {36048257},
issn = {1437-1596},
mesh = {*Body Remains ; Bone and Bones ; DNA ; *DNA Fingerprinting ; Female ; Humans ; Male ; Microsatellite Repeats ; },
abstract = {Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons.},
}
@article {pmid36048238,
year = {2022},
author = {Gochi, L and Kawai, Y and Fujimoto, A},
title = {Comprehensive analysis of microsatellite polymorphisms in human populations.},
journal = {Human genetics},
volume = {},
number = {},
pages = {},
pmid = {36048238},
issn = {1432-1203},
abstract = {Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, and genotyping methods for MS have yet to be established. Here, we analyzed approximately 8.5 million MS regions using a previously developed MS caller for short reads (MIVcall method) for three large publicly available human genome sequencing data sets: the Korean Personal Genome Project, Simons Genome Diversity Project, and Human Genome Diversity Project. Our analysis identified 253,114 polymorphic MS. A comparison among different populations suggests that MS in the coding region evolved by random genetic drift and natural selection. In an analysis of genetic structures, MS clearly revealed population structures as SNPs and detected clusters that were not found by SNPs in African and Oceanian populations. Based on the MS polymorphisms, we selected MS marker candidates for individual identification. Finally, we applied our method to a deep sequenced ancient DNA sample. This study provides a comprehensive picture of MS polymorphisms and application to human population studies.},
}
@article {pmid36046618,
year = {2022},
author = {Behnamian, S and Esposito, U and Holland, G and Alshehab, G and Dobre, AM and Pirooznia, M and Brimacombe, CS and Elhaik, E},
title = {Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years.},
journal = {Cell reports methods},
volume = {2},
number = {8},
pages = {100270},
pmid = {36046618},
issn = {2667-2375},
abstract = {Radiocarbon dating is the gold standard in archeology to estimate the age of skeletons, a key to studying their origins. Many published ancient genomes lack reliable and direct dates, which results in obscure and contradictory reports. We developed the temporal population structure (TPS), a DNA-based dating method for genomes ranging from the Late Mesolithic to today, and applied it to 3,591 ancient and 1,307 modern Eurasians. TPS predictions aligned with the known dates and correctly accounted for kin relationships. TPS dating of poorly dated Eurasian samples resolved conflicting reports in the literature, as illustrated by one test case. We also demonstrated how TPS improved the ability to study phenotypic traits over time. TPS can be used when radiocarbon dating is unfeasible or uncertain or to develop alternative hypotheses for samples younger than 10,000 years ago, a limitation that may be resolved over time as ancient data accumulate.},
}
@article {pmid36044903,
year = {2022},
author = {Brace, S and Diekmann, Y and Booth, T and Macleod, R and Timpson, A and Stephen, W and Emery, G and Cabot, S and Thomas, MG and Barnes, I},
title = {Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century.},
journal = {Current biology : CB},
volume = {32},
number = {20},
pages = {4350-4359.e6},
doi = {10.1016/j.cub.2022.08.036},
pmid = {36044903},
issn = {1879-0445},
mesh = {Humans ; Gene Frequency ; *Jews/genetics/history ; Alleles ; *Burial ; },
abstract = {We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews. We identify four alleles associated with genetic disease in Ashkenazi Jewish populations and infer variation in pigmentation traits, including the presence of red hair. Simulations indicate that Ashkenazi-associated genetic disease alleles were already at appreciable frequencies, centuries earlier than previously hypothesized. These findings provide new insights into a significant historical crime, into Ashkenazi population history, and into the origins of genetic diseases associated with modern Jewish populations.},
}
@article {pmid36032329,
year = {2022},
author = {Handsley-Davis, M and Kapellas, K and Jamieson, LM and Hedges, J and Skelly, E and Kaidonis, J and Anastassiadis, P and Weyrich, LS},
title = {Heritage-specific oral microbiota in Indigenous Australian dental calculus.},
journal = {Evolution, medicine, and public health},
volume = {10},
number = {1},
pages = {352-362},
pmid = {36032329},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Aboriginal Australians and Torres Strait Islanders (hereafter respectfully referred to as Indigenous Australians) experience a high burden of chronic non-communicable diseases (NCDs). Increased NCD risk is linked to oral diseases mediated by the oral microbiota, a microbial community influenced by both vertical transmission and lifestyle factors. As an initial step towards understanding the oral microbiota as a factor in Indigenous health, we present the first investigation of oral microbiota in Indigenous Australian adults.<br><br>METHODOLOGY: Dental calculus samples from Indigenous Australians with periodontal disease (PD; n&#x2009;=&#x2009;13) and non-Indigenous individuals both with (n&#x2009;=&#x2009;19) and without PD (n&#x2009;=&#x2009;20) were characterized using 16S ribosomal RNA gene amplicon sequencing. Alpha and beta diversity, differentially abundant microbial taxa and taxa unique to different participant groups were analysed using QIIME2.<br><br>RESULTS: Samples from Indigenous Australians were more phylogenetically diverse (Kruskal-Wallis H&#x2009;=&#x2009;19.86, P&#x2009;=&#x2009;8.3&#x2009;&#xd7;&#x2009;10[-6]), differed significantly in composition from non-Indigenous samples (PERMANOVA pseudo-F&#x2009;=&#x2009;10.42, P&#x2009;=&#x2009;0.001) and contained a relatively high proportion of unique taxa not previously reported in the human oral microbiota (e.g. Endomicrobia). These patterns were robust to stratification by PD status. Oral microbiota diversity and composition also differed between Indigenous individuals living in different geographic regions.<br><br>CONCLUSIONS AND IMPLICATIONS: Indigenous Australians may harbour unique oral microbiota shaped by their long relationships with Country (ancestral homelands). Our findings have implications for understanding the origins of oral and systemic NCDs and for the inclusion of Indigenous peoples in microbiota research, highlighting the microbiota as a novel field of enquiry to improve Indigenous health.},
}
@article {pmid36031712,
year = {2022},
author = {Canteri, E and Brown, SC and Schmidt, NM and Heller, R and Nogués-Bravo, D and Fordham, DA},
title = {Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia.},
journal = {Global change biology},
volume = {28},
number = {22},
pages = {6602-6617},
doi = {10.1111/gcb.16375},
pmid = {36031712},
issn = {1365-2486},
mesh = {Animals ; Arctic Regions ; Climate Change ; *DNA, Ancient ; Fossils ; Humans ; *Ruminants ; },
abstract = {Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process-explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species-specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process-explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process-explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.},
}
@article {pmid36030812,
year = {2022},
author = {Roca-Rada, X and Tereso, S and Rohrlach, AB and Brito, A and Williams, MP and Umbelino, C and Curate, F and Deveson, IW and Souilmi, Y and Amorim, A and Carvalho, PC and Llamas, B and Teixeira, JC},
title = {A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics.},
journal = {Lancet (London, England)},
volume = {400},
number = {10353},
pages = {691-692},
doi = {10.1016/S0140-6736(22)01476-3},
pmid = {36030812},
issn = {1474-547X},
mesh = {Humans ; *Klinefelter Syndrome ; Osteology ; },
}
@article {pmid36029689,
year = {2022},
author = {Smith-Guzmán, NE},
title = {A paleoepidemiological approach to the challenging differential diagnosis of an isolated 1500-year-old anomalous molar from Panamá.},
journal = {International journal of paleopathology},
volume = {39},
number = {},
pages = {1-13},
doi = {10.1016/j.ijpp.2022.07.002},
pmid = {36029689},
issn = {1879-9825},
mesh = {Humans ; Diagnosis, Differential ; *Syphilis, Congenital ; Molar/diagnostic imaging ; Panama ; *Tooth Abnormalities ; },
abstract = {OBJECTIVE: This study seeks to quantify the presence and prevalence of specific genetic and infectious diseases in the pre-Colombian Panamanian population and uses these data to consider the plausibility of these diseases as causative factors in the development of an abnormal supernumerary cusp morphology in a 1500-year-old isolated molar recovered from Cerro Juan Díaz (Los Santos, Panama).<br><br>MATERIALS: 267 individuals from pre-Columbian sites throughout Panama.<br><br>METHODS: The anomalous tooth was analyzed through macroscopic, odontometric, and radiographic means. Tentative differential diagnosis was performed using inferences from paleopathological features of the broader regional population.<br><br>RESULTS: The regional sample showed evidence of treponemal infection and developmental anomalies in 10.1% and 10.9% of individuals, respectively.<br><br>CONCLUSIONS: While not able to rule out three potential genetic conditions, more evidence was found to support the differential diagnosis of congenital syphilis as the causative agent leading to the development of abnormal supernumerary cusps in the isolated molar.<br><br>SIGNIFICANCE: This study demonstrates how characterizing disease experience in the population can assist in differential diagnoses at the individual level and cautions against the assumption that any one lesion in isolation is unique to only one specific pathological condition.<br><br>LIMITATIONS: The timing discrepancy between clinical descriptions of congenital syphilis and genetic disorders, lack of knowledge on pathophysiological mechanisms of the former, poor preservation of Treponema pathogen ancient DNA, and deficiencies in modern public health data from Panama limit the differential diagnosis.<br><br>Inclusion and serious contemplation of genetic diseases in paleopathological differential diagnoses is necessary.},
}
@article {pmid36015403,
year = {2022},
author = {Bosi, G and De Felice, S and Wilkinson, MJ and Allainguillaume, J and Arru, L and Nascimbene, J and Buldrini, F},
title = {Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {16},
pages = {},
pmid = {36015403},
issn = {2223-7747},
abstract = {The genus Brassica includes some of the most important vegetable and oil crops worldwide. Many Brassica seeds (which can show diagnostic characters useful for species identification) were recovered from two archaeological sites in northern Italy, dated from between the Middle Ages and the Renaissance. We tested the combined use of archaeobotanical keys, ancient DNA barcoding, and references to ancient herbarium specimens to address the issue of diagnostic uncertainty. An unequivocal conventional diagnosis was possible for much of the material recovered, with the samples dominated by five Brassica species and Sinapis. The analysis using ancient DNA was restricted to the seeds with a Brassica-type structure and deployed a variant of multiplexed tandem PCR. The quality of diagnosis strongly depended on the molecular locus used. Nevertheless, many seeds were diagnosed down to species level, in concordance with their morphological identification, using one primer set from the core barcode site (matK). The number of specimens found in the Renaissance herbaria was not high; Brassica nigra, which is of great ethnobotanical importance, was the most common taxon. Thus, the combined use of independent means of species identification is particularly important when studying the early use of closely related crops, such as Brassicaceae.},
}
@article {pmid36014039,
year = {2022},
author = {Pérez, V and Liu, Y and Hengst, MB and Weyrich, LS},
title = {A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36014039},
issn = {2076-2607},
abstract = {High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects-from sample collection to data analysis-and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol-chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.},
}
@article {pmid36012483,
year = {2022},
author = {Sá, L and Almeida, M and Azonbakin, S and Matos, E and Franco-Duarte, R and Gómez-Carballa, A and Salas, A and Laleye, A and Rosa, A and Brehm, A and Richards, MB and Soares, P and Rito, T},
title = {Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade.},
journal = {International journal of molecular sciences},
volume = {23},
number = {16},
pages = {},
pmid = {36012483},
issn = {1422-0067},
mesh = {Africa South of the Sahara ; Climate Change ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; *Enslaved Persons ; Humans ; Phylogeny ; Phylogeography ; },
abstract = {Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries-the time of the Atlantic slave trade-thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the "greening" of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.},
}
@article {pmid36011343,
year = {2022},
author = {Zupanič Pajnič, I and Zupanc, T and Leskovar, T and Črešnar, M and Fattorini, P},
title = {Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach.},
journal = {Genes},
volume = {13},
number = {8},
pages = {},
pmid = {36011343},
issn = {2073-4425},
mesh = {Aged ; *Body Remains ; DNA/genetics ; DNA, Ancient ; *Eye Color/genetics ; *Hair Color/genetics ; Humans ; Polymerase Chain Reaction ; World War II ; },
abstract = {To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.},
}
@article {pmid36009790,
year = {2022},
author = {Churchill, SE and Keys, K and Ross, AH},
title = {Midfacial Morphology and Neandertal-Modern Human Interbreeding.},
journal = {Biology},
volume = {11},
number = {8},
pages = {},
pmid = {36009790},
issn = {2079-7737},
abstract = {Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.},
}
@article {pmid36008480,
year = {2022},
author = {Modzelewski, AJ and Gan Chong, J and Wang, T and He, L},
title = {Mammalian genome innovation through transposon domestication.},
journal = {Nature cell biology},
volume = {24},
number = {9},
pages = {1332-1340},
pmid = {36008480},
issn = {1476-4679},
support = {R01 NS120287/NS/NINDS NIH HHS/United States ; R01 CA139067/CA/NCI NIH HHS/United States ; U24 HG012070/HG/NHGRI NIH HHS/United States ; R01 GM114414/GM/NIGMS NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; U01 HG009391/HG/NHGRI NIH HHS/United States ; R21 OD027053/OD/NIH HHS/United States ; R01 HG007175/HG/NHGRI NIH HHS/United States ; K99 HD096108/HD/NICHD NIH HHS/United States ; U24 ES026699/ES/NIEHS NIH HHS/United States ; R00 HD096108/HD/NICHD NIH HHS/United States ; U01 CA200060/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HD106809/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; *DNA Transposable Elements/genetics ; *Domestication ; Evolution, Molecular ; Mammals ; },
abstract = {Since the discovery of transposons, their sheer abundance in host genomes has puzzled many. While historically viewed as largely harmless 'parasitic' DNAs during evolution, transposons are not a mere record of ancient genome invasion. Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome sequences introduced by transposon activities provide raw material for genome innovation and document the distinct evolutionary path of each species.},
}
@article {pmid36008437,
year = {2022},
author = {Slon, V and Clark, JL and Friesem, DE and Orbach, M and Porat, N and Meyer, M and Kandel, AW and Shimelmitz, R},
title = {Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {14528},
pmid = {36008437},
issn = {2045-2322},
support = {694707/ERC_/European Research Council/International ; },
mesh = {Animals ; Archaeology ; Biological Evolution ; Caves ; *DNA, Ancient ; Fossils ; Humans ; *Hyaenidae ; Infant, Newborn ; Israel ; },
abstract = {Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.},
}
@article {pmid36007054,
year = {2022},
author = {Lazaridis, I and Alpaslan-Roodenberg, S and Acar, A and Açıkkol, A and Agelarakis, A and Aghikyan, L and Akyüz, U and Andreeva, D and Andrijašević, G and Antonović, D and Armit, I and Atmaca, A and Avetisyan, P and Aytek, A&#x130; and Bacvarov, K and Badalyan, R and Bakardzhiev, S and Balen, J and Bejko, L and Bernardos, R and Bertsatos, A and Biber, H and Bilir, A and Bodružić, M and Bonogofsky, M and Bonsall, C and Borić, D and Borovinić, N and Bravo Morante, G and Buttinger, K and Callan, K and Candilio, F and Carić, M and Cheronet, O and Chohadzhiev, S and Chovalopoulou, ME and Chryssoulaki, S and Ciobanu, I and Čondić, N and Constantinescu, M and Cristiani, E and Culleton, BJ and Curtis, E and Davis, J and Demcenco, TI and Dergachev, V and Derin, Z and Deskaj, S and Devejyan, S and Djordjević, V and Duffett Carlson, KS and Eccles, LR and Elenski, N and Engin, A and Erdoğan, N and Erir-Pazarcı, S and Fernandes, DM and Ferry, M and Freilich, S and Frînculeasa, A and Galaty, ML and Gamarra, B and Gasparyan, B and Gaydarska, B and Genç, E and Gültekin, T and Gündüz, S and Hajdu, T and Heyd, V and Hobosyan, S and Hovhannisyan, N and Iliev, I and Iliev, L and Iliev, S and İvgin, &#x130; and Janković, I and Jovanova, L and Karkanas, P and Kavaz-Kındığılı, B and Kaya, EH and Keating, D and Kennett, DJ and Deniz Kesici, S and Khudaverdyan, A and Kiss, K and Kılıç, S and Klostermann, P and Kostak Boca Negra Valdes, S and Kovačević, S and Krenz-Niedbała, M and Krznarić Škrivanko, M and Kurti, R and Kuzman, P and Lawson, AM and Lazar, C and Leshtakov, K and Levy, TE and Liritzis, I and Lorentz, KO and Łukasik, S and Mah, M and Mallick, S and Mandl, K and Martirosyan-Olshansky, K and Matthews, R and Matthews, W and McSweeney, K and Melikyan, V and Micco, A and Michel, M and Milašinović, L and Mittnik, A and Monge, JM and Nekhrizov, G and Nicholls, R and Nikitin, AG and Nikolov, V and Novak, M and Olalde, I and Oppenheimer, J and Osterholtz, A and Özdemir, C and Özdoğan, KT and Öztürk, N and Papadimitriou, N and Papakonstantinou, N and Papathanasiou, A and Paraman, L and Paskary, EG and Patterson, N and Petrakiev, I and Petrosyan, L and Petrova, V and Philippa-Touchais, A and Piliposyan, A and Pocuca Kuzman, N and Potrebica, H and Preda-Bălănică, B and Premužić, Z and Price, TD and Qiu, L and Radović, S and Raeuf Aziz, K and Rajić Šikanjić, P and Rasheed Raheem, K and Razumov, S and Richardson, A and Roodenberg, J and Ruka, R and Russeva, V and Şahin, M and Şarbak, A and Savaş, E and Schattke, C and Schepartz, L and Selçuk, T and Sevim-Erol, A and Shamoon-Pour, M and Shephard, HM and Sideris, A and Simalcsik, A and Simonyan, H and Sinika, V and Sirak, K and Sirbu, G and Šlaus, M and Soficaru, A and Söğüt, B and Sołtysiak, A and Sönmez-Sözer, &#xc7; and Stathi, M and Steskal, M and Stewardson, K and Stocker, S and Suata-Alpaslan, F and Suvorov, A and Szécsényi-Nagy, A and Szeniczey, T and Telnov, N and Temov, S and Todorova, N and Tota, U and Touchais, G and Triantaphyllou, S and Türker, A and Ugarković, M and Valchev, T and Veljanovska, F and Videvski, Z and Virag, C and Wagner, A and Walsh, S and Włodarczak, P and Workman, JN and Yardumian, A and Yarovoy, E and Yavuz, AY and Yılmaz, H and Zalzala, F and Zettl, A and Zhang, Z and Çavuşoğlu, R and Rohland, N and Pinhasi, R and Reich, D and Davtyan, R},
title = {Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6609},
pages = {982-987},
doi = {10.1126/science.abq0762},
pmid = {36007054},
issn = {1095-9203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Archaeology ; Armenia ; Cyprus ; DNA, Ancient ; *Farmers/history ; *Gene Flow ; History, Ancient ; *Human Migration/history ; Mesopotamia ; },
abstract = {We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.},
}
@article {pmid36007048,
year = {2022},
author = {Curry, A},
title = {Ancient DNA from the Near East probes a cradle of civilization.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6609},
pages = {908-909},
doi = {10.1126/science.ade5539},
pmid = {36007048},
issn = {1095-9203},
mesh = {*Civilization/history ; *DNA, Ancient ; *Farms/history ; History, Ancient ; Humans ; *Language/history ; Middle East ; },
abstract = {Studies seek clues to origins of farming, early languages.},
}
@article {pmid36007032,
year = {2022},
author = {Arbuckle, BS and Schwandt, Z},
title = {Ancient genomes and West Eurasian history.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6609},
pages = {922-923},
doi = {10.1126/science.add9059},
pmid = {36007032},
issn = {1095-9203},
mesh = {Asia ; DNA, Ancient ; Europe ; *Genome, Human ; History, Ancient ; Humans ; *Sequence Analysis, DNA ; },
abstract = {Storytelling with ancient DNA reveals challenges and potential for writing new histories.},
}
@article {pmid36006373,
year = {2022},
author = {Dai, SS and Sulaiman, X and Isakova, J and Xu, WF and Abdulloevich, NT and Afanasevna, ME and Ibrohimovich, KB and Chen, X and Yang, WK and Wang, MS and Shen, QK and Yang, XY and Yao, YG and Aldashev, AA and Saidov, A and Chen, W and Cheng, LF and Peng, MS and Zhang, YP},
title = {The Genetic Echo of the Tarim Mummies in Modern Central Asians.},
journal = {Molecular biology and evolution},
volume = {39},
number = {9},
pages = {},
pmid = {36006373},
issn = {1537-1719},
mesh = {Asians/genetics ; *DNA, Ancient ; Ethnicity ; Gene Flow ; Genetics, Population ; Humans ; *Mummies ; },
abstract = {The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria-Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian-related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.},
}
@article {pmid35999365,
year = {2022},
author = {Kreier, F},
title = {Ancient tooth DNA reveals how 'cold sore' herpes virus has evolved.},
journal = {Nature},
volume = {609},
number = {7925},
pages = {21-22},
pmid = {35999365},
issn = {1476-4687},
mesh = {*DNA, Ancient/analysis ; DNA, Viral/analysis/genetics ; *Evolution, Molecular ; *Herpes Labialis/history/virology ; *Herpesvirus 1, Human/genetics/isolation &amp; purification ; History, Ancient ; *Tooth/metabolism ; },
}
@article {pmid35998599,
year = {2022},
author = {Schuenemann, VJ},
title = {Ancient DNA: Pathogens caught in the Minoan labyrinth.},
journal = {Current biology : CB},
volume = {32},
number = {16},
pages = {R886-R889},
doi = {10.1016/j.cub.2022.07.032},
pmid = {35998599},
issn = {1879-0445},
mesh = {Biological Evolution ; DNA, Ancient ; Genomics ; History, Ancient ; Humans ; *Plague ; *Typhoid Fever ; },
abstract = {Ancient DNA methodologies enable research on past prevalence and evolutionary history of pathogens. A new study found plague and typhoid fever-causing bacteria in Minoan Crete, showcasing both the potential and the limitations of the growing field of ancient pathogen genomics.},
}
@article {pmid35991555,
year = {2022},
author = {Collen, EJ and Johar, AS and Teixeira, JC and Llamas, B},
title = {The immunogenetic impact of European colonization in the Americas.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {918227},
pmid = {35991555},
issn = {1664-8021},
abstract = {The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.},
}
@article {pmid35960716,
year = {2022},
author = {Illanes, G and Fariello, MI and Spangenberg, L and Mordecki, E and Naya, H},
title = {Testing the existence of an unadmixed ancestor from a specific population t generations ago.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0271097},
pmid = {35960716},
issn = {1932-6203},
mesh = {*Genetics, Population ; Genome, Human ; Humans ; *Polymorphism, Single Nucleotide ; Uruguay ; },
abstract = {The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples.},
}
@article {pmid35951485,
year = {2023},
author = {Walton, K and Scarsbrook, L and Mitchell, KJ and Verry, AJF and Marshall, BA and Rawlence, NJ and Spencer, HG},
title = {Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {118-130},
doi = {10.1111/1755-0998.13696},
pmid = {35951485},
issn = {1755-0998},
mesh = {Animals ; Phylogeny ; New Zealand ; Phylogeography ; *Gastropoda/genetics ; Mollusca/genetics ; DNA ; },
abstract = {Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.},
}
@article {pmid35944486,
year = {2022},
author = {Wang, R and Wang, CC},
title = {Human genetics: The dual origin of Three Kingdoms period Koreans.},
journal = {Current biology : CB},
volume = {32},
number = {15},
pages = {R844-R847},
doi = {10.1016/j.cub.2022.06.044},
pmid = {35944486},
issn = {1879-0445},
mesh = {*Asians/genetics ; *DNA, Ancient ; Genetics, Population ; Genome ; History, Ancient ; Humans ; Republic of Korea ; },
abstract = {The genetic history of Koreans remains poorly understood due to a lack of ancient DNA. A new paleo-genomic study shows that population stratification in 4[th]-5[th] century South Korean populations was linked to a varied proportion of indigenous Jomon-related ancestry, which does not survive in present-day Koreans.},
}
@article {pmid35943423,
year = {2022},
author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV},
title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.},
journal = {Molecular ecology},
volume = {31},
number = {19},
pages = {4979-4990},
doi = {10.1111/mec.16642},
pmid = {35943423},
issn = {1365-294X},
mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; DNA, Ancient ; *Dinoflagellida/genetics ; Ecosystem ; Genome ; },
abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we utilized aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE to 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence aDNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.},
}
@article {pmid35933511,
year = {2022},
author = {Petrou, EL and Kopperl, R and Lepofsky, D and Rodrigues, AT and Yang, D and Moss, ML and Speller, CF and Hauser, L},
title = {Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13512},
pmid = {35933511},
issn = {2045-2322},
mesh = {Animals ; *DNA, Ancient ; Fisheries ; *Fishes/genetics ; Food Chain ; Seafood ; },
abstract = {Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.},
}
@article {pmid35931723,
year = {2022},
author = {Silva, NM and Kreutzer, S and Souleles, A and Triantaphyllou, S and Kotsakis, K and Urem-Kotsou, D and Halstead, P and Efstratiou, N and Kotsos, S and Karamitrou-Mentessidi, G and Adaktylou, F and Chondroyianni-Metoki, A and Pappa, M and Ziota, C and Sampson, A and Papathanasiou, A and Vitelli, K and Cullen, T and Kyparissi-Apostolika, N and Lanz, AZ and Peters, J and Rio, J and Wegmann, D and Burger, J and Currat, M and Papageorgopoulou, C},
title = {Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13474},
pmid = {35931723},
issn = {2045-2322},
support = {31003A_156853/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Bayes Theorem ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; Greece ; History, Ancient ; Humans ; *Mitochondria/genetics ; Population Dynamics ; },
abstract = {The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.},
}
@article {pmid35923939,
year = {2022},
author = {Royle, TCA and Guiry, EJ and Zhang, H and Clark, LT and Missal, SM and Rabinow, SA and James, M and Yang, DY},
title = {Documenting the short-tailed albatross (Phoebastria albatrus) clades historically present in British Columbia, Canada, through ancient DNA analysis of archaeological specimens.},
journal = {Ecology and evolution},
volume = {12},
number = {8},
pages = {e9116},
pmid = {35923939},
issn = {2045-7758},
abstract = {The short-tailed albatross (Phoebastria albatrus) is a threatened seabird whose present-day range encompasses much of the North Pacific. Within this species, there are two genetic clades (Clades 1 and 2) that have distinctive morphologies and foraging ecologies. Due to a global population collapse in the late 19th and early 20th centuries, the frequency of these clades among the short-tailed albatross population that historically foraged off British Columbia, Canada, is unclear. To document the species' historical genetic structure in British Columbia, we applied ancient DNA (aDNA) analysis to 51 archaeological short-tailed albatross specimens from the Yuquot site (Borden site number: DjSp-1) that span the past four millennia. We obtained a 141 bp cytochrome b sequence from 43 of the 51 (84.3%) analyzed specimens. Analyses of these sequences indicate 40 of the specimens belong to Clade 1, while 2 belong to Clade 2. We also identified a single specimen with a novel cytochrome b haplotype. Our results indicate that during the past four millennia most of the short-tailed albatrosses foraging near Yuquot belonged to Clade 1, while individuals from other lineages made more limited use of the area. Comparisons with the results of previous aDNA analyses of archaeological albatrosses from Japanese sites suggest the distribution of Clades 1 and 2 differed. While both albatross clades foraged extensively in the Northwest Pacific, Clade 1 albatrosses appear to have foraged along the west coast of Vancouver Island to a greater extent. Due to their differing distributions, these clades may be exposed to different threats.},
}
@article {pmid35922549,
year = {2023},
author = {Gregory, MD and Berman, KF},
title = {Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition.},
journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology},
volume = {48},
number = {1},
pages = {236-237},
pmid = {35922549},
issn = {1740-634X},
mesh = {Humans ; *DNA, Ancient ; *Cognition ; Brain ; },
}
@article {pmid35921988,
year = {2022},
author = {Zhu, S and Chen, Z and Hu, S and Wang, W and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Fu, Q},
title = {Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis).},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {49},
number = {11},
pages = {1076-1079},
doi = {10.1016/j.jgg.2022.07.005},
pmid = {35921988},
issn = {1673-8527},
mesh = {*DNA, Ancient ; *Genetic Variation ; China ; },
}
@article {pmid35914369,
year = {2022},
author = {Doniec, A and Januła, M and Grzmil, P and Kupiec, T},
title = {Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes.},
journal = {Forensic science international. Genetics},
volume = {60},
number = {},
pages = {102751},
doi = {10.1016/j.fsigen.2022.102751},
pmid = {35914369},
issn = {1878-0326},
mesh = {*Body Remains ; DNA/analysis/genetics ; DNA Fingerprinting ; Humans ; *Microsatellite Repeats ; Real-Time Polymerase Chain Reaction ; Y Chromosome/chemistry ; },
abstract = {In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.},
}
@article {pmid35907246,
year = {2022},
author = {Pérez-Escobar, OA and Tusso, S and Przelomska, NAS and Wu, S and Ryan, P and Nesbitt, M and Silber, MV and Preick, M and Fei, Z and Hofreiter, M and Chomicki, G and Renner, SS},
title = {Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication.},
journal = {Molecular biology and evolution},
volume = {39},
number = {8},
pages = {},
pmid = {35907246},
issn = {1537-1719},
mesh = {Chromosome Mapping ; *Citrullus/genetics ; Domestication ; Genomics ; Seeds/genetics ; },
abstract = {Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use "egusi-type" watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.},
}
@article {pmid35903348,
year = {2022},
author = {Erven, JAM and Çakirlar, C and Bradley, DG and Raemaekers, DCM and Madsen, O},
title = {Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {872486},
pmid = {35903348},
issn = {1664-8021},
abstract = {Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100-4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.},
}
@article {pmid35901158,
year = {2022},
author = {O'Grady, C},
title = {Ancient Europeans farmed dairy-but couldn't digest milk.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6605},
pages = {456},
doi = {10.1126/science.ade1300},
pmid = {35901158},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; *Dairying/history ; Digestion ; Europe ; *Farms/history ; History, Ancient ; Humans ; *Lactase/genetics ; *Lactose Intolerance/enzymology/genetics/history ; *Milk ; *Selection, Genetic ; Starvation/epidemiology ; *Whites/genetics/history ; },
abstract = {Giant study of ancient pottery and DNA challenges common evolutionary explanation for lactase persistence.},
}
@article {pmid35896571,
year = {2022},
author = {Krajcarz, M and Van Neer, W and Krajcarz, MT and Popović, D and Baca, M and De Cupere, B and Goffette, Q and Küchelmann, HC and Gręzak, A and Iwaszczuk, U and Ottoni, C and Van de Vijver, K and Wilczyński, J and Mulczyk, A and Wiejacki, J and Makowiecki, D and Bocherens, H},
title = {Stable isotopes unveil one millennium of domestic cat paleoecology in Europe.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12775},
pmid = {35896571},
issn = {2045-2322},
support = {101002811 FELIX/ERC_/European Research Council/International ; },
mesh = {Animals ; Carbon Isotopes/analysis ; Cats ; Diet ; Ecology ; *Ecosystem ; Europe ; *Isotopes ; Nitrogen Isotopes/analysis ; },
abstract = {The domestic cat is the world's most popular pet and one of the most detrimental predators in terrestrial ecosystems. Effective protection of wildlife biodiversity demands detailed tracking of cat trophic ecology, and stable isotopes serve as a powerful proxy in dietary studies. However, a variable diet can make an isotopic pattern unreadable in opportunistic predators. To evaluate the usefulness of the isotopic method in cat ecology, we measured C and N isotope ratios in hundreds of archaeological cat bones. We determined trends in cat trophic paleoecology in northern Europe by exploiting population-scale patterns in animals from diverse locations. Our dataset shows a high variability of isotopic signals related to the socio-economic and/or geomorphological context. This points toward regularities in isotopic patterns across past cat populations. We provide a generalized guide to interpret the isotopic ecology of cats, emphasizing that regional isotopic baselines have a major impact on the isotopic signal.},
}
@article {pmid35882233,
year = {2022},
author = {Neumann, GU and Skourtanioti, E and Burri, M and Nelson, EA and Michel, M and Hiss, AN and McGeorge, PJP and Betancourt, PP and Spyrou, MA and Krause, J and Stockhammer, PW},
title = {Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete.},
journal = {Current biology : CB},
volume = {32},
number = {16},
pages = {3641-3649.e8},
doi = {10.1016/j.cub.2022.06.094},
pmid = {35882233},
issn = {1879-0445},
mesh = {Genome, Bacterial ; Greece ; Humans ; Phylogeny ; *Salmonella enterica/genetics ; *Yersinia pestis/genetics ; },
abstract = {During the late 3[rd] millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.[1-4] However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.[5] The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,[5-8] circulated across Eurasia at least from the onset of the 3[rd] millennium BCE,[9-13] but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y. pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.},
}
@article {pmid35876520,
year = {2022},
author = {Gibert, JM},
title = {[Small scale evolution].},
journal = {Biologie aujourd'hui},
volume = {216},
number = {1-2},
pages = {41-47},
doi = {10.1051/jbio/2022008},
pmid = {35876520},
issn = {2105-0686},
mesh = {Animals ; Beak/anatomy &amp; histology ; Biological Evolution ; Cats ; Evolution, Molecular ; *Finches/anatomy &amp; histology/genetics ; Genetic Variation ; Mutation ; Phenotype ; *Selection, Genetic ; },
abstract = {Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.},
}
@article {pmid35874301,
year = {2022},
author = {Silvestrini, S and Romandini, M and Marciani, G and Arrighi, S and Carrera, L and Fiorini, A and López-García, JM and Lugli, F and Ranaldo, F and Slon, V and Tassoni, L and Higgins, OA and Bortolini, E and Curci, A and Meyer, M and Meyer, MC and Oxilia, G and Zerboni, A and Benazzi, S and Spinapolice, EE},
title = {Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy.},
journal = {Journal of quaternary science},
volume = {37},
number = {2},
pages = {235-256},
pmid = {35874301},
issn = {0267-8179},
abstract = {The Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.},
}
@article {pmid35868268,
year = {2022},
author = {Liu, Y and Bennett, EA and Fu, Q},
title = {Evolving ancient DNA techniques and the future of human history.},
journal = {Cell},
volume = {185},
number = {15},
pages = {2632-2635},
doi = {10.1016/j.cell.2022.06.009},
pmid = {35868268},
issn = {1097-4172},
mesh = {*DNA, Ancient ; *Genome, Human ; History, Ancient ; Humans ; },
abstract = {Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health.},
}
@article {pmid35857780,
year = {2022},
author = {Gòdia, M and Brogaard, L and Mármol-Sánchez, E and Langhorn, R and Nordang Kieler, I and Jan Reezigt, B and Nikolic Nielsen, L and Rem Jessen, L and Cirera, S},
title = {Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0270067},
pmid = {35857780},
issn = {1932-6203},
mesh = {Animals ; Biomarkers/urine ; Case-Control Studies ; Cats ; Humans ; *MicroRNAs/metabolism ; *Pyelonephritis/diagnosis/genetics/veterinary ; *Renal Insufficiency, Chronic ; },
abstract = {MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression at the post-transcriptional level. miRNAs have been found in urine and have shown diagnostic potential in human nephropathies. Here, we aimed to characterize, for the first time, the feline urinary miRNAome and explore the use of urinary miRNA profiles as non-invasive biomarkers for feline pyelonephritis (PN). Thirty-eight cats were included in a prospective case-control study and classified in five groups: healthy Control cats (n = 11), cats with PN (n = 10), cats with subclinical bacteriuria or cystitis (SB/C, n = 5), cats with ureteral obstruction (n = 7) and cats with chronic kidney disease (n = 5). By small RNA sequencing we identified 212 miRNAs in cat urine, including annotated (n = 137) and putative novel (n = 75) miRNAs. The 15 most highly abundant urinary miRNAs accounted for nearly 71% of all detected miRNAs, most of which were previously identified in feline kidney. Ninety-nine differentially abundant (DA) miRNAs were identified when comparing Control cats to cats with urological conditions and 102 DA miRNAs when comparing PN to other urological conditions. Tissue clustering analysis revealed that the majority of urine samples clustered close to kidney, which confirm the likely cellular origin of the secreted urinary miRNAs. Relevant DA miRNAs were verified by quantitative real-time PCR (qPCR). Eighteen miRNAs discriminated Control cats from cats with a urological condition. Of those, seven miRNAs were DA by both RNAseq and qPCR methods between Control and PN cats (miR-125b-5p, miR-27a-3p, miR-21-5p, miR-27b-3p, miR-125a-5p, miR-17-5p and miR-23a-3p) or DA between Control and SB/C cats (miR-125b-5p). Six additional miRNAs (miR-30b-5p, miR-30c, miR-30e-5p, miR-27a-3p, miR-27b-39 and miR-222) relevant for discriminating PN from other urological conditions were identified by qPCR alone (n = 4) or by both methods (n = 2) (P<0.05). This panel of 13 miRNAs has potential as non-invasive urinary biomarkers for diagnostic of PN and other urological conditions in cats.},
}
@article {pmid35839766,
year = {2022},
author = {Zhang, X and Ji, X and Li, C and Yang, T and Huang, J and Zhao, Y and Wu, Y and Ma, S and Pang, Y and Huang, Y and He, Y and Su, B},
title = {A Late Pleistocene human genome from Southwest China.},
journal = {Current biology : CB},
volume = {32},
number = {14},
pages = {3095-3109.e5},
doi = {10.1016/j.cub.2022.06.016},
pmid = {35839766},
issn = {1879-0445},
mesh = {Animals ; China ; *Deer ; Fossils ; Genome, Human ; *Hominidae ; Humans ; },
abstract = {Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.},
}
@article {pmid35835776,
year = {2022},
author = {Askari, Z and Ruehli, F and Bouwman, A and Shariati, V and Naddaf, SR and Otranto, D and Mas-Coma, S and Rezaeian, M and Boenke, N and Stöllner, T and Aali, A and Mobedi, I and Mowlavi, G},
title = {Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE-6th cent. CE).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12045},
pmid = {35835776},
issn = {2045-2322},
mesh = {Animals ; DNA, Ancient ; Genomics ; *Helminths/genetics ; History, Ancient ; Humans ; Iran ; *Taenia/genetics ; },
abstract = {Palaeoparasitology investigates parasitological infections in animals and humans of past distance by examining biological remains. Palaeofaeces (or coprolites) are biological remains that provide valuable information on the disease, diet, and population movements in ancient times. Today, advances in detecting ancient DNA have cast light on dark corners that microscopy could never reach. The archaeological site of the Chehrabad salt mine of Achaemenid (550-330 BC) and Sassanid (third-seventh century AD) provides remains of various biotic and abiotic samples, including animal coprolites, for multidisciplinary studies. In the present work, we investigated coprolites for helminth eggs and larvae by microscopy and traced their biological agents' DNA by Next Generation Sequencing. Our results revealed various helminths, including Taenia asiatica, the species introduced in the 1990s. Implementing advanced modern molecular techniques like NGS gives a paramount view of pathogenic agents in space and time.},
}
@article {pmid35818010,
year = {2022},
author = {Estrada, O and Richards, SM and Breen, J},
title = {Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2512},
number = {},
pages = {261-267},
doi = {10.1007/978-1-0716-2429-6_15},
pmid = {35818010},
issn = {1940-6029},
mesh = {DNA, Plant/genetics ; Genomics/methods ; *Museums ; *Plants/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.},
}
@article {pmid35779768,
year = {2022},
author = {Psonis, N and Vardinoyannis, K and Poulakakis, N},
title = {High-throughput degraded DNA sequencing of subfossil shells of a critically endangered stenoendemic land snail in the Aegean.},
journal = {Molecular phylogenetics and evolution},
volume = {175},
number = {},
pages = {107561},
doi = {10.1016/j.ympev.2022.107561},
pmid = {35779768},
issn = {1095-9513},
mesh = {Animals ; DNA/genetics ; Endangered Species ; *High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Sequence Analysis, DNA/methods ; *Snails/genetics ; },
abstract = {High-throughput sequencing has enabled the comprehensive genetic exploration of biological diversity, especially by using natural history collections to study hard-to-find, threatened or even extinct-in-the-wild taxa. Mollusk shells are under-exploited as a source for DNA-based approaches, despite their apparent advantages in the field of conservation genetics. More particularly, degraded DNA techniques combined with high-throughput sequencing have never been used to gain insights about the DNA preservation in land snail subfossil or historical shells. Here, we applied degraded DNA analysis on two historical shells of Levantina rechingeri, a stenoendemic Critically Endangered species that has never been found alive, in order to explore the patterns of DNA preservation on land snail shells originating from the eastern Mediterranean, as well as to infer its molecular phylogenetic placement. Our results showed that centuries to decades-old DNA from an empty shell collected in an Aegean island exhibits characteristic post-mortem damage patterns similar to those observed in ancient DNA from eastern Mediterranean terrestrial animals, setting a precedent for future museomics studies on taxa distributed in areas with similar climate. Finally, genome skimming of the empty shell allowed high coverage of multiple nuclear and mitochondrial loci, enabling the phylogenetic placement of the focal taxon, the re-evaluation of its taxonomic classification, and the revealing of a new Aegean land snail lineage, Aristena genus novum. This approach is a non-invasive way to sample DNA from threatened land snail species and suitable to study the evolutionary history of taxa with cryptic ecology, stenoendemics, or extinct-in-the-wild, as well as old museum specimens.},
}
@article {pmid35774991,
year = {2022},
author = {Marinček, P and Wagner, ND and Tomasello, S},
title = {Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?.},
journal = {Applications in plant sciences},
volume = {10},
number = {3},
pages = {e11477},
pmid = {35774991},
issn = {2168-0450},
abstract = {PREMISE: Herbaria harbor a tremendous number of plant specimens that are rarely used for molecular systematic studies, largely due to the difficulty in extracting sufficient amounts of high-quality DNA from the preserved plant material.<br><br>METHODS: We compared the standard Qiagen DNeasy Plant Mini Kit and a specific protocol for extracting ancient DNA (aDNA) (the N-phenacylthiazolium bromide and dithiothreitol [PTB-DTT] extraction method) from two different plant genera (Xanthium and Salix). The included herbarium materials covered about two centuries of plant collections. To analyze the success of DNA extraction using each method, a subset of samples was subjected to a standard library preparation as well as target-enrichment approaches.<br><br>RESULTS: The PTB-DTT method produced a higher DNA yield of better quality than the Qiagen kit; however, extracts from the Qiagen kit over a certain DNA yield and quality threshold produced comparable sequencing results. The sequencing resulted in high proportions of endogenous reads. We were able to successfully sequence 200-year-old samples.<br><br>DISCUSSION: This method comparison revealed that, for younger specimens, DNA extraction using a standard kit might be sufficient. For old and precious herbarium specimens, aDNA extraction methods are better suited to meet the requirements for next-generation sequencing.},
}
@article {pmid35771911,
year = {2022},
author = {Liu, YC and Hunter-Anderson, R and Cheronet, O and Eakin, J and Camacho, F and Pietrusewsky, M and Rohland, N and Ioannidis, A and Athens, JS and Douglas, MT and Ikehara-Quebral, RM and Bernardos, R and Culleton, BJ and Mah, M and Adamski, N and Broomandkhoshbacht, N and Callan, K and Lawson, AM and Mandl, K and Michel, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Kidd, K and Kidd, J and Schurr, TG and Auckland, K and Hill, AVS and Mentzer, AJ and Quinto-Cortés, CD and Robson, K and Kennett, DJ and Patterson, N and Bustamante, CD and Moreno-Estrada, A and Spriggs, M and Vilar, M and Lipson, M and Pinhasi, R and Reich, D},
title = {Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6601},
pages = {72-79},
doi = {10.1126/science.abm6536},
pmid = {35771911},
issn = {1095-9203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Asians/genetics ; Child ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Female ; History, Ancient ; *Human Migration/history ; Humans ; Male ; Micronesia ; Oceania ; },
abstract = {Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.},
}
@article {pmid35771611,
year = {2022},
author = {Liu, X and Orlando, L},
title = {mapDATAge: a ShinyR package to chart ancient DNA data through space and time.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {16},
pages = {3992-3994},
pmid = {35771611},
issn = {1367-4811},
mesh = {*Software ; *DNA, Ancient ; },
abstract = {SUMMARY: Ancient DNA datasets are increasingly difficult to visualize for users lacking computational experience. Here, we describe mapDATAge, which aims to provide user-friendly automated modules for the interactive mapping of allele, haplogroup and/or ancestry distributions through space and time. mapDATAge enhances collaborative data sharing while assisting the assessment and reporting of spatiotemporal patterns of genetic changes.<br><br>mapDATAge is a Shiny R application designed for exploring spatiotemporal patterns in ancient DNA data through a graphical user interface. It is freely available under GNU Public License in Github: https://github.com/xuefenfei712/mapDATAge.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35768506,
year = {2022},
author = {Bergström, A and Stanton, DWG and Taron, UH and Frantz, L and Sinding, MS and Ersmark, E and Pfrengle, S and Cassatt-Johnstone, M and Lebrasseur, O and Girdland-Flink, L and Fernandes, DM and Ollivier, M and Speidel, L and Gopalakrishnan, S and Westbury, MV and Ramos-Madrigal, J and Feuerborn, TR and Reiter, E and Gretzinger, J and Münzel, SC and Swali, P and Conard, NJ and Carøe, C and Haile, J and Linderholm, A and Androsov, S and Barnes, I and Baumann, C and Benecke, N and Bocherens, H and Brace, S and Carden, RF and Drucker, DG and Fedorov, S and Gasparik, M and Germonpré, M and Grigoriev, S and Groves, P and Hertwig, ST and Ivanova, VV and Janssens, L and Jennings, RP and Kasparov, AK and Kirillova, IV and Kurmaniyazov, I and Kuzmin, YV and Kosintsev, PA and Lázničková-Galetová, M and Leduc, C and Nikolskiy, P and Nussbaumer, M and O'Drisceoil, C and Orlando, L and Outram, A and Pavlova, EY and Perri, AR and Pilot, M and Pitulko, VV and Plotnikov, VV and Protopopov, AV and Rehazek, A and Sablin, M and Seguin-Orlando, A and Storå, J and Verjux, C and Zaibert, VF and Zazula, G and Crombé, P and Hansen, AJ and Willerslev, E and Leonard, JA and Götherström, A and Pinhasi, R and Schuenemann, VJ and Hofreiter, M and Gilbert, MTP and Shapiro, B and Larson, G and Krause, J and Dalén, L and Skoglund, P},
title = {Grey wolf genomic history reveals a dual ancestry of dogs.},
journal = {Nature},
volume = {607},
number = {7918},
pages = {313-320},
pmid = {35768506},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; 852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; 310763/ERC_/European Research Council/International ; ERC-2013-STG-337574-UNDEAD/ERC_/European Research Council/International ; ERC-2019-STG-853272-PALAEOFARM/ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Africa ; Animals ; DNA, Ancient/analysis ; *Dogs/genetics ; Domestication ; Europe ; *Genome/genetics ; *Genomics ; History, Ancient ; Middle East ; Mutation ; North America ; *Phylogeny ; Selection, Genetic ; Siberia ; Tumor Suppressor Proteins/genetics ; *Wolves/classification/genetics ; },
abstract = {The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived[1-8]. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.},
}
@article {pmid35751552,
year = {2022},
author = {, and Nijman, IJ and Rosen, BD and Bardou, P and Faraut, T and Cumer, T and Daly, KG and Zheng, Z and Cai, Y and Asadollahpour, H and Kul, B&#xc7; and Zhang, WY and E, G and Ayin, A and Baird, H and Bakhtin, M and Bâlteanu, VA and Barfield, D and Berger, B and Blichfeldt, T and Boink, G and Bugiwati, SRA and Cai, Z and Carolan, S and Clark, E and Cubric-Curik, V and Dagong, MIA and Dorji, T and Drew, L and Guo, J and Hallsson, J and Horvat, S and Kantanen, J and Kawaguchi, F and Kazymbet, P and Khayatzadeh, N and Kim, N and Shah, MK and Liao, Y and Martínez, A and Masangkay, JS and Masaoka, M and Mazza, R and McEwan, J and Milanesi, M and Omar, FM and Nomura, Y and Ouchene-Khelifi, NA and Pereira, F and Sahana, G and Salavati, M and Sasazaki, S and Da Silva, A and Simčič, M and Sölkner, J and Sutherland, A and Tigchelaar, J and Zhang, H and , and Ajmone-Marsan, P and Bradley, DG and Colli, L and Drögemüller, C and Jiang, Y and Lei, C and Mannen, H and Pompanon, F and Tosser-Klopp, G and Lenstra, JA},
title = {Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.},
journal = {Molecular ecology},
volume = {31},
number = {16},
pages = {4364-4380},
doi = {10.1111/mec.16579},
pmid = {35751552},
issn = {1365-294X},
support = {BBS/OS/GC/000012F/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genetic Variation ; Goats/genetics ; Haplotypes/genetics ; Phylogeny ; Y Chromosome/genetics ; },
abstract = {By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.},
}
@article {pmid35749392,
year = {2022},
author = {Toncheva, D and Marinova, M and Borovska, P and Serbezov, D},
title = {Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269628},
pmid = {35749392},
issn = {1932-6203},
mesh = {DNA, Ancient ; Gene Frequency ; Genotype ; Humans ; *Phenylketonurias ; *Symporters ; },
abstract = {Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP-52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes-PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210-32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread.},
}
@article {pmid35746807,
year = {2022},
author = {Nishimura, L and Fujito, N and Sugimoto, R and Inoue, I},
title = {Detection of Ancient Viruses and Long-Term Viral Evolution.},
journal = {Viruses},
volume = {14},
number = {6},
pages = {},
pmid = {35746807},
issn = {1999-4915},
mesh = {*COVID-19 ; DNA, Ancient ; Evolution, Molecular ; Genome, Viral ; Humans ; *Viruses/genetics ; },
abstract = {The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.},
}
@article {pmid35743173,
year = {2022},
author = {Bodner, M and Amory, C and Olivieri, A and Gandini, F and Cardinali, I and Lancioni, H and Huber, G and Xavier, C and Pala, M and Fichera, A and Schnaller, L and Gysi, M and Sarno, S and Pettener, D and Luiselli, D and Richards, MB and Semino, O and Achilli, A and Torroni, A and Parson, W},
title = {Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
pmid = {35743173},
issn = {1422-0067},
mesh = {*DNA, Mitochondrial/genetics ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes/genetics ; Nuclear Family ; Pilot Projects ; Sequence Analysis, DNA ; },
abstract = {The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.},
}
@article {pmid35734848,
year = {2022},
author = {Saldías, E and Valdebenito, G and Zamora, L and Bastías, B and Flores, C and Vila, B and Vinueza, D and Tornero, C and Malgosa, A and Becker, E},
title = {Multidisciplinary analysis of a mummy from the War of the Pacific.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {79},
number = {4},
pages = {451-465},
doi = {10.1127/anthranz/2022/1543},
pmid = {35734848},
issn = {0003-5548},
mesh = {Adult ; Archaeology ; Humans ; Male ; *Mummies ; Peru ; Tomography, X-Ray Computed ; *Wounds, Gunshot ; },
abstract = {The War of the Pacific (1879-1884) was a big scale war between Chile against the alliance of Peru and Bolivia. One of the most important battles, the "Batalla del Campo de la Alianza" was situated in the desert near Tacna, Peru. The conditions of this environment favored the conservation of the dead soldiers after many years. Decades ago, the Natural History Museum of Concepción in Chile, received a naturally mummified individual of a probably Chilean soldier as a donation; its uncertain context was never studied nor confirmed. Considering this, our investigation analyzed this body under exploratory methods, ballistic analysis, archaeological contrast, [14]C radiocarbon dating, ancient DNA, and isotopic analysis to reconstruct the biological profile of this mummy. The results indicated that the mummy belongs to an adult man between 33-39 years of age (> 1.50 m) and has a perimortem wound in the left flank of the abdomen. CT scan and X-rays revealed the presence of a bullet (Comblain II or Gras) hosted near the L2 vertebra. It is possible that the individual died of bleeding from a gunshot wound done by a long-distance firearm projectile from an inferior level, whose trajectory was from left to right, with slight inclination towards the top, and without a projectile exit. Other analyses confirmed the historical context and suggests the Chilean origin of the mummy. Despite the passage of time and other factors, it was possible to reconstruct the death of this individual thanks to technology and approaches from different disciplines.},
}
@article {pmid35732180,
year = {2022},
author = {Gelabert, P and Blazyte, A and Chang, Y and Fernandes, DM and Jeon, S and Hong, JG and Yoon, J and Ko, Y and Oberreiter, V and Cheronet, O and Özdoğan, KT and Sawyer, S and Yang, S and Greytak, EM and Choi, H and Kim, J and Kim, JI and Jeong, C and Bae, K and Bhak, J and Pinhasi, R},
title = {Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea.},
journal = {Current biology : CB},
volume = {32},
number = {15},
pages = {3232-3244.e6},
doi = {10.1016/j.cub.2022.06.004},
pmid = {35732180},
issn = {1879-0445},
mesh = {Archaeology ; *Asians/genetics ; *Ethnicity ; Genome ; History, Ancient ; Humans ; Polymorphism, Single Nucleotide ; },
abstract = {The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.},
}
@article {pmid35731946,
year = {2022},
author = {Översti, S and Palo, JU},
title = {Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages.},
journal = {Genome biology and evolution},
volume = {14},
number = {7},
pages = {},
pmid = {35731946},
issn = {1759-6653},
mesh = {Bayes Theorem ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Evolution, Molecular ; Fossils ; Genetic Variation ; Haplotypes ; Humans ; Phylogeny ; },
abstract = {Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.},
}
@article {pmid35729698,
year = {2022},
author = {Zheng, ZQ and Fu, QM and Liu, YC},
title = {Exploration of adaptation, evolution and domestication of fermentation microorganisms by applying ancient DNA technology.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {5},
pages = {414-423},
doi = {10.16288/j.yczz.22-057},
pmid = {35729698},
issn = {0253-9772},
mesh = {*DNA, Ancient ; Domestication ; Fermentation ; *Fermented Foods ; Humans ; Technology ; },
abstract = {Fermentation production is the most primitive application of microorganisms by humans, which is of great significance in human history. However, due to the lack of molecular evidence, the history of human fermentation production and the evolution and domestication of fermentation microorganisms remain to be further investigated. Taking wine and fermented dairy, the two most common types of fermented foods as examples, we introduce the archaeology evidence of fermented foods and the evolution and domestication of fermented microorganisms, introduce the research status of paleomicrobiology and fermented paleomicroorganisms, and explore the feasibility and challenges of the research of ancient fermented microorganisms applying microbial ancient DNA technology, as well as the application potential of ancient DNA capture technology in this field.},
}
@article {pmid35729694,
year = {2022},
author = {Ping, WJ and Liu, YC and Fu, QM},
title = {Exploring the evolution of archaic humans through sedimentary ancient DNA.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {5},
pages = {362-369},
doi = {10.16288/j.yczz.22-032},
pmid = {35729694},
issn = {0253-9772},
mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Genome, Human ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; },
abstract = {Recent success in the retrieval of nuclear DNA of ancient humans and animals from cave sediments paves the way for genome-wide studies of past populations directly from sediments. In three studies, nuclear genomes of different species were obtained from the sediments of multiple archeological caves and their genetic histories were revealed, including an unknown population replacement of Neanderthals from Estatuas cave in Spain, which was recovered using a new DNA capture approach. By extending sediments as a source of DNA beyond fossils, this breakthrough is of particular significance to the field of ancient human genomics, which brings about more possibilities for exploring the history of past population migration, evolution and adaptation within larger time-scales and geographical areas where no fossil remains exist. Here, we mainly review the significance of the technical advances in retrieving ancient nuclear DNA from sediments and present new insights into the genetic history of Neanderthals revealed by this technique. By combining ancient genomes retrieved from fossils and additional mitochondrial DNA extracted from sediments of archaeological sites, we may begin investigating diverse archaic populations and examine their genetic relationships, movements and replacements in detail.},
}
@article {pmid35719876,
year = {2022},
author = {Rodrigues Soares, AE and Boroffka, N and Schröder, O and Sverchkov, L and Benecke, N and Günther, T},
title = {Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.},
journal = {Royal Society open science},
volume = {9},
number = {6},
pages = {220104},
pmid = {35719876},
issn = {2054-5703},
abstract = {Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.},
}
@article {pmid35715597,
year = {2022},
author = {Graham, F},
title = {Daily briefing: Ancient DNA traces origin of Black Death.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-01703-1},
pmid = {35715597},
issn = {1476-4687},
}
@article {pmid35710940,
year = {2022},
author = {Long, GS and Klunk, J and Duggan, AT and Tapson, M and Giuffra, V and Gazzè, L and Fornaciari, A and Duchene, S and Fornaciari, G and Clermont, O and Denamur, E and Golding, GB and Poinar, H},
title = {A 16[th] century Escherichia coli draft genome associated with an opportunistic bile infection.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {599},
pmid = {35710940},
issn = {2399-3642},
mesh = {Animals ; Bile ; Escherichia coli/genetics ; *Escherichia coli Infections/genetics/microbiology ; Genome, Bacterial ; Mice ; *Opportunistic Infections ; },
abstract = {Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16[th] century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.},
}
@article {pmid35709925,
year = {2022},
author = {Raveane, A and Molinaro, L and Aneli, S and Capodiferro, MR and de Gennaro, L and Ongaro, L and Rambaldi Migliore, N and Soffiati, S and Scarano, T and Torroni, A and Achilli, A and Ventura, M and Pagani, L and Capelli, C and Olivieri, A and Bertolini, F and Semino, O and Montinaro, F},
title = {Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy.},
journal = {Genomics},
volume = {114},
number = {4},
pages = {110405},
doi = {10.1016/j.ygeno.2022.110405},
pmid = {35709925},
issn = {1089-8646},
mesh = {Archaeology ; *DNA, Ancient ; *Genome, Human ; Humans ; Iran ; Italy ; },
abstract = {Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.},
}
@article {pmid35709264,
year = {2022},
author = {Gibbons, A},
title = {Ancient DNA reveals Black Death source.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6599},
pages = {1254-1255},
doi = {10.1126/science.add4865},
pmid = {35709264},
issn = {1095-9203},
mesh = {Burial/history ; DNA, Ancient ; *Epidemics/history ; History, Medieval ; Humans ; Kyrgyzstan/epidemiology ; *Plague/epidemiology/history ; *Yersinia pestis/isolation &amp; purification ; },
abstract = {Graves in Kyrgyzstan hold early victims of plague that swept medieval Europe.},
}
@article {pmid35705867,
year = {2022},
author = {Callaway, E},
title = {Ancient DNA traces origin of Black Death.},
journal = {Nature},
volume = {606},
number = {7915},
pages = {635-636},
pmid = {35705867},
issn = {1476-4687},
mesh = {*DNA, Ancient ; *DNA, Bacterial ; History, Medieval ; Humans ; *Plague/epidemiology/genetics/history/microbiology ; },
}
@article {pmid35705810,
year = {2022},
author = {Spyrou, MA and Musralina, L and Gnecchi Ruscone, GA and Kocher, A and Borbone, PG and Khartanovich, VI and Buzhilova, A and Djansugurova, L and Bos, KI and Kühnert, D and Haak, W and Slavin, P and Krause, J},
title = {The source of the Black Death in fourteenth-century central Eurasia.},
journal = {Nature},
volume = {606},
number = {7915},
pages = {718-724},
pmid = {35705810},
issn = {1476-4687},
support = {771234/ERC_/European Research Council/International ; },
mesh = {Archaeology ; Cemeteries ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; History, Medieval ; Humans ; Kyrgyzstan/epidemiology ; Pandemics/history ; Phylogeny ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/classification/pathogenicity ; },
abstract = {The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences[1,2]. Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan[1,3-9]. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals[9]. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.},
}
@article {pmid35702131,
year = {2022},
author = {Mohit, and Sharma, I and Sharma, V and Kumar, S and Rastogi, G and Dutt, P and Shrivastava, A and Rai, N and Chand, P},
title = {Empirical assessment of allele frequencies of genome wide association study variants associated with obstructive sleep apnea.},
journal = {American journal of translational research},
volume = {14},
number = {5},
pages = {3464-3471},
pmid = {35702131},
issn = {1943-8141},
abstract = {OBJECTIVE: Obstructive Sleep Apnea (OSA) is a heterogeneous disorder with a complex interplay of genetic and environmental factors. Over the years, with advancement in genotyping and sequencing techniques, various loci have shown an association with OSA. It is pertinent to understand the status of these associated variants in different ethnic groups. The aim of the study was to assess the genetic affinity among different population groups by evaluating the risk allele frequencies of variants associated with OSA.<br><br>METHOD: The variants associated with OSA were obtained from the GWAS catalog with a significant p value of <5 &#xd7; 10[-7]; 95 variants were obtained (www.ebi.ac.uk/gwas). Further, the variants were narrowed down on the basis of risk allele frequencies (>5%). The fst was calculated to assess the genetic affinity between super population groups and among the sub-population groups present in the 1000 genome project.<br><br>RESULT: The fst values observed indicated all super populations were genetically related (SAS, AMR, EAS and EUR) except in the African (AFR) population group. Further, the closely related super population i.e., SAS, AMR, EAS and EUR when bifurcated on the basis of sub-population groups shows population stratification and SAS population groups form separate clusters on the MDS plot.<br><br>CONCLUSION: The study highlights genetic heterogeneity among different population groups that gets diluted and results are biased when the samples are pooled irrespective of their endogamous groups. Our results provide insight to researchers to target specific endogamous groups for future studies on OSA.},
}
@article {pmid35698034,
year = {2022},
author = {Kutschera, VE and Kierczak, M and van der Valk, T and von Seth, J and Dussex, N and Lord, E and Dehasque, M and Stanton, DWG and Khoonsari, PE and Nystedt, B and Dalén, L and Díez-Del-Molino, D},
title = {GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {228},
pmid = {35698034},
issn = {1471-2105},
support = {P2SKP3_165031/SNSF_/Swiss National Science Foundation/Switzerland ; P300PA_177845/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; *Computational Biology ; Endangered Species ; *Genome ; Genomics ; Reproducibility of Results ; Software ; },
abstract = {BACKGROUND: Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.<br><br>RESULTS: Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).<br><br>CONCLUSIONS: GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.},
}
@article {pmid35695771,
year = {2022},
author = {Huang, Y and Ringbauer, H},
title = {hapCon: estimating contamination of ancient genomes by copying from reference haplotypes.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {15},
pages = {3768-3777},
pmid = {35695771},
issn = {1367-4811},
mesh = {Male ; Humans ; Haplotypes ; Sequence Analysis, DNA/methods ; *Genome ; *Software ; DNA, Ancient ; },
abstract = {MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches.<br><br>RESULTS: We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&amp;Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1&#xd7; for SNP capture data (1240k) and 0.02&#xd7; for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as &#x223c;45&#xa0;000 and various global ancestries.<br><br>We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35692842,
year = {2022},
author = {Xue, J and Wang, W and Shao, J and Dai, X and Sun, Z and Gardner, JD and Chen, L and Guo, X and Di, N and Pei, X and Wu, X and Zhang, G and Cui, C and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Zhang, L and He, N and Fu, Q},
title = {Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {909267},
pmid = {35692842},
issn = {1664-8021},
abstract = {Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin. Our results show that the populations inhabiting Shimao City had close genetic connections with an earlier population in the Middle Neolithic Yangshao period of northern Shaanxi Province, revealing a mostly local origin for the Shimao Society. In addition, among the populations in other regions of the Yellow River basin, the Shimao-related populations had the closest maternal affinity with the contemporaneous Taosi populations from the Longshan period. The Shimao-related populations also shared more affinity with present-day northern Han populations than with the minorities and southern Han in China. Our study provides a new perspective on the genetic origins and structure of the Shimao people and the population dynamics in the Middle Yellow River basin during the Neolithic period.},
}
@article {pmid35687599,
year = {2022},
author = {Poma, A and Cesare, P and Bonfigli, A and Volpe, AR and Colafarina, S and Vecchiotti, G and Forgione, A and Zarivi, O},
title = {A qPCR-duplex assay for sex determination in ancient DNA.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269913},
pmid = {35687599},
issn = {1932-6203},
mesh = {Amelogenin/genetics ; DNA/analysis/genetics ; *DNA, Ancient ; Humans ; Male ; Real-Time Polymerase Chain Reaction ; *Sex Determination Analysis/methods ; },
abstract = {Molecular biology techniques are increasingly being used in sex identification of skeletal remains when traditional anthropometric analyzes are not successful in identifying sex of remains that are incomplete, fragmented and /or of immature individuals. In the present work, we investigated the possibility of determining sex by using the qPCR-duplex method for both ancient and modern DNA samples. This method involves the co-amplification of two genes in a single reaction system and the subsequent analysis of the fusion curves; the gene sequences used for the construction of suitable primers are those of steroid sulfatase (STS) and testis specific protein Y-linked 1 (TSPY) genes which turned out to be two sensitive markers as they have a detection limit of 60 pg and 20 pg respectively on modern DNA. The validity of the method was verified on modern DNA in which gender was identified in all the samples with 100% accuracy; thus, allowing for the same results as the classic method with amelogenin, but in a faster and more immediate way, as it allows for sex determination solely by analyzing the denaturation curves without having to perform an electrophoretic run. The proposed molecular technique proves to be sensitive and precise even on degraded DNA, in fact on 9 archaeological finds dating from the VII-XII century in which sex had been identified through anthropometric analysis, it confirmed the sex of 8 out of 9 finds correctly.},
}
@article {pmid35681049,
year = {2022},
author = {Schulte, L and Meucci, S and Stoof-Leichsenring, KR and Heitkam, T and Schmidt, N and von Hippel, B and Andreev, AA and Diekmann, B and Biskaborn, BK and Wagner, B and Melles, M and Pestryakova, LA and Alsos, IG and Clarke, C and Krutovsky, KV and Herzschuh, U},
title = {Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {570},
pmid = {35681049},
issn = {2399-3642},
mesh = {DNA, Ancient ; Ecosystem ; *Larix/genetics ; Siberia ; Trees ; },
abstract = {Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.},
}
@article {pmid35671731,
year = {2022},
author = {Choin, J and Quintana-Murci, L},
title = {Paleogenomics: The demographic past of prehistoric Europeans.},
journal = {Current biology : CB},
volume = {32},
number = {11},
pages = {R535-R538},
doi = {10.1016/j.cub.2022.04.081},
pmid = {35671731},
issn = {1879-0445},
mesh = {DNA, Ancient ; Demography ; Europe ; *Genome, Human ; *Genomics ; History, Ancient ; Humans ; Paleontology ; },
abstract = {Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe.},
}
@article {pmid35652762,
year = {2022},
author = {Nagler, M and Podmirseg, SM and Ascher-Jenull, J and Sint, D and Traugott, M},
title = {Why eDNA fractions need consideration in biomonitoring.},
journal = {Molecular ecology resources},
volume = {22},
number = {7},
pages = {2458-2470},
pmid = {35652762},
issn = {1755-0998},
mesh = {Biodiversity ; Biological Monitoring ; DNA Barcoding, Taxonomic ; *DNA, Environmental ; Environmental Monitoring ; },
abstract = {The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.},
}
@article {pmid35635751,
year = {2022},
author = {Chintalapati, M and Patterson, N and Moorjani, P},
title = {The spatiotemporal patterns of major human admixture events during the European Holocene.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35635751},
issn = {2050-084X},
support = {R35 GM142978/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeology ; DNA, Ancient ; Europe ; *Genome, Human ; *Human Migration ; Humans ; Iran ; },
abstract = {Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.},
}
@article {pmid35627311,
year = {2022},
author = {Abondio, P and Cilli, E and Luiselli, D},
title = {Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods.},
journal = {Genes},
volume = {13},
number = {5},
pages = {},
pmid = {35627311},
issn = {2073-4425},
mesh = {*Genome ; Haplotypes/genetics ; Linkage Disequilibrium ; *Selection, Genetic ; Whole Genome Sequencing ; },
abstract = {Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework.},
}
@article {pmid35618734,
year = {2022},
author = {Scorrano, G and Viva, S and Pinotti, T and Fabbri, PF and Rickards, O and Macciardi, F},
title = {Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {6468},
pmid = {35618734},
issn = {2045-2322},
mesh = {Archaeology ; Body Remains ; *DNA, Ancient ; *Exanthema ; Humans ; Italy ; },
abstract = {The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius' eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian' genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.},
}
@article {pmid35617951,
year = {2022},
author = {Maróti, Z and Neparáczki, E and Schütz, O and Maár, K and Varga, GIB and Kovács, B and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Horváth, C and Varga, S and Költő, L and Raskó, I and Nagy, PL and Balogh, C and Zink, A and Maixner, F and Götherström, A and George, R and Szalontai, C and Szenthe, G and Gáll, E and Kiss, AP and Gulyás, B and Kovacsóczy, BN and Gál, SS and Tomka, P and Török, T},
title = {The genetic origin of Huns, Avars, and conquering Hungarians.},
journal = {Current biology : CB},
volume = {32},
number = {13},
pages = {2858-2870.e7},
doi = {10.1016/j.cub.2022.04.093},
pmid = {35617951},
issn = {1879-0445},
mesh = {Asians ; *Gene Pool ; *Genetics, Population ; Haplotypes ; Humans ; Hungary ; },
abstract = {Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5[th] and 9[th] centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this "immigrant core" of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the "immigrant core" of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common "proto-Ugric" gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring "native European" ancestry.},
}
@article {pmid35609205,
year = {2022},
author = {Demarchi, B and Stiller, J and Grealy, A and Mackie, M and Deng, Y and Gilbert, T and Clarke, J and Legendre, LJ and Boano, R and Sicheritz-Pontén, T and Magee, J and Zhang, G and Bunce, M and Collins, MJ and Miller, G},
title = {Ancient proteins resolve controversy over the identity of Genyornis eggshell.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {e2109326119},
doi = {10.1073/pnas.2109326119},
pmid = {35609205},
issn = {1091-6490},
abstract = {SignificanceThe controversy over the taxonomic identity of the eggs exploited by Australia's first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless "mihirung" Genyornis and a large megapode Progura, had proven impossible using morphological and geochemical methods. Ancient DNA sequencing remains inconclusive because of the age and burial temperature of the eggshell. In contrast, ancient protein sequences recovered from the eggshell enabled estimation of the evolutionary affinity between the egg and a range of extant taxa. The eggs are those of a Galloanseres (a group that includes extinct Dromornithidae, as well as extant landfowl and waterfowl), Genyornis, and not of the megapode (Megapodiidae, crown Galliformes).},
}
@article {pmid35588742,
year = {2022},
author = {Ariano, B and Mattiangeli, V and Breslin, EM and Parkinson, EW and McLaughlin, TR and Thompson, JE and Power, RK and Stock, JT and Mercieca-Spiteri, B and Stoddart, S and Malone, C and Gopalakrishnan, S and Cassidy, LM and Bradley, DG},
title = {Ancient Maltese genomes and the genetic geography of Neolithic Europe.},
journal = {Current biology : CB},
volume = {32},
number = {12},
pages = {2668-2680.e6},
pmid = {35588742},
issn = {1879-0445},
support = {/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Agriculture ; *Archaeology ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; *Genome, Human ; Geography ; History, Ancient ; Human Migration ; Humans ; },
abstract = {Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.},
}
@article {pmid35580179,
year = {2022},
author = {Slavin, P and Sebbane, F},
title = {Emergence and spread of ancestral Yersinia pestis in Late-Neolithic and Bronze-Age Eurasia, ca. 5,000 to 1,500 y B.P.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {21},
pages = {e2204044119},
pmid = {35580179},
issn = {1091-6490},
mesh = {Asia ; DNA, Ancient ; Europe ; Humans ; *Plague/epidemiology ; *Yersinia pestis/genetics ; *Yersinia pseudotuberculosis/genetics ; },
}
@article {pmid35578825,
year = {2022},
author = {Childebayeva, A and Rohrlach, AB and Barquera, R and Rivollat, M and Aron, F and Szolek, A and Kohlbacher, O and Nicklisch, N and Alt, KW and Gronenborn, D and Meller, H and Friederich, S and Prüfer, K and Deguilloux, MF and Krause, J and Haak, W},
title = {Population Genetics and Signatures of Selection in Early Neolithic European Farmers.},
journal = {Molecular biology and evolution},
volume = {39},
number = {6},
pages = {},
pmid = {35578825},
issn = {1537-1719},
mesh = {Agriculture ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; *Farmers ; Genetics, Population ; History, Ancient ; *Human Migration ; Humans ; },
abstract = {Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.},
}
@article {pmid35573598,
year = {2022},
author = {Zhang, X and Yang, L and Zhao, X and Xiang, H},
title = {The complete mitochondrial genome of an ancient cattle (Bos taurus) from Taosi site, China, and its phylogenetic assessment.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {5},
pages = {804-806},
pmid = {35573598},
issn = {2380-2359},
abstract = {The complete mitochondrial genome (mitogenome) of one 4000-years-old cattle from Taosi site was determined by high throughput sequencing. The mitogenome was 16,336 bp in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The protein-coding genes had two types of start codons (ATG and ATA) and three types of stop codons (TAA, TAG, and AGA). The overall base composition of the genome was 33%-A, 27%-T, 26%-C, 14%-G. The matrilineal genealogical analysis based on mitogenome revealed that the 4000-years-old cattle from Taosi site was domestic taurine cattle. In this study, we not only reported a complete mitogenome for a 4000-years-old bovine remain from the middle Yellow River region but also provided the mitogenomic evidence for the close phylogenetic relationship between the early taurine cattle in Northern China and modern domestic cattle.},
}
@article {pmid35571044,
year = {2022},
author = {Sehrawat, JS and Agrawal, S and Sankhyan, D and Singh, M and Kumar, S and Prakash, S and Rajpal, R and Chaubey, G and Thangaraj, K and Rai, N},
title = {Pinpointing the Geographic Origin of 165-Year-Old Human Skeletal Remains Found in Punjab, India: Evidence From Mitochondrial DNA and Stable Isotope Analysis.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {813934},
pmid = {35571044},
issn = {1664-8021},
abstract = {In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ[18]O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ[18]O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers.},
}
@article {pmid35563041,
year = {2022},
author = {Heraclides, A and Fernández-Domínguez, E},
title = {Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods.},
journal = {International journal of molecular sciences},
volume = {23},
number = {9},
pages = {},
pmid = {35563041},
issn = {1422-0067},
mesh = {DNA, Ancient ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.},
}
@article {pmid35559028,
year = {2022},
author = {Ávila-Arcos, MC and de la Fuente Castro, C and Nieves-Colón, MA and Raghavan, M},
title = {Recommendations for Sustainable Ancient DNA Research in the Global South: Voices From a New Generation of Paleogenomicists.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {880170},
pmid = {35559028},
issn = {1664-8021},
support = {R35 GM143094/GM/NIGMS NIH HHS/United States ; },
abstract = {Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in "high impact" journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against 'helicopter science', such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos.},
}
@article {pmid35557944,
year = {2022},
author = {Buisan, R and Moriano, J and Andirkó, A and Boeckx, C},
title = {A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {824740},
pmid = {35557944},
issn = {2296-634X},
abstract = {Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of "archaic" haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.},
}
@article {pmid35552521,
year = {2022},
author = {Callaway, E},
title = {Ancient DNA maps 'dawn of farming'.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35552521},
issn = {1476-4687},
}
@article {pmid35550934,
year = {2022},
author = {Rath, K and Käßner, A and Melisch, C and Powers, N and Tichomirowa, M and Nagy, M and Friedrich, R and Riege, J and Rothe, J},
title = {Genetic and isotope analysis of a triple burial from medieval St. Peter's cemetery in Cölln/Berlin.},
journal = {Forensic science international. Genetics},
volume = {59},
number = {},
pages = {102718},
doi = {10.1016/j.fsigen.2022.102718},
pmid = {35550934},
issn = {1878-0326},
mesh = {Berlin ; *Burial/history ; *Cemeteries/history ; History, Medieval ; Humans ; Isotopes ; Male ; Whites ; },
abstract = {The German capital Berlin originates from the two medieval settlements Berlin and Cölln on either side of the river Spree. Whereas Berlin is world famous, there is very little awareness of former Cölln. From 2007-2009, during excavations of the earliest cemetery of this forgotten medieval town; 3,126 graves were discovered containing the remains of 3,717 individuals. Amongst those graves was an unusual triple burial. This grave was exceptional due to the relative postures of the skeletons and their extensive facial injuries. Here we present genetic and isotope data for this grave. Genetic results confirmed all of them as biological male individuals and ruled out their biological kinship. Combining genetic ancestry information with strontium isotope data we furthermore determined that two of the men most likely originated from the Berlin-Brandenburg region, whereas a more distant origin of the third individual can be debated.},
}
@article {pmid35543411,
year = {2022},
author = {Cai, D and Zhu, S and Gong, M and Zhang, N and Wen, J and Liang, Q and Sun, W and Shao, X and Guo, Y and Cai, Y and Zheng, Z and Zhang, W and Hu, S and Wang, X and Tian, H and Li, Y and Liu, W and Yang, M and Yang, J and Wu, D and Orlando, L and Jiang, Y},
title = {Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35543411},
issn = {2050-084X},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Equidae/genetics ; *Fossils ; Genome ; Genomics ; Horses/genetics ; Phylogeny ; },
abstract = {The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.},
}
@article {pmid35538842,
year = {2022},
author = {Verry, AJF and Mitchell, KJ and Rawlence, NJ},
title = {Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus).},
journal = {Biology letters},
volume = {18},
number = {5},
pages = {20220013},
pmid = {35538842},
issn = {1744-957X},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; *Genetic Variation ; Haplotypes ; Phylogeny ; Phylogeography ; *Refugium ; },
abstract = {Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.},
}
@article {pmid35537469,
year = {2022},
author = {Fleskes, RE and Bader, AC and Tsosie, KS and Wagner, JK and Claw, KG and Garrison, NA},
title = {Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives.},
journal = {Annual review of genomics and human genetics},
volume = {23},
number = {},
pages = {627-652},
doi = {10.1146/annurev-genom-120621-090239},
pmid = {35537469},
issn = {1545-293X},
support = {R35 HG011319/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA, Ancient ; *Genomics ; Humans ; Informed Consent ; *Paleontology ; Research Personnel ; },
abstract = {Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities,such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process.},
}
@article {pmid35537455,
year = {2022},
author = {Segawa, T and Yonezawa, T and Mori, H and Kohno, A and Kudo, Y and Akiyoshi, A and Wu, J and Tokanai, F and Sakamoto, M and Kohno, N and Nishihara, H},
title = {Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.},
journal = {Current biology : CB},
volume = {32},
number = {11},
pages = {2494-2504.e5},
doi = {10.1016/j.cub.2022.04.034},
pmid = {35537455},
issn = {1879-0445},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genomics ; Japan ; Paleontology ; Phylogeny ; *Wolves/anatomy &amp; histology/genetics ; },
abstract = {Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.},
}
@article {pmid35526849,
year = {2022},
author = {Malyarchuk, AB and Andreeva, TV and Kuznetsova, IL and Kunizheva, SS and Protasova, MS and Uralsky, LI and Tyazhelova, TV and Gusev, FE and Manakhov, AD and Rogaev, EI},
title = {Genomics of Ancient Pathogens: First Advances and Prospects.},
journal = {Biochemistry. Biokhimiia},
volume = {87},
number = {3},
pages = {242-258},
pmid = {35526849},
issn = {1608-3040},
mesh = {DNA, Ancient ; *Genomics/methods ; History, Ancient ; Humans ; Mycobacterium leprae/genetics ; Paleontology ; *Yersinia pestis/genetics ; },
abstract = {Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.},
}
@article {pmid35508651,
year = {2022},
author = {Gelabert, P and Schmidt, RW and Fernandes, DM and Karsten, JK and Harper, TK and Madden, GD and Ledogar, SH and Sokhatsky, M and Oota, H and Kennett, DJ and Pinhasi, R},
title = {Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7242},
pmid = {35508651},
issn = {2045-2322},
support = {PACE #70245/MCCC_/Marie Curie/United Kingdom ; },
mesh = {Agriculture ; *DNA, Ancient ; Europe ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Ukraine ; },
abstract = {The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000-3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935-825 cal BCE). Results reveal that the CTCC individuals' ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980-825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.},
}
@article {pmid35506242,
year = {2022},
author = {Martínez-García, L and Ferrari, G and Hufthammer, AK and Jakobsen, KS and Jentoft, S and Barrett, JH and Star, B},
title = {Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene.},
journal = {Biology letters},
volume = {18},
number = {5},
pages = {20220021},
pmid = {35506242},
issn = {1744-957X},
mesh = {Animals ; Climate Change ; *DNA, Ancient ; Fishes ; *Gadus morhua/genetics ; Temperature ; },
abstract = {Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, [14]C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.},
}
@article {pmid35506233,
year = {2022},
author = {Yarlagadda, K and Zachwieja, AJ and de Flamingh, A and Phungviwatnikul, T and Rivera-Colón, AG and Roseman, C and Shackelford, L and Swanson, KS and Malhi, RS},
title = {Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1974},
pages = {20220052},
pmid = {35506233},
issn = {1471-2954},
mesh = {Animals ; Diet ; Dogs ; Feces ; India ; *Microbiota ; South Africa ; },
abstract = {Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.},
}
@article {pmid35494246,
year = {2022},
author = {Yu, H and van de Loosdrecht, MS and Mannino, MA and Talamo, S and Rohrlach, AB and Childebayeva, A and Villalba-Mouco, V and Aron, F and Brandt, G and Burri, M and Freund, C and Radzeviciute, R and Stahl, R and Wissgott, A and Fewlass, H and Tagliacozzo, A and Piperno, M and Tusa, S and Collina, C and Schimmenti, V and Di Salvo, R and Prüfer, K and Posth, C and Hublin, JJ and Gronenborn, D and Binder, D and Jeong, C and Haak, W and Krause, J},
title = {Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily.},
journal = {iScience},
volume = {25},
number = {5},
pages = {104244},
pmid = {35494246},
issn = {2589-0042},
abstract = {Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell'Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.},
}
@article {pmid35482488,
year = {2022},
author = {Ausmees, K and Sanchez-Quinto, F and Jakobsson, M and Nettelblad, C},
title = {An empirical evaluation of genotype imputation of ancient DNA.},
journal = {G3 (Bethesda, Md.)},
volume = {12},
number = {6},
pages = {},
pmid = {35482488},
issn = {2160-1836},
mesh = {Alleles ; *DNA, Ancient ; Gene Frequency ; *Genotype ; Humans ; Software ; },
abstract = {With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.},
}
@article {pmid35476992,
year = {2022},
author = {Kędzior, M and Garcia, AK and Li, M and Taton, A and Adam, ZR and Young, JN and Kaçar, B},
title = {Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time.},
journal = {Cell reports},
volume = {39},
number = {4},
pages = {110726},
doi = {10.1016/j.celrep.2022.110726},
pmid = {35476992},
issn = {2211-1247},
support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteria/genetics ; Carbon Isotopes ; *Ribulose-Bisphosphate Carboxylase/chemistry/genetics ; },
abstract = {The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.},
}
@article {pmid35456493,
year = {2022},
author = {Dehasque, M and Pečnerová, P and Kempe Lagerholm, V and Ersmark, E and Danilov, GK and Mortensen, P and Vartanyan, S and Dalén, L},
title = {Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.},
journal = {Genes},
volume = {13},
number = {4},
pages = {},
pmid = {35456493},
issn = {2073-4425},
mesh = {Bone and Bones ; DNA/genetics ; *DNA, Ancient ; *Silicon Dioxide ; Uracil ; },
abstract = {Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.},
}
@article {pmid35456371,
year = {2022},
author = {Gînguță, A and Kovács, B and Tihanyi, B and Maár, K and Schütz, O and Maróti, Z and Varga, GIB and Kiss, AP and Stanciu, I and Török, T and Neparáczki, E},
title = {Maternal Lineages of Gepids from Transylvania.},
journal = {Genes},
volume = {13},
number = {4},
pages = {},
pmid = {35456371},
issn = {2073-4425},
mesh = {Archaeology ; Cemeteries ; *Gene Pool ; *Genetics, Population ; Humans ; Whites ; },
abstract = {According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is explored for the first time, providing new insights into the genetic makeup of this archaic group. The retrieved genetic data showed mainly the presence of Northwestern European mitochondrial ancient lineages in the Gepid group and all population genetic analyses reiterated the same genetic structure, showing that early ancient mitogenomes from Europe were the major contributors to the Gepid maternal genetic pool.},
}
@article {pmid35446704,
year = {2022},
author = {Lopez-Valdivia, I and Perkins, AC and Schneider, HM and Vallebueno-Estrada, M and Burridge, JD and González-Orozco, E and Montufar, A and Montiel, R and Lynch, JP and Vielle-Calzada, JP},
title = {Gradual domestication of root traits in the earliest maize from Tehuacán.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {17},
pages = {e2110245119},
pmid = {35446704},
issn = {1091-6490},
mesh = {*Domestication ; Mexico ; Phenotype ; *Zea mays/genetics ; },
abstract = {Efforts to understand the phenotypic transition that gave rise to maize from teosinte have mainly focused on the analysis of aerial organs, with little insights into possible domestication traits affecting the root system. Archeological excavations in San Marcos cave (Tehuacán, Mexico) yielded two well-preserved 5,300 to 4,970 calibrated y B.P. specimens (SM3 and SM11) corresponding to root stalks composed of at least five nodes with multiple nodal roots and, in case, a complete embryonic root system. To characterize in detail their architecture and anatomy, we used laser ablation tomography to reconstruct a three-dimensional segment of their nodal roots and a scutellar node, revealing exquisite preservation of the inner tissue and cell organization and providing reliable morphometric parameters for cellular characteristics of the stele and cortex. Whereas SM3 showed multiple cortical sclerenchyma typical of extant maize, the scutellar node of the SM11 embryonic root system completely lacked seminal roots, an attribute found in extant teosinte and in two specific maize mutants: root with undetectable meristem1 (rum1) and rootless concerning crown and seminal roots (rtcs). Ancient DNA sequences of SM10—a third San Marcos specimen of equivalent age to SM3 and SM11—revealed the presence of mutations in the transcribed sequence of both genes, offering the possibility for some of these mutations to be involved in the lack of seminal roots of the ancient specimens. Our results indicate that the root system of the earliest maize from Tehuacán resembled teosinte in traits important for maize drought adaptation.},
}
@article {pmid35446690,
year = {2022},
author = {Rivollat, M and Thomas, A and Ghesquière, E and Rohrlach, AB and Späth, E and Pemonge, MH and Haak, W and Chambon, P and Deguilloux, MF},
title = {Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {18},
pages = {e2120786119},
pmid = {35446690},
issn = {1091-6490},
mesh = {Archaeology ; Burial/history ; *Cemeteries ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; Genomics ; History, Ancient ; Humans ; Male ; },
abstract = {The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery.},
}
@article {pmid35445261,
year = {2022},
author = {Vallini, L and Marciani, G and Aneli, S and Bortolini, E and Benazzi, S and Pievani, T and Pagani, L},
title = {Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.},
journal = {Genome biology and evolution},
volume = {14},
number = {4},
pages = {},
pmid = {35445261},
issn = {1759-6653},
mesh = {Africa ; Animals ; Anthropology, Cultural ; Europe ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Siberia ; },
abstract = {The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.},
}
@article {pmid35440148,
year = {2022},
author = {Brand, CM and Colbran, LL and Capra, JA},
title = {Predicting Archaic Hominin Phenotypes from Genomic Data.},
journal = {Annual review of genomics and human genetics},
volume = {23},
number = {},
pages = {591-612},
doi = {10.1146/annurev-genom-111521-121903},
pmid = {35440148},
issn = {1545-293X},
support = {T32 HG009495/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; DNA, Ancient ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Phenotype ; },
abstract = {Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.},
}
@article {pmid35422088,
year = {2022},
author = {Guiry, EJ and James, M and Cheung, C and Royle, TCA},
title = {Four millennia of long-term individual foraging site fidelity in a highly migratory marine predator.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {368},
pmid = {35422088},
issn = {2399-3642},
mesh = {Animals ; *Birds ; Geography ; },
abstract = {Theory and field studies suggest that long-term individual foraging site fidelity (IFSF) may be an important adaptation to competition from increasing population. However, the driving mechanisms and extent of long-term IFSF in wild populations of long-lived, migratory animals has been logistically difficult to study, with only a few confirmed instances. Temporal isotopic datasets can reveal long-term patterns in geographical foraging behaviour. We investigate the isotopic compositions of endangered short-tailed albatross (Phoebastria albatrus) over four millennia leading up to their near-extinction. Although not exhibited by short-tailed albatross today, we show past sub-populations displayed a high-degree of long-term IFSF, focusing on the same locations for hundreds of generations. This is the first large-scale evidence for the deep antiquity of long-term IFSF and suggests that it's density-driven. Globally, as populations of species like short-tailed albatross continue to recover from overexploitation, potential for resurgence of geographic specialization may increase exposure to localized hazards, requiring closer conservation monitoring.},
}
@article {pmid35421701,
year = {2022},
author = {Bonsu, DOM and Afoakwah, CB and Abedi, M and Higgins, D and Austin, JJ},
title = {Ethics reporting in forensic science research publications - A review.},
journal = {Forensic science international},
volume = {335},
number = {},
pages = {111290},
doi = {10.1016/j.forsciint.2022.111290},
pmid = {35421701},
issn = {1872-6283},
mesh = {*Forensic Sciences ; Humans ; *Informed Consent ; },
abstract = {An essential element of compliance with ethical standards in scientific research is the reporting of a verifiable declaration of ethical approval and, when human subjects are involved - informed consent, in published works. The level of reporting of ethical permission for research published in forensic and investigative sciences journals has not been explored to date. Hence, we examined the reporting of ethical approval and informed consent in original research utilising human or animal subjects published in six forensic science journals from 2010 to 2019. We identified 10,192 articles and retained 3010 that satisfied the inclusion criteria of utilising human (91.2%), or animal (7.0%) or both (1.8%) subjects or tissues in experiments. Just over a third (1079/3010) of all studies declared obtaining ethical approval, with 927 (85.9%) of those indicating the name of the ethical committee, but only 392 (36%) provided an approval code. Furthermore, while consent was said to have been sought in 527 (17.5%) of studies, only 155 of those reported that written informed consent was obtained, eleven stated oral (verbal) consent, while the remaining 357 studies (67.7%) did not report the process used to gain consent. Ethical approval reporting rates differed between different research types, availability of financial support and whether authors were affiliated to academia or industry. The results demonstrate a low level of declaration of ethical approval and informed consent in forensic science research and publication, requiring urgent rectification. We support the adoption of the model proposed by Forensic Science International: Genetics as baseline recommendations to facilitate consistent nomenclature, transparency, and standard of ethical reporting in forensic science.},
}
@article {pmid35413261,
year = {2022},
author = {Schlebusch, CM},
title = {Genomics: Testing the limits of de-extinction.},
journal = {Current biology : CB},
volume = {32},
number = {7},
pages = {R324-R327},
doi = {10.1016/j.cub.2022.03.023},
pmid = {35413261},
issn = {1879-0445},
mesh = {DNA, Ancient ; *Extinction, Biological ; Genome ; *Genomics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Resurrecting extinct species through de-extinction by genome editing requires full and unbiased information from the extinct species' genome. A new study establishes a framework to assess how much of an extinct species genome can be recovered by ancient DNA sequencing and which factors influence recovery.},
}
@article {pmid35412864,
year = {2022},
author = {Andrades Valtueña, A and Neumann, GU and Spyrou, MA and Musralina, L and Aron, F and Beisenov, A and Belinskiy, AB and Bos, KI and Buzhilova, A and Conrad, M and Djansugurova, LB and Dobeš, M and Ernée, M and Fernández-Eraso, J and Frohlich, B and Furmanek, M and Hałuszko, A and Hansen, S and Harney, &#xc9; and Hiss, AN and Hübner, A and Key, FM and Khussainova, E and Kitov, E and Kitova, AO and Knipper, C and Kühnert, D and Lalueza-Fox, C and Littleton, J and Massy, K and Mittnik, A and Mujika-Alustiza, JA and Olalde, I and Papac, L and Penske, S and Peška, J and Pinhasi, R and Reich, D and Reinhold, S and Stahl, R and Stäuble, H and Tukhbatova, RI and Vasilyev, S and Veselovskaya, E and Warinner, C and Stockhammer, PW and Haak, W and Krause, J and Herbig, A},
title = {Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {17},
pages = {e2116722119},
pmid = {35412864},
issn = {1091-6490},
mesh = {Animal Husbandry/history ; Animals ; DNA, Ancient ; Genetic Variation ; *Genome, Bacterial ; History, Ancient ; Human Migration/history ; Humans ; Phylogeny ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/classification/genetics/isolation &amp; purification ; },
abstract = {The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.},
}
@article {pmid35402880,
year = {2022},
author = {Fischer, CE and Pemonge, MH and Ducoussau, I and Arzelier, A and Rivollat, M and Santos, F and Barrand Emam, H and Bertaud, A and Beylier, A and Ciesielski, E and Dedet, B and Desenne, S and Duday, H and Chenal, F and Gailledrat, E and Goepfert, S and Gorgé, O and Gorgues, A and Kuhnle, G and Lambach, F and Lefort, A and Mauduit, A and Maziere, F and Oudry, S and Paresys, C and Pinard, E and Plouin, S and Richard, I and Roth-Zehner, M and Roure, R and Thevenet, C and Thomas, Y and Rottier, S and Deguilloux, MF and Pruvost, M},
title = {Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics.},
journal = {iScience},
volume = {25},
number = {4},
pages = {104094},
pmid = {35402880},
issn = {2589-0042},
abstract = {The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.},
}
@article {pmid35398984,
year = {2022},
author = {Suchan, T and Chauvey, L and Poullet, M and Tonasso-Calvière, L and Schiavinato, S and Clavel, P and Clavel, B and Lepetz, S and Seguin-Orlando, A and Orlando, L},
title = {Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.},
journal = {Molecular ecology resources},
volume = {22},
number = {6},
pages = {2262-2274},
doi = {10.1111/1755-0998.13619},
pmid = {35398984},
issn = {1755-0998},
mesh = {Animals ; *Cytosine ; DNA Damage ; DNA Methylation ; *DNA, Ancient ; Equidae/genetics ; Horses/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.},
}
@article {pmid35389750,
year = {2022},
author = {Marciniak, S and Bergey, CM and Silva, AM and Hałuszko, A and Furmanek, M and Veselka, B and Velemínský, P and Vercellotti, G and Wahl, J and Zariņa, G and Longhi, C and Kolář, J and Garrido-Pena, R and Flores-Fernández, R and Herrero-Corral, AM and Simalcsik, A and Müller, W and Sheridan, A and Miliauskienė, &#x17d; and Jankauskas, R and Moiseyev, V and Köhler, K and Király, &#xc1; and Gamarra, B and Cheronet, O and Szeverényi, V and Kiss, V and Szeniczey, T and Kiss, K and Zoffmann, ZK and Koós, J and Hellebrandt, M and Maier, RM and Domboróczki, L and Virag, C and Novak, M and Reich, D and Hajdu, T and von Cramon-Taubadel, N and Pinhasi, R and Perry, GH},
title = {An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {15},
pages = {e2106743119},
pmid = {35389750},
issn = {1091-6490},
mesh = {Adult ; *Agriculture/history ; *Body Height/genetics ; Child ; DNA, Ancient ; Europe ; *Farmers/history ; Genetic Variation ; Genomics ; *Health/history ; History, Ancient ; Humans ; Paleopathology ; *Skeleton/anatomy &amp; histology ; },
abstract = {Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.},
}
@article {pmid35383854,
year = {2022},
author = {Di, D and Simon Thomas, J and Currat, M and Nunes, JM and Sanchez-Mazas, A},
title = {Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35383854},
issn = {1537-1719},
mesh = {DNA ; DNA, Ancient ; Europe ; *Genetic Predisposition to Disease ; *HLA Antigens/genetics ; Histocompatibility Antigens Class II ; Humans ; *Plague/genetics ; Yersinia pestis ; },
abstract = {In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059-4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.},
}
@article {pmid35382600,
year = {2022},
author = {Barrett, JH and Khamaiko, N and Ferrari, G and Cuevas, A and Kneale, C and Hufthammer, AK and Pálsdóttir, AH and Star, B},
title = {Walruses on the Dnieper: new evidence for the intercontinental trade of Greenlandic ivory in the Middle Ages.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1972},
pages = {20212773},
pmid = {35382600},
issn = {1471-2954},
mesh = {Animals ; Archaeology ; *DNA, Ancient ; Geography ; Russia ; *Walruses/genetics ; },
abstract = {Mediaeval walrus hunting in Iceland and Greenland-driven by Western European demand for ivory and walrus hide ropes-has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine-combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.},
}
@article {pmid35366416,
year = {2022},
author = {Gnecchi-Ruscone, GA and Szécsényi-Nagy, A and Koncz, I and Csiky, G and Rácz, Z and Rohrlach, AB and Brandt, G and Rohland, N and Csáky, V and Cheronet, O and Szeifert, B and Rácz, T&#xc1; and Benedek, A and Bernert, Z and Berta, N and Czifra, S and Dani, J and Farkas, Z and Hága, T and Hajdu, T and Jászberényi, M and Kisjuhász, V and Kolozsi, B and Major, P and Marcsik, A and Kovacsóczy, BN and Balogh, C and Lezsák, GM and Ódor, JG and Szelekovszky, M and Szeniczey, T and Tárnoki, J and Tóth, Z and Tutkovics, EK and Mende, BG and Geary, P and Pohl, W and Vida, T and Pinhasi, R and Reich, D and Hofmanová, Z and Jeong, C and Krause, J},
title = {Ancient genomes reveal origin and rapid trans-Eurasian migration of 7[th] century Avar elites.},
journal = {Cell},
volume = {185},
number = {8},
pages = {1402-1413.e21},
pmid = {35366416},
issn = {1097-4172},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Asians/genetics ; *DNA, Ancient ; *Genetics, Population ; Genome ; History, Ancient ; Human Migration/history ; Humans ; Sulfur ; },
abstract = {The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.},
}
@article {pmid35359699,
year = {2022},
author = {Molodtseva, AS and Makunin, AI and Salomashkina, VV and Kichigin, IG and Vorobieva, NV and Vasiliev, SK and Shunkov, MV and Tishkin, AA and Grushin, SP and Anijalg, P and Tammeleht, E and Keis, M and Boeskorov, GG and Mamaev, N and Okhlopkov, IM and Kryukov, AP and Lyapunova, EA and Kholodova, MV and Seryodkin, IV and Saarma, U and Trifonov, VA and Graphodatsky, AS},
title = {Phylogeography of ancient and modern brown bears from eastern Eurasia.},
journal = {Biological journal of the Linnean Society. Linnean Society of London},
volume = {135},
number = {4},
pages = {722-733},
pmid = {35359699},
issn = {0024-4066},
support = {206194/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.},
}
@article {pmid35356467,
year = {2022},
author = {Arizmendi Cárdenas, YO and Neuenschwander, S and Malaspinas, AS},
title = {Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12784},
pmid = {35356467},
issn = {2167-8359},
abstract = {Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.},
}
@article {pmid35356424,
year = {2022},
author = {Xiong, J and Du, P and Chen, G and Tao, Y and Zhou, B and Yang, Y and Wang, H and Yu, Y and Chang, X and Allen, E and Sun, C and Zhou, J and Zou, Y and Xu, Y and Meng, H and Tan, J and Li, H and Wen, S},
title = {Sex-Biased Population Admixture Mediated Subsistence Strategy Transition of Heishuiguo People in Han Dynasty Hexi Corridor.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {827277},
pmid = {35356424},
issn = {1664-8021},
abstract = {The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE-220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oβ-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.},
}
@article {pmid35342764,
year = {2022},
author = {Kim, K and Kim, DH and Kim, KY},
title = {Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {5344418},
pmid = {35342764},
issn = {2314-6141},
mesh = {*DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; },
abstract = {Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.},
}
@article {pmid35336803,
year = {2022},
author = {Horsburgh, KA and Beckett, DB and Gosling, AL},
title = {Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups.},
journal = {Biology},
volume = {11},
number = {3},
pages = {},
pmid = {35336803},
issn = {2079-7737},
abstract = {We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.},
}
@article {pmid35324275,
year = {2022},
author = {Gibbons, A},
title = {Southern roots for the Maya-and the maize that fed them.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6587},
pages = {1325},
doi = {10.1126/science.abq1704},
pmid = {35324275},
issn = {1095-9203},
abstract = {Migrants from the south may have helped spread early farming in Central America, ancient DNA suggests.},
}
@article {pmid35318319,
year = {2022},
author = {Kennett, DJ and Lipson, M and Prufer, KM and Mora-Marín, D and George, RJ and Rohland, N and Robinson, M and Trask, WR and Edgar, HHJ and Hill, EC and Ray, EE and Lynch, P and Moes, E and O'Donnell, L and Harper, TK and Kate, EJ and Ramos, J and Morris, J and Gutierrez, SM and Ryan, TM and Culleton, BJ and Awe, JJ and Reich, D},
title = {South-to-north migration preceded the advent of intensive farming in the Maya region.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1530},
pmid = {35318319},
issn = {2041-1723},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Agriculture ; Central America ; Colombia ; *DNA, Ancient ; Forests ; Humans ; },
abstract = {The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.},
}
@article {pmid35312358,
year = {2022},
author = {Severson, AL and Byrd, BF and Mallott, EK and Owings, AC and DeGiorgio, M and de Flamingh, A and Nijmeh, C and Arellano, MV and Leventhal, A and Rosenberg, NA and Malhi, RS},
title = {Ancient and modern genomics of the Ohlone Indigenous population of California.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {13},
pages = {e2111533119},
pmid = {35312358},
issn = {1091-6490},
support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeology ; DNA, Ancient ; Genetics, Population ; *Genomics ; History, Ancient ; Humans ; *Indigenous Peoples ; Linguistics ; San Francisco ; },
abstract = {SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.},
}
@article {pmid35307645,
year = {2022},
author = {Fu, M and Li, Y},
title = {The origin and domestication history of domestic horses and the domestication characteristics of breeds.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {3},
pages = {216-229},
doi = {10.16288/j.yczz.21-260},
pmid = {35307645},
issn = {0253-9772},
mesh = {Animals ; Animals, Domestic/genetics ; *Breeding ; DNA, Mitochondrial/genetics ; *Domestication ; *Horses/genetics ; Phylogeny ; },
abstract = {The horse (Equus caballus) was domesticated thousands of years after dog, cattle, pig, sheep, and goat. Importantly, it represents the domestic animal that mostly impacted the development of human civilization. Its excellent loading and moving ability prompted the changes from fixed farming mode into mobile sharing mode. Accordingly, its domestication history deserves considerable attention. So far, many issues have long been controversial, due to the extinction of the closest wild relatives and the dramatic reduction of genetic diversity. With the continuous development of sequencing technology and the utilization of ancient samples, we got more clues to the origin and domestication process. In this review, we summarize 1) current progresses on the domestication history revealed by nuclear genes, mtDNA, Y chromosome, and ancient DNA, 2) the characteristics of population structure and diversification among modern breeds, 3) the genetic basis of important phenotypes, such as coat color, speed, and body size. The overall aim of the review is to provide in-depth insights into the studies of horse domestication, the preservation and utilization of genetic resources, the direction of breeding improvement, and the development of modern horse industry in future.},
}
@article {pmid35306727,
year = {2022},
author = {Scarsbrook, L and Verry, AJF and Walton, K and Hitchmough, RA and Rawlence, NJ},
title = {Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16434},
pmid = {35306727},
issn = {1365-294X},
abstract = {Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898-2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-computed tomography reconstructions. All "large gecko" specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue-derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.},
}
@article {pmid35306671,
year = {2022},
author = {Schwörer, C and Leunda, M and Alvarez, N and Gugerli, F and Sperisen, C},
title = {The untapped potential of macrofossils in ancient plant DNA research.},
journal = {The New phytologist},
volume = {235},
number = {2},
pages = {391-401},
pmid = {35306671},
issn = {1469-8137},
mesh = {Animals ; *DNA, Ancient ; DNA, Plant/genetics ; Lakes ; *Permafrost ; Plants/genetics ; },
abstract = {The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.},
}
@article {pmid35294015,
year = {2022},
author = {Biddanda, A and Steinrücken, M and Novembre, J},
title = {Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.},
journal = {Genetics},
volume = {221},
number = {1},
pages = {},
pmid = {35294015},
issn = {1943-2631},
support = {R01 HG007089/HG/NHGRI NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; T32 GM07197/GF/NIH HHS/United States ; },
mesh = {Archaeology/*methods ; Genetics, Population/*methods ; Genotype ; Haplotypes ; Humans ; Linkage Disequilibrium ; Population Density ; },
abstract = {Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.},
}
@article {pmid35288946,
year = {2022},
author = {Her, C and Rezaei, HR and Hughes, S and Naderi, S and Duffraisse, M and Mashkour, M and Naghash, HR and Bălășescu, A and Luikart, G and Jordan, S and Özüt, D and Kence, A and Bruford, MW and Tresset, A and Vigne, JD and Taberlet, P and Hänni, C and Pompanon, F},
title = {Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros.},
journal = {Animal genetics},
volume = {53},
number = {3},
pages = {452-459},
doi = {10.1111/age.13191},
pmid = {35288946},
issn = {1365-2052},
mesh = {Animals ; Cytochromes b/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Phylogeny ; Sheep/genetics ; *Sheep, Domestic/genetics ; Turkey ; },
abstract = {We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).},
}
@article {pmid35288565,
year = {2022},
author = {Zhou, BF and Yuan, S and Crowl, AA and Liang, YY and Shi, Y and Chen, XY and An, QQ and Kang, M and Manos, PS and Wang, B},
title = {Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1320},
pmid = {35288565},
issn = {2041-1723},
mesh = {Ecosystem ; Forests ; *Genome, Plastid/genetics ; Phylogeny ; *Quercus ; },
abstract = {Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia.},
}
@article {pmid35279516,
year = {2022},
author = {Lorentz, KO and Kamel, G and Lemmers, SAM and Miyauchi, Y and Çubukçu, E and Alpagut, A and Büyükkarakaya, AM},
title = {Synchrotron Radiation Fourier Transform Infrared (SR-FTIR) spectroscopy in exploring ancient human hair from Roman period Juliopolis: Preservation status and alterations of organic compounds.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {274},
number = {},
pages = {121026},
doi = {10.1016/j.saa.2022.121026},
pmid = {35279516},
issn = {1873-3557},
mesh = {Archaeology/methods ; *Body Remains ; Fourier Analysis ; Hair/chemistry ; Humans ; Organic Chemicals ; Spectroscopy, Fourier Transform Infrared/methods ; *Synchrotrons ; },
abstract = {We explore the preservation status and alterations of organic compounds in Roman period human hairstrandsfrom a specific individual (M196) excavated at Juliopolis (JP). How do these organic compounds present in this c. 2000-year-old human hair compare to those present in modern hair? Alterations to organic compounds in archaeological human hair are caused by biological degradative processes dependent on multifactorial processes acting on the hair since the deposition of a body in a mortuary context. We investigate the type of organic compounds present using Synchrotron Radiation Fourier Transform Infrared (SR-FTIR). Juliopolis (Iuliopolis) is an ancient multiperiod city, located in the Çayırhan district of Nallıhan, northwest of Ankara. The Juliopolis necropolis from which M196 was recovered was in use throughout the Hellenistic, Roman, and Byzantine periods, and yielded over 700 tombs with numerous human remains. One tomb (M196) contained human remains of exceptional preservation status, including substantial amounts of hair. Human hair from archaeological contexts is not only extremely rare, but importantly, has high analytical value, with potential for analysis of diet, geographical origins, ancient DNA, metal exposure, and other aspects of life in a time-resolved manner. These data make significant contributions to the life history of the individual (osteobiography), as well as contribute towards key archaeological questions. As these analyses are in their majority destructive, prior evaluation of the preservation of sufficient amounts of the organic compounds on which many such analyses rely upon is crucial, to avoid unnecessary loss of precious ancient samples. The results of our SR-FTIR analyses at SESAME synchrotron show that keratin in the JP M196 is more degraded in comparison to the modern reference sample. However, the results also point to clear potential for further analyses with techniques relying on organic compound preservation, such as C and N isotopic analyses for diet, and aDNA.},
}
@article {pmid35273713,
year = {2022},
author = {Singh, H and Shipra, and Sharma, V and Sharma, I and Sharma, A and Modeel, S and Gupta, N and Gupta, G and Pandita, AK and Butt, MF and Sharma, R and Pandita, S and Singh, V and Rai, E and Ikegawa, S and Sharma, S},
title = {The first study of epidemiology of adolescent idiopathic scoliosis shows lower prevalence in females of Jammu and Kashmir, India.},
journal = {American journal of translational research},
volume = {14},
number = {2},
pages = {1100-1106},
pmid = {35273713},
issn = {1943-8141},
abstract = {UNLABELLED: AIS is a heterogeneous 3D spinal deformity with Cobb angle ≥10°. It affects children in the age group of 10-16 years globally with 2-3% prevalence and significant female predominance. The exact etiology of AIS is not known however, it is supposed to be associated with factors such as anthropometric, metabolic, neuromuscular abnormalities and genetics.<br><br>OBJECTIVES: To determine the prevalence of AIS and association of anthropometric factors with AIS in the studied population group.<br><br>METHODOLOGY: Scoliosis screening of 9,500 individuals was carried out at different educational institutions of Jammu region in Jammu and Kashmir, India using a scoliosis-meter. The subjects were later examined radiologically.<br><br>RESULTS: In population of the region, AIS was most prevalent among all types of scoliosis with overall prevalence of 0.61%. The prevalence was observed to be lower in females (0.31%) than males (0.88%). Based on angle of trunk rotation (ATR), lumbar curves were more prevalent than thoracic curves. Average Cobb angle in males and females were 24.9&#xb0; and 22.6&#xb0;, respectively. BMI showed significant association with AIS in the age group of 12-16 years (P value =0.028). Furthermore, height was significantly associated with AIS in the overall screened population (P-value =0.029).<br><br>CONCLUSIONS: The AIS patients in the Jammu region of India have unique clinical features. In contrast to the global prevalence data, the prevalence of AIS in females in the region was less in comparison to males. Based on epidemiological literature and our findings, we hypothesized that genetic factors might be a major contributor in the AIS pathogenesis along with other confounding factors such as height, BMI, ethnicity, etc.},
}
@article {pmid35271794,
year = {2022},
author = {Lin, J and Duchêne, D and Carøe, C and Smith, O and Ciucani, MM and Niemann, J and Richmond, D and Greenwood, AD and MacPhee, R and Zhang, G and Gopalakrishnan, S and Gilbert, MTP},
title = {Probing the genomic limits of de-extinction in the Christmas Island rat.},
journal = {Current biology : CB},
volume = {32},
number = {7},
pages = {1650-1656.e3},
pmid = {35271794},
issn = {1879-0445},
mesh = {Animals ; Australia ; Biological Evolution ; Extinction, Biological ; *Genome ; *Genomics ; Norway ; Phylogeny ; Rats ; },
abstract = {Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.[1,2] Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.[3-5] We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.},
}
@article {pmid35263821,
year = {2022},
author = {Zavala, EI and Aximu-Petri, A and Richter, J and Nickel, B and Vernot, B and Meyer, M},
title = {Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA.},
journal = {Molecular ecology resources},
volume = {22},
number = {6},
pages = {2196-2207},
doi = {10.1111/1755-0998.13607},
pmid = {35263821},
issn = {1755-0998},
mesh = {*DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; *Genomics ; Nucleic Acid Hybridization/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains or sediments in single studies. Nevertheless, demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here, we explored the possibility of improving the economics of sample preparation via multiplex capture, that is, the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the reamplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination.},
}
@article {pmid35256608,
year = {2022},
author = {Vågene, &#xc5;J and Honap, TP and Harkins, KM and Rosenberg, MS and Giffin, K and Cárdenas-Arroyo, F and Leguizamón, LP and Arnett, J and Buikstra, JE and Herbig, A and Krause, J and Stone, AC and Bos, KI},
title = {Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1195},
pmid = {35256608},
issn = {2041-1723},
mesh = {Animals ; *Caniformia/genetics ; DNA, Ancient ; Humans ; *Mycobacterium/genetics ; *Mycobacterium tuberculosis/genetics ; Racial Groups ; South America/epidemiology ; *Tuberculosis/epidemiology/microbiology ; },
abstract = {Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.},
}
@article {pmid35240033,
year = {2022},
author = {Hong, JH and Oh, CS and Kim, S and Kang, IU and Shin, DH},
title = {Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area.},
journal = {Animal bioscience},
volume = {35},
number = {8},
pages = {1141-1150},
pmid = {35240033},
issn = {2765-0189},
abstract = {OBJECTIVE: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea.<br><br>METHODS: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software.<br><br>RESULTS: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia.<br><br>CONCLUSION: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseonperiod horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.},
}
@article {pmid35238427,
year = {2022},
author = {Nores, R and Tavella, MP and Fabra, M and Demarchi, DA},
title = {Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {34},
number = {7},
pages = {e23733},
doi = {10.1002/ajhb.23733},
pmid = {35238427},
issn = {1520-6300},
mesh = {Argentina ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; *Indians, South American/genetics ; },
abstract = {OBJECTIVES: The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene.<br><br>METHODS: We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of C&#xf3;rdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes.<br><br>RESULTS: Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly.<br><br>CONCLUSIONS: The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of C&#xf3;rdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.},
}
@article {pmid35210171,
year = {2022},
author = {Jäger, HY and Maixner, F and Pap, I and Szikossy, I and Pálfi, G and Zink, AR},
title = {Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {137},
number = {},
pages = {102181},
doi = {10.1016/j.tube.2022.102181},
pmid = {35210171},
issn = {1873-281X},
mesh = {Female ; Humans ; *Coinfection/microbiology ; DNA, Bacterial/genetics/analysis ; Hungary ; *Midwifery ; *Mycobacterium tuberculosis/genetics ; Phylogeny ; *Tuberculosis/diagnosis/history ; History, 18th Century ; Metagenome ; },
abstract = {The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors.},
}
@article {pmid35208912,
year = {2022},
author = {Reynoso-García, J and Narganes-Storde, Y and Santiago-Rodriguez, TM and Toranzos, GA},
title = {Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations.},
journal = {Microorganisms},
volume = {10},
number = {2},
pages = {},
pmid = {35208912},
issn = {2076-2607},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; 5R25GM061151-20/NH/NIH HHS/United States ; },
abstract = {Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman's large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.},
}
@article {pmid35205259,
year = {2022},
author = {Messelodi, D and Giuliani, C and Cipriani, F and Armuzzi, S and di Palmo, E and Garagnani, P and Bertelli, L and Astolfi, A and Luiselli, D and Ricci, G and Pession, A},
title = {C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205259},
issn = {2073-4425},
mesh = {*Asthma/epidemiology/genetics ; Child ; *Complement C5/genetics ; *GTPase-Activating Proteins/genetics ; Gene Frequency ; *Genetic Predisposition to Disease ; Genotype ; Humans ; Italy ; Polymorphism, Single Nucleotide ; },
abstract = {Asthma is a complex and heterogeneous disease, caused by the interaction between genetic and environmental factors with a predominant allergic background in children. The role of specific genes in asthmatic bronchial reactivity is still not clear, probably because of the many common pathways shared with other allergic disorders. This study is focused on 11 SNPs possibly related to asthma that were previously identified in a GWAS study. The genetic variability of these SNPs has been analysed in a population of 773 Italian healthy controls, and the presence of an association between the polymorphisms and the asthma onset was evaluated performing genotyping analysis on 108 children affected with asthma compared with the controls. Moreover, a pool of 171 patients with only allergic rhinoconjunctivitis has been included in the case-control analysis. The comparison of allele frequencies in asthmatic patients versus healthy controls identified two SNPs-rs1162394 (p = 0.019) and rs25681 (p = 0.044)-associated with the asthmatic condition, which were not differentially distributed in the rhinoconjunctivitis group. The rs25681 SNP, together with three other SNPs, also resulted in not being homogenously distributed in the Italian population. The significantly higher frequency of the rs25681 and rs1162394 SNPs (located, respectively, in the C5 and SRGAP3 genes) in the asthmatic population suggests an involvement of these genes in the asthmatic context, playing a role in increasing the inflammatory condition that may influence asthma onset and clinical course.},
}
@article {pmid35205247,
year = {2022},
author = {Loreille, O and Tillmar, A and Brandhagen, MD and Otterstatter, L and Irwin, JA},
title = {Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205247},
issn = {2073-4425},
mesh = {DNA, Mitochondrial/analysis/genetics ; Famous Persons ; Female ; *Genome, Mitochondrial ; Hair/chemistry ; Heteroplasmy ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide ; Russia ; },
abstract = {This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina's lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas' maternal lineage, including the well-known point heteroplasmy at position 16169.},
}
@article {pmid35205223,
year = {2022},
author = {Niiranen, L and Leciej, D and Edlund, H and Bernhardsson, C and Fraser, M and Quinto, FS and Herzig, KH and Jakobsson, M and Walkowiak, J and Thalmann, O},
title = {Epigenomic Modifications in Modern and Ancient Genomes.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205223},
issn = {2073-4425},
mesh = {Animals ; DNA Methylation/genetics ; *DNA, Ancient ; Epigenesis, Genetic/genetics ; *Epigenomics ; Genome/genetics ; },
abstract = {Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.},
}
@article {pmid35201891,
year = {2022},
author = {Wohns, AW and Wong, Y and Jeffery, B and Akbari, A and Mallick, S and Pinhasi, R and Patterson, N and Reich, D and Kelleher, J and McVean, G},
title = {A unified genealogy of modern and ancient genomes.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6583},
pages = {eabi8264},
doi = {10.1126/science.abi8264},
pmid = {35201891},
issn = {1095-9203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Africa ; Chromosomes, Human, Pair 20/genetics ; Computer Simulation ; *DNA, Ancient ; Databases, Nucleic Acid ; Datasets as Topic ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; *Genome, Human ; *Genomics ; Geography ; Haplotypes ; Human Migration ; Humans ; Mutation ; *Pedigree ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Statistics, Nonparametric ; },
abstract = {The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.},
}
@article {pmid35197631,
year = {2022},
author = {Lipson, M and Sawchuk, EA and Thompson, JC and Oppenheimer, J and Tryon, CA and Ranhorn, KL and de Luna, KM and Sirak, KA and Olalde, I and Ambrose, SH and Arthur, JW and Arthur, KJW and Ayodo, G and Bertacchi, A and Cerezo-Román, JI and Culleton, BJ and Curtis, MC and Davis, J and Gidna, AO and Hanson, A and Kaliba, P and Katongo, M and Kwekason, A and Laird, MF and Lewis, J and Mabulla, AZP and Mapemba, F and Morris, A and Mudenda, G and Mwafulirwa, R and Mwangomba, D and Ndiema, E and Ogola, C and Schilt, F and Willoughby, PR and Wright, DK and Zipkin, A and Pinhasi, R and Kennett, DJ and Manthi, FK and Rohland, N and Patterson, N and Reich, D and Prendergast, ME},
title = {Ancient DNA and deep population structure in sub-Saharan African foragers.},
journal = {Nature},
volume = {603},
number = {7900},
pages = {290-296},
pmid = {35197631},
issn = {1476-4687},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Africa South of the Sahara ; Archaeology ; *Blacks/genetics/history ; *DNA, Ancient/analysis ; Gene Flow/genetics ; *Genetics, Population ; Genome, Human/genetics ; History, Ancient ; Humans ; },
abstract = {Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa[1-4]. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations[3,5]. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.},
}
@article {pmid35197586,
year = {2022},
author = {},
title = {Ancient DNA illuminates how humans travelled and interacted in Stone Age Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35197586},
issn = {1476-4687},
}
@article {pmid35183376,
year = {2022},
author = {Cuenca-Cambronero, M and Courtney-Mustaphi, CJ and Greenway, R and Heiri, O and Hudson, CM and King, L and Lemmen, KD and Moosmann, M and Muschick, M and Ngoepe, N and Seehausen, O and Matthews, B},
title = {An integrative paleolimnological approach for studying evolutionary processes.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {6},
pages = {488-496},
doi = {10.1016/j.tree.2022.01.007},
pmid = {35183376},
issn = {1872-8383},
mesh = {*Biological Evolution ; *Ecosystem ; },
abstract = {The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evolutionary perspective, such analyses provide important insights into the chronology of past environmental conditions, the dynamics of phenotypic evolution, and species diversification. Here, we review recent advances in paleolimnological, paleogenetic, and molecular approaches and highlight how their integrative use can help us better understand the ecological and evolutionary responses of species and communities to environmental change.},
}
@article {pmid35178874,
year = {2022},
author = {Jiménez-Mena, B and Flávio, H and Henriques, R and Manuzzi, A and Ramos, M and Meldrup, D and Edson, J and Pálsson, S and Ásta Ólafsdóttir, G and Ovenden, JR and Nielsen, EE},
title = {Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {2105-2119},
pmid = {35178874},
issn = {1755-0998},
mesh = {Animals ; DNA/genetics ; Genetics, Population ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Hunting ; Sequence Analysis, DNA/methods ; },
abstract = {Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.},
}
@article {pmid35176104,
year = {2022},
author = {Rauf, S and Austin, JJ and Higgins, D and Khan, MR},
title = {Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel.},
journal = {PloS one},
volume = {17},
number = {2},
pages = {e0264125},
pmid = {35176104},
issn = {1932-6203},
mesh = {Chromosomes, Human, Y/*genetics ; DNA Fingerprinting/*methods ; Ethnicity/*genetics ; Female ; *Forensic Genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Pakistan ; *Phenotype ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Sex Determination Processes ; },
abstract = {Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.},
}
@article {pmid35175801,
year = {2022},
author = {Stone, AC},
title = {Genomes in motionOrigin: A Genetic History of the Americas Jennifer Raff Twelve, 2022. 368 pp.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6582},
pages = {727},
doi = {10.1126/science.abn7262},
pmid = {35175801},
issn = {1095-9203},
abstract = {Ancient DNA sheds light on the peopling of the Americas.},
}
@article {pmid35171192,
year = {2022},
author = {Antkowiak, PL and Koch, J and Rzepka, P and Nguyen, BH and Strauss, K and Stark, WJ and Grass, RN},
title = {Anhydrous calcium phosphate crystals stabilize DNA for dry storage.},
journal = {Chemical communications (Cambridge, England)},
volume = {58},
number = {19},
pages = {3174-3177},
doi = {10.1039/d2cc00414c},
pmid = {35171192},
issn = {1364-548X},
mesh = {Biocompatible Materials/*chemistry ; Calcium Phosphates/*chemistry ; DNA/*chemistry ; Materials Testing ; },
abstract = {The resilience of ancient DNA (aDNA) in bone gives rise to the preservation of synthetic DNA with bioinorganic materials such as calcium phosphate (CaP). Accelerated aging experiments at elevated temperature and humidity displayed a positive effect of co-precipitated, crystalline dicalcium phosphate on the stability of synthetic DNA in contrast to amorphous CaP. Quantitative PXRD in combination with SEM and EDX measurements revealed distinct CaP phase transformations of calcium phosphate dihydrate (brushite) to anhydrous dicalcium phosphate (monetite) influencing DNA stability.},
}
@article {pmid35167699,
year = {2022},
author = {Oh, CS and Seo, M and Lee, HJ and Kim, MJ and Lim, DS and Shin, DH},
title = {GENETIC ANALYSIS OF ANCIENT CLONORCHIS SINENSIS EGGS ATTAINED FROM GORYEONG MUMMY OF JOSEON DYNASTY PERIOD.},
journal = {The Journal of parasitology},
volume = {108},
number = {1},
pages = {70-78},
doi = {10.1645/21-49},
pmid = {35167699},
issn = {1937-2345},
mesh = {Animals ; Clonorchiasis/*history/parasitology ; Clonorchis sinensis/classification/*genetics ; DNA, Helminth/chemistry/genetics ; History, Ancient ; Mummies/*parasitology ; Ovum ; Phylogeny ; Republic of Korea ; },
abstract = {Although Clonorchis sinensis is a parasite that still infects many people in East Asia, its genetics remain largely unknown. We conducted ancient DNA analysis of C. sinensis eggs obtained from a Joseon period mummy newly discovered in South Korea. Clonorchis sinensis DNA was amplified for internal transcribed spacer 1, cytochrome c oxidase subunit 1, and NADH dehydrogenase subunit 2 and 5 genes. The results of BLAST/NCBI showed that the consensus sequences were 98.24 to 100% identical to the modern and ancient C. sinensis sequences reported from Korea, China, Japan, and other Asian countries. Our report helps to fill in the genetic profile of ancient C. sinensis strains that infected East Asian people hundreds of years ago.},
}
@article {pmid35165121,
year = {2022},
author = {Li, J and Zhao, B and Huang, T and Qin, Z and Wang, SM},
title = {Human BRCA pathogenic variants were originated during recent human history.},
journal = {Life science alliance},
volume = {5},
number = {5},
pages = {},
pmid = {35165121},
issn = {2575-1077},
mesh = {Animals ; BRCA1 Protein/*genetics ; BRCA2 Protein/*genetics ; Biological Evolution ; DNA, Ancient/analysis ; Databases, Genetic ; Evolution, Molecular ; Female ; Genetic Predisposition to Disease/genetics ; Germ-Line Mutation/genetics ; Haplotypes/genetics ; Humans ; Mutation ; },
abstract = {BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.},
}
@article {pmid35145268,
year = {2022},
author = {Izdebski, A and Guzowski, P and Poniat, R and Masci, L and Palli, J and Vignola, C and Bauch, M and Cocozza, C and Fernandes, R and Ljungqvist, FC and Newfield, T and Seim, A and Abel-Schaad, D and Alba-Sánchez, F and Björkman, L and Brauer, A and Brown, A and Czerwiński, S and Ejarque, A and Fiłoc, M and Florenzano, A and Fredh, ED and Fyfe, R and Jasiunas, N and Kołaczek, P and Kouli, K and Kozáková, R and Kupryjanowicz, M and Lagerås, P and Lamentowicz, M and Lindbladh, M and López-Sáez, JA and Luelmo-Lautenschlaeger, R and Marcisz, K and Mazier, F and Mensing, S and Mercuri, AM and Milecka, K and Miras, Y and Noryśkiewicz, AM and Novenko, E and Obremska, M and Panajiotidis, S and Papadopoulou, ML and Pędziszewska, A and Pérez-Díaz, S and Piovesan, G and Pluskowski, A and Pokorny, P and Poska, A and Reitalu, T and Rösch, M and Sadori, L and Sá Ferreira, C and Sebag, D and Słowiński, M and Stančikaitė, M and Stivrins, N and Tunno, I and Veski, S and Wacnik, A and Masi, A},
title = {Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {3},
pages = {297-306},
pmid = {35145268},
issn = {2397-334X},
mesh = {Animals ; DNA, Ancient ; Europe/epidemiology ; Humans ; Pandemics/history ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/genetics ; },
abstract = {The Black Death (1347-1352 CE) is the most renowned pandemic in human history, believed by many to have killed half of Europe's population. However, despite advances in ancient DNA research that conclusively identified the pandemic's causative agent (bacterium Yersinia pestis), our knowledge of the Black Death remains limited, based primarily on qualitative remarks in medieval written sources available for some areas of Western Europe. Here, we remedy this situation by applying a pioneering new approach, 'big data palaeoecology', which, starting from palynological data, evaluates the scale of the Black Death's mortality on a regional scale across Europe. We collected pollen data on landscape change from 261 radiocarbon-dated coring sites (lakes and wetlands) located across 19 modern-day European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that a large portion of the population, upwards of half, died within a few years in the 21 historical regions we studied. While we can confirm that the Black Death had a devastating impact in some regions, we found that it had negligible or no impact in others. These inter-regional differences in the Black Death's mortality across Europe demonstrate the significance of cultural, ecological, economic, societal and climatic factors that mediated the dissemination and impact of the disease. The complex interplay of these factors, along with the historical ecology of plague, should be a focus of future research on historical pandemics.},
}
@article {pmid35131896,
year = {2022},
author = {Dulias, K and Foody, MGB and Justeau, P and Silva, M and Martiniano, R and Oteo-García, G and Fichera, A and Rodrigues, S and Gandini, F and Meynert, A and Donnelly, K and Aitman, TJ and , and Chamberlain, A and Lelong, O and Kozikowski, G and Powlesland, D and Waddington, C and Mattiangeli, V and Bradley, DG and Bryk, J and Soares, P and Wilson, JF and Wilson, G and Moore, H and Pala, M and Edwards, CJ and Richards, MB},
title = {Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {8},
pages = {},
pmid = {35131896},
issn = {1091-6490},
support = {MC_PC_15080/MRC_/Medical Research Council/United Kingdom ; G0901467/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G0802729/MRC_/Medical Research Council/United Kingdom ; G0400116/MRC_/Medical Research Council/United Kingdom ; 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeology ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; England ; Europe ; Female ; Fossils ; Gene Pool ; Genome, Human/genetics ; Genomics ; Haplotypes ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Ireland ; Male ; Paternal Inheritance/*genetics ; Scotland ; },
abstract = {Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.},
}
@article {pmid35119154,
year = {2022},
author = {Kearns, AM and Campana, MG and Slikas, B and Berry, L and Saitoh, T and Cibois, A and Fleischer, RC},
title = {Conservation genomics and systematics of a near-extinct island radiation.},
journal = {Molecular ecology},
volume = {31},
number = {7},
pages = {1995-2012},
doi = {10.1111/mec.16382},
pmid = {35119154},
issn = {1365-294X},
mesh = {Animals ; Conservation of Natural Resources ; *DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; *Genomics ; Geography ; Inbreeding ; Phylogeny ; },
abstract = {Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mitochondrial DNA (mtDNA), nuclear single nucleotide polymorphisms (SNPs) support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographical structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that pre-date modern anthropogenic threats require further study with denser population sampling. Our study highlights the value that conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragment their ranges and contribute to rapid declines in population abundances.},
}
@article {pmid35109894,
year = {2022},
author = {Guellil, M and Keller, M and Dittmar, JM and Inskip, SA and Cessford, C and Solnik, A and Kivisild, T and Metspalu, M and Robb, JE and Scheib, CL},
title = {An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {22},
pmid = {35109894},
issn = {1474-760X},
support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; *Haemophilus Vaccines ; Haemophilus influenzae/genetics ; Humans ; Infant ; Phylogeny ; *Plague ; Serogroup ; },
abstract = {BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available.<br><br>RESULTS: We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550&#x2009;CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill.<br><br>CONCLUSIONS: Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.},
}
@article {pmid35098251,
year = {2021},
author = {Westbury, MV and Barnett, R and Sandoval-Velasco, M and Gowe, G and Vieira, FG and de Manuel, M and Hansen, AJ and Yamaguch, N and Werdelin, L and Marques-Bonet, T and Gilbert, MTP and Lorenzen, ED},
title = {A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives [version 2; peer review: 2 approved].},
journal = {Open research Europe},
volume = {1},
number = {},
pages = {25},
pmid = {35098251},
issn = {2732-5121},
support = {681396/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths.<br><br>METHODS: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 &#xb1; 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships.<br><br>RESULTS: We confirm a deep divergence (~20.65 Ma) within sabretoothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae.<br><br>CONCLUSIONS: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.},
}
@article {pmid35090588,
year = {2022},
author = {Plassais, J and vonHoldt, BM and Parker, HG and Carmagnini, A and Dubos, N and Papa, I and Bevant, K and Derrien, T and Hennelly, LM and Whitaker, DT and Harris, AC and Hogan, AN and Huson, HJ and Zaibert, VF and Linderholm, A and Haile, J and Fest, T and Habib, B and Sacks, BN and Benecke, N and Outram, AK and Sablin, MV and Germonpré, M and Larson, G and Frantz, L and Ostrander, EA},
title = {Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.},
journal = {Current biology : CB},
volume = {32},
number = {4},
pages = {889-897.e9},
pmid = {35090588},
issn = {1879-0445},
support = {/WT_/Wellcome Trust/United Kingdom ; Z99 HG999999/ImNIH/Intramural NIH HHS/United States ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Alleles ; Animals ; Body Size/genetics ; Breeding ; *Canidae/genetics ; Humans ; *Wolves/genetics ; },
abstract = {Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.[1] Although dogs of variable size are found in the archeological record,[2-4] the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.[5] Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.[6-10] Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.[8] The identification of a functional mutation associated with IGF1 has thus far proven elusive.[6][,][10][,][11] Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.},
}
@article {pmid35084493,
year = {2022},
author = {Martiniano, R and De Sanctis, B and Hallast, P and Durbin, R},
title = {Placing Ancient DNA Sequences into Reference Phylogenies.},
journal = {Molecular biology and evolution},
volume = {39},
number = {2},
pages = {},
pmid = {35084493},
issn = {1537-1719},
support = {/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Base Sequence ; *Chromosomes, Human, Y ; *DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Haplotypes ; Humans ; Likelihood Functions ; Male ; *Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.},
}
@article {pmid35060661,
year = {2022},
author = {Nieves-Colón, MA},
title = {Anthropological genetic insights on Caribbean population history.},
journal = {Evolutionary anthropology},
volume = {31},
number = {3},
pages = {118-137},
doi = {10.1002/evan.21935},
pmid = {35060661},
issn = {1520-6505},
mesh = {Anthropology ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Genetic Variation ; *Genetics, Population ; Humans ; West Indies ; },
abstract = {As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present-day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post-contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present-day Caribbean peoples.},
}
@article {pmid35058955,
year = {2021},
author = {Yu, N and Sun, H and Yang, J and Li, R},
title = {The Diesel Tree Sindora glabra Genome Provides Insights Into the Evolution of Oleoresin Biosynthesis.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {794830},
pmid = {35058955},
issn = {1664-462X},
abstract = {Sindora glabra is an economically important tree that produces abundant oleoresin in the trunk. Here, we present a high-quality chromosome-scale assembly of S. glabra genome by combining Illumina HiSeq, Pacific Biosciences sequencing, and Hi-C technologies. The size of S. glabra genome was 1.11 Gb, with a contig N50 of 1.27 Mb and 31,944 predicted genes. This is the first sequenced genome of the subfamily Caesalpinioideae. As a sister taxon to Papilionoideae, S. glabra underwent an ancient genome triplication shared by core eudicots and further whole-genome duplication shared by early-legume in the last 73.3 million years. S. glabra harbors specific genes and expanded genes largely involved in stress responses and biosynthesis of secondary metabolites. Moreover, 59 terpene backbone biosynthesis genes and 64 terpene synthase genes were identified, which together with co-expressed transcription factors could contribute to the diversity and specificity of terpene compounds and high terpene content in S. glabra stem. In addition, 63 disease resistance NBS-LRR genes were found to be unique in S. glabra genome and their expression levels were correlated with the accumulation of terpene profiles, suggesting potential defense function of terpenes in S. glabra. These together provide new resources for understanding genome evolution and oleoresin production.},
}
@article {pmid35052700,
year = {2021},
author = {Abondio, P and Sarno, S and Giuliani, C and Laganà, V and Maletta, R and Bernardi, L and Bruno, F and Colao, R and Puccio, G and Frangipane, F and Borroni, B and Van Broeckhoven, C and Luiselli, D and Bruni, A},
title = {Amyloid Precursor Protein A713T Mutation in Calabrian Patients with Alzheimer's Disease: A Population Genomics Approach to Estimate Inheritance from a Common Ancestor.},
journal = {Biomedicines},
volume = {10},
number = {1},
pages = {},
pmid = {35052700},
issn = {2227-9059},
abstract = {Mutation A713T in the amyloid precursor protein (APP) has been linked to cases of Alzheimer's disease (AD), cerebral amyloid angiopathy (CAA) and cerebrovascular disease. Despite its rarity, it has been observed in several families from the same geographical area, in the Calabria region in Southern Italy. Genotyping of 720,000 genome-wide SNPs with the HumanOmniExpress BeadChip was performed for six patients that were representative of apparently unrelated Calabrian families, as well as a Belgian subject of Italian descent (all with the same A713T mutation and disease). Their genomic structure and genetic relationships were analyzed. Demographic reconstruction and coalescent theory were applied to estimate the time of the most recent common ancestor (tMRCA) among patients. Results show that all A713T carriers fell into the genetic variability of Southern Italy and were not more closely related to each other than to any other healthy Calabrian individual. However, five out of seven patients shared a 1.7 Mbp-long DNA segment centered on the A713T mutation, making it possible to estimate a tMRCA for its common origin in the Calabrian region dating back over 1000 years. The analysis of affected individuals with methodologies based on human population genomics thus provides informative insights in support of clinical observations and biomedical research.},
}
@article {pmid35052476,
year = {2022},
author = {De Angelis, F and Romboni, M and Veltre, V and Catalano, P and Martínez-Labarga, C and Gazzaniga, V and Rickards, O},
title = {First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First-Third Centuries AD).},
journal = {Genes},
volume = {13},
number = {1},
pages = {},
pmid = {35052476},
issn = {2073-4425},
mesh = {Adolescent ; Bacteria/*classification/genetics/isolation &amp; purification ; Bone and Bones/*metabolism/*microbiology ; Child ; Child, Preschool ; DNA, Ancient/*analysis/isolation &amp; purification ; Female ; Genome, Human ; Genomics/*methods ; Humans ; Infant ; Male ; Paleopathology ; Rome ; Whole Genome Sequencing ; },
abstract = {This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first-third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.},
}
@article {pmid35052469,
year = {2022},
author = {Zavala, EI and Thomas, JT and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Meyers, KK and Barrit-Ross, S and Aximu-Petri, A and Richter, J and Nickel, B and Berg, GE and McMahon, TP and Meyer, M and Marshall, C},
title = {Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns.},
journal = {Genes},
volume = {13},
number = {1},
pages = {},
pmid = {35052469},
issn = {2073-4425},
mesh = {Body Remains/*metabolism ; DNA Fingerprinting/*methods ; DNA, Ancient/*analysis/isolation &amp; purification ; *Forensic Genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Korean War ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; World War II ; },
abstract = {The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.},
}
@article {pmid35052455,
year = {2022},
author = {Deng, MX and Xiao, B and Yuan, JX and Hu, JM and Kim, KS and Westbury, MV and Lai, XL and Sheng, GL},
title = {Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer.},
journal = {Genes},
volume = {13},
number = {1},
pages = {},
pmid = {35052455},
issn = {2073-4425},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/analysis/*genetics ; Deer/*genetics ; *Evolution, Molecular ; Fossils ; *Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; *Phylogeny ; },
abstract = {The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.},
}
@article {pmid35049133,
year = {2022},
author = {Capo, E and Monchamp, ME and Coolen, MJL and Domaizon, I and Armbrecht, L and Bertilsson, S},
title = {Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.},
journal = {Environmental microbiology},
volume = {24},
number = {5},
pages = {2201-2209},
pmid = {35049133},
issn = {1462-2920},
mesh = {Biodiversity ; DNA ; *Ecosystem ; Geologic Sediments/microbiology ; Humans ; Lakes/microbiology ; *Microbiota/genetics ; },
abstract = {In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.},
}
@article {pmid35047996,
year = {2021},
author = {Handsley-Davis, M and Skelly, E and Johnson, NW and Kapellas, K and Lalloo, R and Kroon, J and Weyrich, LS},
title = {Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {641328},
pmid = {35047996},
issn = {2673-4842},
abstract = {Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4-17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences in microbial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management options for Australian Aboriginal and Torres Strait Islander children and communities.},
}
@article {pmid35038768,
year = {2022},
author = {Stuart, KC and Sherwin, WB and Austin, JJ and Bateson, M and Eens, M and Brandley, MC and Rollins, LA},
title = {Historical museum samples enable the examination of divergent and parallel evolution during invasion.},
journal = {Molecular ecology},
volume = {31},
number = {6},
pages = {1836-1852},
pmid = {35038768},
issn = {1365-294X},
mesh = {Australia ; Climate Change ; Ecosystem ; *Introduced Species ; *Museums ; },
abstract = {During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.},
}
@article {pmid35038748,
year = {2022},
author = {Aneli, S and Saupe, T and Montinaro, F and Solnik, A and Molinaro, L and Scaggion, C and Carrara, N and Raveane, A and Kivisild, T and Metspalu, M and Scheib, CL and Pagani, L},
title = {The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.},
journal = {Molecular biology and evolution},
volume = {39},
number = {2},
pages = {},
pmid = {35038748},
issn = {1537-1719},
mesh = {*DNA, Mitochondrial/genetics ; Europe ; Italy ; },
abstract = {The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula.},
}
@article {pmid35037474,
year = {2022},
author = {Rayo, E and Ferrari, G and Neukamm, J and Akgül, G and Breidenstein, AM and Cooke, M and Phillips, C and Bouwman, AS and Rühli, FJ and Schuenemann, VJ},
title = {Non-destructive extraction of DNA from preserved tissues in medical collections.},
journal = {BioTechniques},
volume = {72},
number = {2},
pages = {60-64},
doi = {10.2144/btn-2021-0014},
pmid = {35037474},
issn = {1940-9818},
mesh = {*DNA/genetics ; Fixatives ; Humans ; *Preservation, Biological/methods ; Retrospective Studies ; Sequence Analysis, DNA/methods ; },
abstract = {Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.},
}
@article {pmid35016010,
year = {2022},
author = {Murchie, TJ and Karpinski, E and Eaton, K and Duggan, AT and Baleka, S and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN},
title = {Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments.},
journal = {Current biology : CB},
volume = {32},
number = {4},
pages = {851-860.e7},
doi = {10.1016/j.cub.2021.12.023},
pmid = {35016010},
issn = {1879-0445},
mesh = {Animals ; DNA, Ancient ; *DNA, Environmental ; DNA, Mitochondrial/genetics ; Ecosystem ; Fossils ; *Genome, Mitochondrial ; Horses/genetics ; *Mammoths/genetics ; *Permafrost ; Phylogeny ; },
abstract = {Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.[1] In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.[2] Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia[3]-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.[4][,][5] However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,[6-12] in paleodietary reconstructions,[13-19] and facilitated genomic reconstructions from cave contexts.[8][,][20-22] Murchie et al.[6][,][23] used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.[24] Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 40,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.},
}
@article {pmid35003706,
year = {2021},
author = {Oliva, A and Tobler, R and Llamas, B and Souilmi, Y},
title = {Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment.},
journal = {Ecology and evolution},
volume = {11},
number = {24},
pages = {18743-18748},
pmid = {35003706},
issn = {2045-7758},
abstract = {Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA-mem parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA-aln is still the gold-standard for ancient DNA read alignment .},
}
@article {pmid34988402,
year = {2022},
author = {Baleka, S and Varela, L and Tambusso, PS and Paijmans, JLA and Mothé, D and Stafford, TW and Fariña, RA and Hofreiter, M},
title = {Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA.},
journal = {iScience},
volume = {25},
number = {1},
pages = {103559},
pmid = {34988402},
issn = {2589-0042},
abstract = {The extinct Gomphotheriidae is the only proboscidean family that colonized South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, ancient DNA (aDNA) preservation decreases in warmer regions. Despite the poor preservation conditions for aDNA in humid, sub-tropical climates, we recovered ∼3,000 bp of mtDNA of Notiomastodon platensis from the Arroyo del Vizcaíno site, Uruguay. Our calibrated phylogeny places Notiomastodon as a sister taxon to Elephantidae, with a divergence time of ∼13.5 Ma. Additionally, a total evidence analysis combining morphological and paleogenetic data shows that the three most diverse clades within Proboscidea diverged during the early Miocene, coinciding with the formation of a land passage between Africa and Eurasia. Our results are a further step toward aDNA analyses on Pleistocene samples from subtropical regions and provide a framework for proboscidean evolution.},
}
@article {pmid34988387,
year = {2021},
author = {Sarhan, MS and Lehmkuhl, A and Straub, R and Tett, A and Wieland, G and Francken, M and Zink, A and Maixner, F},
title = {Ancient DNA diffuses from human bones to cave stones.},
journal = {iScience},
volume = {24},
number = {12},
pages = {103397},
pmid = {34988387},
issn = {2589-0042},
abstract = {Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.},
}
@article {pmid34969841,
year = {2022},
author = {Massilani, D and Morley, MW and Mentzer, SM and Aldeias, V and Vernot, B and Miller, C and Stahlschmidt, M and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Conard, NJ and Wurz, S and Henshilwood, CS and Vasquez, J and Essel, E and Nagel, S and Richter, J and Nickel, B and Roberts, RG and Pääbo, S and Slon, V and Goldberg, P and Meyer, M},
title = {Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {1},
pages = {},
pmid = {34969841},
issn = {1091-6490},
mesh = {Animals ; *Caves ; *DNA, Ancient ; *Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; },
abstract = {Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.},
}
@article {pmid34963129,
year = {2022},
author = {Pedersen, MW and Antunes, C and De Cahsan, B and Moreno-Mayar, JV and Sikora, M and Vinner, L and Mann, D and Klimov, PB and Black, S and Michieli, CT and Braig, HR and Perotti, MA},
title = {Ancient Human Genomes and Environmental DNA from the Cement Attaching 2,000-Year-Old Head Lice Nits.},
journal = {Molecular biology and evolution},
volume = {39},
number = {2},
pages = {},
pmid = {34963129},
issn = {1537-1719},
support = {BB/N001400/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N001443/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *DNA, Environmental ; Genome, Human ; Genome-Wide Association Study ; Humans ; Infant, Newborn ; *Pediculus/genetics ; Skull ; },
abstract = {Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500-2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.},
}
@article {pmid34953252,
year = {2022},
author = {Thomas, ZA and Mooney, S and Cadd, H and Baker, A and Turney, C and Schneider, L and Hogg, A and Haberle, S and Green, K and Weyrich, LS and Perez, V and Moore, NE and Zawadzki, A and Kelloway, SJ and Khan, SJ},
title = {Corrigendum to "Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands" [Sci. Total Environ. 802 (2021)149542].},
journal = {The Science of the total environment},
volume = {811},
number = {},
pages = {152367},
doi = {10.1016/j.scitotenv.2021.152367},
pmid = {34953252},
issn = {1879-1026},
}
@article {pmid34951605,
year = {2021},
author = {Anagnostou, P and Capocasa, M and Brisighelli, F and Battaggia, C and Destro Bisol, G},
title = {The emerging complexity of Open Science: assessing Intelligent Data Openness in Genomic Anthropology and Human Genomics.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {99},
number = {},
pages = {135-152},
doi = {10.4436/JASS.99016},
pmid = {34951605},
issn = {2037-0644},
abstract = {In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.},
}
@article {pmid34949860,
year = {2022},
author = {Carlin, N},
title = {A grave matter of ancient kinship in Neolithic Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {510-512},
pmid = {34949860},
issn = {1476-4687},
mesh = {*Archaeology ; *DNA, Ancient ; United Kingdom ; },
}
@article {pmid34947853,
year = {2021},
author = {Haarkötter, C and Saiz, M and Gálvez, X and Medina-Lozano, MI and Álvarez, JC and Lorente, JA},
title = {Usefulness of Microbiome for Forensic Geolocation: A Review.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {34947853},
issn = {2075-1729},
abstract = {Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.},
}
@article {pmid34937939,
year = {2022},
author = {Fowler, C and Olalde, I and Cummings, V and Armit, I and Büster, L and Cuthbert, S and Rohland, N and Cheronet, O and Pinhasi, R and Reich, D},
title = {A high-resolution picture of kinship practices in an Early Neolithic tomb.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {584-587},
pmid = {34937939},
issn = {1476-4687},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
mesh = {Adult ; Archaeology ; *Burial ; Child ; *DNA, Ancient ; Female ; Humans ; Male ; Mothers ; Pedigree ; },
abstract = {To explore kinship practices at chambered tombs in Early Neolithic Britain, here we combined archaeological and genetic analyses of 35 individuals who lived about 5,700 years ago and were entombed at Hazleton North long cairn[1]. Twenty-seven individuals are part of the first extended pedigree reconstructed from ancient DNA, a five-generation family whose many interrelationships provide statistical power to document kinship practices that were invisible without direct genetic data. Patrilineal descent was key in determining who was buried in the tomb, as all 15 intergenerational transmissions were through men. The presence of women who had reproduced with lineage men and the absence of adult lineage daughters suggest virilocal burial and female exogamy. We demonstrate that one male progenitor reproduced with four women: the descendants of two of those women were buried in the same half of the tomb over all generations. This suggests that maternal sub-lineages were grouped into branches whose distinctiveness was recognized during the construction of the tomb. Four men descended from non-lineage fathers and mothers who also reproduced with lineage male individuals, suggesting that some men adopted the children of their reproductive partners by other men into their patriline. Eight individuals were not close biological relatives of the main lineage, raising the possibility that kinship also encompassed social bonds independent of biological relatedness.},
}
@article {pmid34937885,
year = {2022},
author = {Bradley, DG},
title = {Bronze Age genomes reveal migration to Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {512-513},
pmid = {34937885},
issn = {1476-4687},
mesh = {*DNA, Ancient ; *Human Migration ; United Kingdom ; },
}
@article {pmid34937536,
year = {2021},
author = {Andreeva, T and Manakhov, A and Kunizheva, S and Rogaev, E},
title = {Genetic Evidence of Authenticity of a Hair Shaft Relic from the Portrait of Tsesarevich Alexei, Son of the Last Russian Emperor.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {12},
pages = {1572-1578},
doi = {10.1134/S0006297921120063},
pmid = {34937536},
issn = {1608-3040},
mesh = {DNA, Mitochondrial/*genetics ; *Forensic Anthropology ; *Forensic Genetics ; *Hair ; *High-Throughput Nucleotide Sequencing ; Humans ; Russia ; },
abstract = {To determine the value of an art piece, authenticity of the artwork must be verified. We demonstrate here a genetic approach to determine origin of a historic relic in the museum piece. We tested two hair shafts of unknown origin framed into a watercolor portrait of Tsesarevich Alexei Romanov, son of the last Russian Tzar Nicholas II, which is a unique item kept in the State Historical Museum. Genetic identification of the hair shafts was performed by analysis of mitochondrial DNA (mtDNA) markers using both massive parallel genomic sequencing and multiplex targeted PCR, followed by Sanger sequencing. In previous works, we reconstructed the complete mtDNA sequence inherited to Alexei Romanov through the Queen Victoria lineage [Rogaev et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 5258-5263]. DNA extracts were obtained from the two thin hair shafts and used for comparative genetic analysis. Despite the very low quantity and quality of the DNA templates retrieved from the historical single hair shaft specimen, informative mtDNA sequences were determined. The mtDNA haplotype in the hair shafts corresponds to the mtDNA haplotype of Tsarevich Alexei, his sisters, and his mother, Empress Alexandra Feodorovna. This haplotype remains unique in the currently available mtDNA databases. Our results reveal that the hair relic from the portrait is associated with the family of the last Russian Emperor Nicholas II. The study is an example of first application of the genetic methodology for verification of the value of museum artwork items.},
}
@article {pmid34937535,
year = {2021},
author = {Zhur, KV and Trifonov, VA and Prokhortchouk, EB},
title = {Progress and Prospects in Epigenetic Studies of Ancient DNA.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {12},
pages = {1563-1571},
doi = {10.1134/S0006297921120051},
pmid = {34937535},
issn = {1608-3040},
mesh = {Animals ; *DNA Methylation ; *DNA, Ancient ; *Epigenesis, Genetic ; Epigenomics/trends ; *Evolution, Molecular ; Human Migration ; Humans ; Neanderthals/*genetics ; },
abstract = {Development of technologies for high-throughput whole-genome sequencing and improvement of sample preparation techniques made it possible to study ancient DNA (aDNA) from archaeological samples over a million year old. The studies of aDNA have shed light on the history of human migration, replacement of populations, interbreeding of Cro-Magnons with Neanderthals and Denisovans, evolution of human pathogens, etc. Equally important is the possibility to investigate epigenetic modifications of ancient genomes, which has allowed to obtain previously inaccessible information on gene expression, nucleosome positioning, and DNA methylation. Analysis of methylation status of certain genomic sites can predict an individual's age at death and reconstruct some phenotypic features, as it was done for the Denisovan genome, and even to elucidate unfavorable environmental factors that had affected this archaic individual. In this review, we discuss current progress in epigenetic studies of aDNA, including methodological approaches and promising research directions in this field.},
}
@article {pmid34933781,
year = {2022},
author = {Bianciotto, V and Selosse, MA and Martos, F and Marmeisse, R},
title = {Herbaria preserve plant microbiota responses to environmental changes.},
journal = {Trends in plant science},
volume = {27},
number = {2},
pages = {120-123},
doi = {10.1016/j.tplants.2021.11.012},
pmid = {34933781},
issn = {1878-4372},
mesh = {*Microbiota ; *Plants ; },
abstract = {Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.},
}
@article {pmid34932923,
year = {2021},
author = {Renom, P and de-Dios, T and Civit, S and Llovera, L and Sánchez-Gracia, A and Lizano, E and Rando, JC and Marquès-Bonet, T and Kergoat, GJ and Casanovas-Vilar, I and Lalueza-Fox, C},
title = {Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives.},
journal = {Biology letters},
volume = {17},
number = {12},
pages = {20210533},
pmid = {34932923},
issn = {1744-957X},
mesh = {Animals ; Islands ; *Phylogeny ; Rats ; Spain ; },
abstract = {Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000-944 000), points toward an island colonization during the Günz-Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.},
}
@article {pmid34931883,
year = {2021},
author = {Der Sarkissian, C and Velsko, IM and Fotakis, AK and Vågene, &#xc5;J and Hübner, A and Fellows Yates, JA},
title = {Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.},
journal = {mSystems},
volume = {6},
number = {6},
pages = {e0131521},
pmid = {34931883},
issn = {2379-5077},
abstract = {Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions &amp; Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.},
}
@article {pmid34927609,
year = {2021},
author = {Parker, CE and Bos, KI and Haak, W and Krause, J},
title = {Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {177},
pages = {},
doi = {10.3791/63250},
pmid = {34927609},
issn = {1940-087X},
mesh = {*Archaeology/methods ; Bone and Bones/chemistry ; DNA/genetics ; *DNA, Ancient/analysis ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {The methods presented here seek to maximize the chances for the recovery of human DNA from ancient archaeological remains while limiting input sample material. This was done by targeting anatomical sampling locations previously determined to yield the highest amounts of ancient DNA (aDNA) in a comparative analysis of DNA recovery across the skeleton. Prior research has suggested that these protocols maximize the chances for the successful recovery of ancient human and pathogen DNA from archaeological remains. DNA yields were previously assessed by Parker et al. 2020 in a broad survey of aDNA preservation across multiple skeletal elements from 11 individuals recovered from the medieval (radiocarbon dated to a period of circa (ca.) 1040-1400 CE, calibrated 2-sigma range) graveyard at Krakauer Berg, an abandoned medieval settlement near Peißen Germany. These eight sampling spots, which span five skeletal elements (pars petrosa, permanent molars, thoracic vertebra, distal phalanx, and talus) successfully yielded high-quality ancient human DNA, where yields were significantly greater than the overall average across all elements and individuals. Yields were adequate for use in most common downstream population genetic analyses. Our results support the preferential use of these anatomical sampling locations for most studies involving the analyses of ancient human DNA from archaeological remains. Implementation of these methods will help to minimize the destruction of precious archaeological specimens.},
}
@article {pmid34906355,
year = {2022},
author = {Liu, X and Zhang, Y and Liu, W and Li, Y and Pan, J and Pu, Y and Han, J and Orlando, L and Ma, Y and Jiang, L},
title = {A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses.},
journal = {Current biology : CB},
volume = {32},
number = {2},
pages = {480-487.e6},
pmid = {34906355},
issn = {1879-0445},
mesh = {Animals ; Body Size/genetics ; Genome ; Horses/genetics ; Mice ; Mutation ; *Nucleotides ; *Polymorphism, Single Nucleotide ; T-Box Domain Proteins/genetics ; Transcription Factors/genetics ; },
abstract = {Chinese ponies are endemic to the mountainous areas of southwestern China and were first reported in the archaeological record at the Royal Tomb of Zhongshan King, Mancheng, dated to approximately ∼2,100 YBP.[1] Previous work has started uncovering the genetic basis of size variation in western ponies and horses, revealing a limited number of loci, including HMGA2,[2]LCORL/NCAPG,[3]ZFAT, and LASP1.[4,5] Whether the same genetic pathways also drive the small body size of Chinese ponies, which show striking anatomical differences to Shetland ponies,[6] remains unclear.[2,7] To test this, we combined whole-genome sequences of 187 horses across China. Statistical analyses revealed top association between genetic variation at the T-box transcription factor 3 (TBX3) and the body size. Fine-scale analysis across an extended population of 189 ponies and 574 horses narrowed down the association to one A/G SNP at an enhancer region upstream of the TBX3 (ECA8:20,644,555, p = 2.34e-39). Luciferase assays confirmed the single-nucleotide G mutation upregulating TBX3 expression, and enhancer-knockout mice exhibited shorter limbs than wild-type littermates (p < 0.01). Re-analysis of ancient DNA data showed that the G allele, which is most frequent in modern horses, first occurred some ∼2,300 years ago and rose in frequency since. This supports selection for larger size in Asia from approximately the beginning of the Chinese Empire. Overall, this study characterized the causal regulatory mutation underlying small body size in Chinese ponies and revealed size as one of the main selection targets of past Chinese breeders.},
}
@article {pmid34902603,
year = {2022},
author = {Zhang, M and Liu, Y and Li, Z and Lü, P and Gardner, JD and Ye, M and Wang, J and Yang, M and Shao, J and Wang, W and Dai, Q and Cao, P and Yang, R and Liu, F and Feng, X and Zhang, L and Li, E and Shi, Y and Chen, Z and Zhu, S and Zhai, W and Deng, T and Duan, Z and Bennett, EA and Hu, S and Fu, Q},
title = {Ancient DNA reveals the maternal genetic history of East Asian domestic pigs.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {49},
number = {6},
pages = {537-546},
doi = {10.1016/j.jgg.2021.11.014},
pmid = {34902603},
issn = {1673-8527},
mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Sus scrofa/genetics ; Swine/genetics ; },
abstract = {Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.},
}
@article {pmid34893875,
year = {2022},
author = {Garg, KM and Chattopadhyay, B and Cros, E and Tomassi, S and Benedick, S and Edwards, DP and Rheindt, FE},
title = {Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland.},
journal = {Molecular biology and evolution},
volume = {39},
number = {1},
pages = {},
pmid = {34893875},
issn = {1537-1719},
mesh = {Animals ; Genome ; Islands ; Phylogeny ; Population Dynamics ; *Rivers ; *Songbirds/genetics ; },
abstract = {Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.},
}
@article {pmid34887902,
year = {2021},
author = {Zhang, X and Yang, L and Hou, L and Li, H and Xiang, H and Zhao, X},
title = {Ancient Mitogenomes Reveal the Domestication and Distribution of Cattle During the Longshan Culture Period in North China.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {759827},
pmid = {34887902},
issn = {1664-8021},
abstract = {Cattle, as an important tool for agricultural production in ancient China, have a complex history of domestication and distribution in China. Although it is generally accepted that ancient Chinese taurine cattle originated from the Near East, the explanation regarding their spread through China and whether or not this spread was associated with native aurochs during ancient times are still unclear. In this study, we obtained three nearly complete mitochondrial genomes (mitogenomes) from bovine remains dating back ca. 4,000 years at the Taosi and Guchengzhai sites in North China. For the first time at the mitogenome level, phylogenetic analyses confirmed the approximately 4,000-year-old bovines from North China as taurine cattle. All ancient cattle from both sites belonged to the T3 haplogroup, suggesting their origin from the Near East. The high affinity between ancient samples and southern Chinese taurine cattle indicated that ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. A rapid decrease in the female effective population size ca. 4.65 thousand years ago (kya) and a steep increase ca. 1.99 kya occurred in Chinese taurine cattle. Overall, these results provide increasing evidence of the origin of cattle in the middle Yellow River region of China.},
}
@article {pmid34883299,
year = {2022},
author = {Haas, C and Körner, C and Sulzer, A and Kratzer, A},
title = {19th century family saga re-told by DNA recovered from postcard stamps.},
journal = {Forensic science international},
volume = {330},
number = {},
pages = {111129},
doi = {10.1016/j.forsciint.2021.111129},
pmid = {34883299},
issn = {1872-6283},
mesh = {Child ; Chromosomes, Human, Y ; DNA ; *DNA Fingerprinting ; DNA, Ancient ; Family ; Humans ; Male ; *Microsatellite Repeats ; },
abstract = {Old postcards with stamps might help unravelling historical family stories and relationships. By employing ancient DNA recovered from world war I postage stamps, we disprove a family saga of an illegitimate child born in 1887. We developed a protocol to collect DNA from saliva, trapped and protected on the backside of postage stamps glued on postcards. With replicate STR analyses we were able to assemble almost full autosomal and Y-STR profiles of three male, deceased family members. The illegitimate child turned out to be a legitimate child of a later married couple.},
}
@article {pmid34880234,
year = {2021},
author = {Murchie, TJ and Monteath, AJ and Mahony, ME and Long, GS and Cocker, S and Sadoway, T and Karpinski, E and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN},
title = {Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {7120},
pmid = {34880234},
issn = {2041-1723},
mesh = {Animals ; Canada ; Climate Change ; *DNA, Ancient ; *DNA, Environmental ; Ecosystem ; Equidae/genetics ; Fossils ; Horses/genetics ; Human Activities ; Mammoths/*genetics ; Metagenome ; Plants/genetics ; Yukon Territory ; },
abstract = {The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.},
}
@article {pmid34850680,
year = {2021},
author = {Cristiani, E and Radini, A and Zupancich, A and Gismondi, A and D'Agostino, A and Ottoni, C and Carra, M and Vukojičić, S and Constantinescu, M and Antonović, D and Price, TD and Borić, D},
title = {Wild cereal grain consumption among Early Holocene foragers of the Balkans predates the arrival of agriculture.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34850680},
issn = {2050-084X},
support = {/WT_/Wellcome Trust/United Kingdom ; 209869/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Agriculture/*history ; Balkan Peninsula ; Domestication ; *Edible Grain ; Farmers/*history ; *Feeding Behavior ; History, Ancient ; Humans ; Tooth/anatomy &amp; histology ; },
abstract = {Forager focus on wild cereal plants has been documented in the core zone of domestication in southwestern Asia, while evidence for forager use of wild grass grains remains sporadic elsewhere. In this paper, we present starch grain and phytolith analyses of dental calculus from 60 Mesolithic and Early Neolithic individuals from five sites in the Danube Gorges of the central Balkans. This zone was inhabited by likely complex Holocene foragers for several millennia before the appearance of the first farmers ~6200 cal BC. We also analyzed forager ground stone tools (GSTs) for evidence of plant processing. Our results based on the study of dental calculus show that certain species of Poaceae (species of the genus Aegilops) were used since the Early Mesolithic, while GSTs exhibit traces of a developed grass grain processing technology. The adoption of domesticated plants in this region after ~6500 cal BC might have been eased by the existing familiarity with wild cereals.},
}
@article {pmid34850636,
year = {2022},
author = {Smith, RW and Non, AL},
title = {Assessing the achievements and uncertain future of paleoepigenomics.},
journal = {Epigenomics},
volume = {14},
number = {4},
pages = {167-173},
doi = {10.2217/epi-2021-0382},
pmid = {34850636},
issn = {1750-192X},
mesh = {*DNA Methylation ; Epigenesis, Genetic ; *Epigenomics ; Humans ; },
}
@article {pmid34848867,
year = {2021},
author = {Tsosie, KS and Bader, AC and Fox, K and Bolnick, DA and Garrison, NA and Smith, RWA},
title = {Ancient-DNA researchers write their own rules.},
journal = {Nature},
volume = {600},
number = {7887},
pages = {37},
doi = {10.1038/d41586-021-03542-y},
pmid = {34848867},
issn = {1476-4687},
mesh = {*DNA, Ancient ; Ethics, Research ; Humans ; *Research Personnel ; Writing ; },
}
@article {pmid34848866,
year = {2021},
author = {Somel, M and Altınışık, NE and Özer, F and Ávila-Arcos, MC},
title = {Collaborate equitably in ancient DNA research and beyond.},
journal = {Nature},
volume = {600},
number = {7887},
pages = {37},
doi = {10.1038/d41586-021-03541-z},
pmid = {34848866},
issn = {1476-4687},
mesh = {*DNA, Ancient ; },
}
@article {pmid34843568,
year = {2021},
author = {Nath, S and Zilm, P and Jamieson, L and Kapellas, K and Goswami, N and Ketagoda, K and Weyrich, LS},
title = {Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0260433},
pmid = {34843568},
issn = {1932-6203},
mesh = {Animals ; Australia ; Dental Caries/microbiology/*therapy ; Dysbiosis/microbiology/*therapy ; Humans ; Mice, Inbred BALB C ; Microbiota ; Mouth/*microbiology ; Periodontal Diseases/microbiology/*therapy ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Oral microbiome transplantation (OMT) is a novel concept of introducing health-associated oral microbiota into the oral cavity of a diseased patient. The premise is to reverse the state of oral dysbiosis, and restore the ecological balance to maintain a stable homeostasis with the host immune system. This study will assess the effectiveness, feasibility, and safety of OMT using an interdisciplinary approach.<br><br>METHODS/DESIGN: To find donors suitable for microbial transplantation, supragingival plaque samples will be collected from 600 healthy participants. Each sample (200&#x3bc;L) will subsequently be examined in two ways: 1) 100&#x3bc;L of the sample will undergo high-throughput 16S rRNA gene amplicon sequencing and shotgun sequencing to identify the composition and characterisation of a healthy supragingival microbiome, 2) the remaining 100&#x3bc;L of the plaque sample will be mixed with 25% artificial saliva medium and inoculated into a specialised in-vitro flow cell model containing a hydroxyapatite disk. To obtain sufficient donor plaque, the samples would be grown for 14 days and further analysed microscopically and sequenced to examine and confirm the growth and survival of the microbiota. Samples with the healthiest microbiota would then be incorporated in a hydrogel delivery vehicle to enable transplantation of the donor oral microbiota. The third step would be to test the effectiveness of OMT in caries and periodontitis animal models for efficacy and safety for the treatment of oral diseases.<br><br>DISCUSSION: If OMTs are found to be successful, it can form a new treatment method for common oral diseases such as dental caries and periodontitis. OMTs may have the potential to modulate the oral microbiota and shift the ecological imbalances to a healthier state.},
}
@article {pmid34833105,
year = {2021},
author = {Sharma, M and Chopra, C and Mehta, M and Sharma, V and Mallubhotla, S and Sistla, S and Sistla, JC and Bhushan, I},
title = {An Insight into Vaginal Microbiome Techniques.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {34833105},
issn = {2075-1729},
abstract = {There is a unique microbial community in the female lower genital tract known as the vaginal microbiota, which varies in composition and density and provides significant benefits during pregnancy, reproductive cyclicity, healthy newborn delivery, protection from preterm birth, infections such as UTIs, bacterial vaginosis, and so on, and improves the efficacy of treatments for vaginal cancers. Methods: It is necessary to know how the vaginal microbiome is composed in order to make an accurate diagnosis of the diseases listed above. A microbiome's members are difficult to classify, and the way microbial communities function and influence host-pathogen interactions are difficult to understand. More and more metagenomic studies are able to unravel such complexities due to advances in high-throughput sequencing and bioinformatics. When it comes to vaginal microbiota research, we'll be looking at the use of modern techniques and strategies that can be used to investigate variations in vaginal microbiota in order to detect diseases earlier, better treat vaginal disorders, and boost women's health. Discussion: The discussed techniques and strategies may improve the treatment of vaginal disorders and may be beneficial for women's overall health.},
}
@article {pmid34832510,
year = {2021},
author = {Raele, DA and Panzarino, G and Sarcinelli, G and Cafiero, MA and Maria Tunzi, A and Dellù, E},
title = {Genetic Evidence of the Black Death in the Abbey of San Leonardo (Apulia Region, Italy): Tracing the Cause of Death in Two Individuals Buried with Coins.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34832510},
issn = {2076-0817},
abstract = {The Abbey of San Leonardo in Siponto (Apulia, Southern Italy) was an important religious and medical center during the Middle Ages. It was a crossroads for pilgrims heading along the Via Francigena to the Sanctuary of Monte Sant'Angelo and for merchants passing through the harbor of Manfredonia. A recent excavation of Soprintendenza Archeologica della Puglia investigated a portion of the related cemetery, confirming its chronology to be between the end of the 13th and beginning of the 14th century. Two single graves preserved individuals accompanied by numerous coins dating back to the 14th century, hidden in clothes and in a bag tied to the waist. The human remains of the individuals were analyzed in the Laboratorio di Antropologia Fisica of Soprintendenza ABAP della città metropolitana di Bari. Three teeth from each individual were collected and sent to the Istituto Zooprofilattico Sperimentale di Puglia e Basilicata to study infectious diseases such as malaria, plague, tuberculosis, epidemic typhus and Maltese fever (Brucellosis), potentially related to the lack of inspection of the bodies during burial procedures. DNA extracted from six collected teeth and two additional unrelated human teeth (negative controls) were analyzed using PCR to verify the presence of human DNA (β-globulin) and of pathogens such as Plasmodium spp., Yersinia pestis, Mycobacterium spp., Rickettsia spp. and Brucella spp. The nucleotide sequence of the amplicon was determined to confirm the results. Human DNA was successfully amplified from all eight dental extracts and two different genes of Y. pestis were amplified and sequenced in 4 out of the 6 teeth. Molecular analyses ascertained that the individuals buried in San Leonardo were victims of the Black Death (1347-1353) and the data confirmed the lack of inspection of the corpses despite the presence of numerous coins. This study represents molecular evidence, for the first time, of Southern Italy's involvement in the second wave of the plague pandemic.},
}
@article {pmid34824815,
year = {2021},
author = {Baca, M and Popović, D and Lemanik, A and Fewlass, H and Talamo, S and Zima, J and Ridush, B and Popov, V and Nadachowski, A},
title = {The Tien Shan vole (Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe.},
journal = {Ecology and evolution},
volume = {11},
number = {22},
pages = {16113-16125},
pmid = {34824815},
issn = {2045-7758},
abstract = {Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.},
}
@article {pmid34805800,
year = {2021},
author = {Ning, C and Zhang, F and Cao, Y and Qin, L and Hudson, MJ and Gao, S and Ma, P and Li, W and Zhu, S and Li, C and Li, T and Xu, Y and Li, C and Robbeets, M and Zhang, H and Cui, Y},
title = {Ancient genome analyses shed light on kinship organization and mating practice of Late Neolithic society in China.},
journal = {iScience},
volume = {24},
number = {11},
pages = {103352},
pmid = {34805800},
issn = {2589-0042},
abstract = {Anthropology began in the late nineteenth century with an emphasis on kinship as a key factor in human evolution. From the 1960s, archaeologists attempted increasingly sophisticated ways of reconstructing prehistoric kinship but ancient DNA analysis has transformed the field, making it possible, to directly examine kin relations from human skeletal remains. Here, we retrieved genomic data from four Late Neolithic individuals in central China associated with the Late Neolithic Longshan culture. We provide direct evidence of consanguineous mating in ancient China, revealing inbreeding among the Longshan populations. By combining ancient genomic data with anthropological and archaeological evidence, we further show that Longshan society household was built based on the extended beyond the nuclear family, coinciding with intensified social complexity during the Longshan period, perhaps showing the transformation of large communities through a new role of genetic kinship-based extended family units.},
}
@article {pmid34793228,
year = {2021},
author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Ramsey, CB and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R},
title = {Response to Comment on "A global environmental crisis 42,000 years ago".},
journal = {Science (New York, N.Y.)},
volume = {374},
number = {6570},
pages = {eabh3655},
doi = {10.1126/science.abh3655},
pmid = {34793228},
issn = {1095-9203},
abstract = {Our paper about the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks’ assertions of misrepresentation are especially disappointing given his limited examination of the material.},
}
@article {pmid34793203,
year = {2021},
author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Bronk Ramsey, C and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R},
title = {Response to Comment on "A global environmental crisis 42,000 years ago".},
journal = {Science (New York, N.Y.)},
volume = {374},
number = {6570},
pages = {eabi9756},
doi = {10.1126/science.abi9756},
pmid = {34793203},
issn = {1095-9203},
abstract = {Our study on the exact timing and the potential climatic, environmental, and evolutionary consequences of the Laschamps Geomagnetic Excursion has generated the hypothesis that geomagnetism represents an unrecognized driver in environmental and evolutionary change. It is important for this hypothesis to be tested with new data, and encouragingly, none of the studies presented by Picin et al. undermine our model.},
}
@article {pmid34791203,
year = {2022},
author = {Moreno-Mayar, JV},
title = {FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets.},
journal = {G3 (Bethesda, Md.)},
volume = {12},
number = {1},
pages = {},
pmid = {34791203},
issn = {2160-1836},
mesh = {Alleles ; Computational Biology ; *Genomics ; *Software ; },
abstract = {Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyze their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualization of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.},
}
@article {pmid34784770,
year = {2021},
author = {Zhang, H and Sun, Y and Zeng, Q and Crowe, SA and Luo, H},
title = {Snowball Earth, population bottleneck and Prochlorococcus evolution.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1963},
pages = {20211956},
pmid = {34784770},
issn = {1471-2954},
mesh = {Earth, Planet ; Genome, Bacterial ; Oceans and Seas ; Phylogeny ; *Prochlorococcus/genetics/metabolism ; Seawater/chemistry ; },
abstract = {Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that this Prochlorococcus genome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibited Prochlorococcus growth and proliferation, and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations accumulated across genomic regions and inherited by descendant lineages. Prochlorococcus adaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. Key metabolic innovation includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event may have altered the physiological characters of Prochlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.},
}
@article {pmid34783162,
year = {2022},
author = {Lyu, W and Dai, X and Beaumont, M and Yu, F and He, Z},
title = {Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data.},
journal = {Molecular ecology resources},
volume = {22},
number = {4},
pages = {1362-1379},
doi = {10.1111/1755-0998.13553},
pmid = {34783162},
issn = {1755-0998},
mesh = {Animals ; Bayes Theorem ; *Chickens/genetics ; *DNA, Ancient ; Evolution, Molecular ; Gene Frequency ; Models, Genetic ; Selection, Genetic ; },
abstract = {With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for the detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in an overestimation of the effect of natural selection. To address these issues, we introduce a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.},
}
@article {pmid34782694,
year = {2021},
author = {Guellil, M and Rinaldo, N and Zedda, N and Kersten, O and Gonzalez Muro, X and Stenseth, NC and Gualdi-Russo, E and Bramanti, B},
title = {Bioarchaeological insights into the last plague of Imola (1630-1632).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22253},
pmid = {34782694},
issn = {2045-2322},
mesh = {Adult ; *Archaeology/history ; Child ; Child, Preschool ; DNA, Ancient ; DNA, Bacterial ; *Disease Outbreaks/history ; Female ; Geography, Medical ; History, 17th Century ; Humans ; Italy/epidemiology ; Male ; Metagenome ; Metagenomics ; Plague/*epidemiology/history/*microbiology ; Yersinia pestis/genetics ; },
abstract = {The plague of 1630-1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell'Osservanza, which date back to the outbreak of 1630-1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto.},
}
@article {pmid34779123,
year = {2022},
author = {Ferrari, G and Atmore, LM and Jentoft, S and Jakobsen, KS and Makowiecki, D and Barrett, JH and Star, B},
title = {An accurate assignment test for extremely low-coverage whole-genome sequence data.},
journal = {Molecular ecology resources},
volume = {22},
number = {4},
pages = {1330-1344},
doi = {10.1111/1755-0998.13551},
pmid = {34779123},
issn = {1755-0998},
mesh = {Animals ; *Butterflies/genetics ; Ecotype ; *Gadus morhua/genetics ; Genome/genetics ; Haplotypes ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/methods ; },
abstract = {Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.},
}
@article {pmid34773064,
year = {2021},
author = {Yurtman, E and Özer, O and Yüncü, E and Dağtaş, ND and Koptekin, D and Çakan, YG and Özkan, M and Akbaba, A and Kaptan, D and Atağ, G and Vural, KB and Gündem, CY and Martin, L and Kılınç, GM and Ghalichi, A and Açan, SC and Yaka, R and Sağlıcan, E and Lagerholm, VK and Krzewińska, M and Günther, T and Morell Miranda, P and Pişkin, E and Şevketoğlu, M and Bilgin, CC and Atakuman, &#xc7; and Erdal, YS and Sürer, E and Altınışık, NE and Lenstra, JA and Yorulmaz, S and Abazari, MF and Hoseinzadeh, J and Baird, D and Bıçakçı, E and Çevik, &#xd6; and Gerritsen, F and Özbal, R and Götherström, A and Somel, M and Togan, &#x130; and Özer, F},
title = {Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1279},
pmid = {34773064},
issn = {2399-3642},
mesh = {Animals ; Archaeology ; Cell Nucleus ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Demography ; *Domestication ; *Polymorphism, Genetic ; Sheep, Domestic/*genetics ; Turkey ; },
abstract = {Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.},
}
@article {pmid34764978,
year = {2021},
author = {Piro, M},
title = {Aspects of Molecular Genetics in Dromedary Camel.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {723181},
pmid = {34764978},
issn = {1664-8021},
abstract = {Dromedary camels are unique in their morphological and physiological characteristics and are capable of providing milk and meat even under extreme environmental conditions. Like other species, the dromedary camel has also benefitted from the development of the molecular genetics to increase the knowledge about different aspect in camel genetics (genetic variation, molecular marker, parentage control, gene of interest, whole genome, dating…etc.). In this paper we review the different molecular genetic technics used in this particular species and future prospects. Dromedary genetic studies started in the end of the 1980s with phenotypic evaluation and the attempts to highlight the protein and biochemical diversity. In the 2000s, with the development of molecular markers such as microsatellites, genetic diversity of different types in several countries were estimated and microsatellites were also used for parentage control. In terms of genetic characterization, microsatellites revealed a defined global structure, differentiating East African and South Arabian dromedaries from North African, North Arabian, and South Asian individuals, respectively. Also, mitochondrialDNA sequence analysis of ancient DNA proved to be crucial in resolving domestication processes in dromedaries. Ancient and modern DNA revealed dynamics of domestication and cross-continental dispersion of the dromedary. Nuclear SNPs, single nucleotide polymorphisms changes that occur approximately each 1000 bps in the mammalian genome were also applied in some studies in dromedary. These markers are a very useful alternative to microsatellites and have been employed in some studies on genetic diversity and relevant phenotypic traits in livestock. Finally, thanks to the use of Next Generation Sequencing (NGS) the whole-genome assemblies of the dromedary (Camelus dromedarius) and a work to establish the organization of the dromedary genome at chromosome level were recently published.},
}
@article {pmid34759290,
year = {2021},
author = {Morin, J and Royle, TCA and Zhang, H and Speller, C and Alcaide, M and Morin, R and Ritchie, M and Cannon, A and George, M and George, M and Yang, D},
title = {Indigenous sex-selective salmon harvesting demonstrates pre-contact marine resource management in Burrard Inlet, British Columbia, Canada.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {21160},
pmid = {34759290},
issn = {2045-2322},
mesh = {Animals ; British Columbia ; Hunting ; Male ; *Oncorhynchus keta ; Rivers ; *Seafood ; },
abstract = {To gain insight into pre-contact Coast Salish fishing practices, we used new palaeogenetic analytical techniques to assign sex identifications to salmonid bones from four archaeological sites in Burrard Inlet (Tsleil-Waut), British Columbia, Canada, dating between about 2300-1000 BP (ca. 400 BCE-CE 1200). Our results indicate that male chum salmon (Oncorhynchus keta) were preferentially targeted at two of the four sampled archaeological sites. Because a single male salmon can mate with several females, selectively harvesting male salmon can increase a fishery's maximum sustainable harvest. We suggest such selective harvesting of visually distinctive male spawning chum salmon was a common practice, most effectively undertaken at wooden weirs spanning small salmon rivers and streams. We argue that this selective harvesting of males is indicative of an ancient and probably geographically widespread practice for ensuring sustainable salmon populations. The archaeological data presented here confirms earlier ethnographic accounts describing the selective harvest of male salmon.},
}
@article {pmid34748674,
year = {2022},
author = {Salis, AT and Bray, SCE and Lee, MSY and Heiniger, H and Barnett, R and Burns, JA and Doronichev, V and Fedje, D and Golovanova, L and Harington, CR and Hockett, B and Kosintsev, P and Lai, X and Mackie, Q and Vasiliev, S and Weinstock, J and Yamaguchi, N and Meachen, JA and Cooper, A and Mitchell, KJ},
title = {Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge.},
journal = {Molecular ecology},
volume = {31},
number = {24},
pages = {6407-6421},
doi = {10.1111/mec.16267},
pmid = {34748674},
issn = {1365-294X},
mesh = {Humans ; Horses/genetics ; Animals ; *Ursidae/genetics ; *Lions ; Phylogeny ; DNA, Mitochondrial/genetics ; North America ; },
abstract = {The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.},
}
@article {pmid34745073,
year = {2021},
author = {Urban, C and Blom, AA and Pfrengle, S and Walker-Meikle, K and Stone, AC and Inskip, SA and Schuenemann, VJ},
title = {One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {762263},
pmid = {34745073},
issn = {1664-302X},
abstract = {Hansen's disease (leprosy), mainly caused by infection with Mycobacterium leprae, has accompanied humanity for thousands of years. Although currently rare in Europe, there are over 200,000 new infections annually in South East Asia, Africa, and South America. Over the years many disciplines - palaeopathology, ancient DNA and other ancient biomolecules, and history - have contributed to a better understanding of leprosy's past, in particular its history in medieval Europe. We discuss their contributions and potential, especially in relation to the role of inter-species transmission, an unexplored phenomenon in the disease's history. Here, we explore the potential of interdisciplinary approaches that understand disease as a biosocial phenomenon, which is a product of both infection with M. leprae and social behaviours that facilitate transmission and spread. Genetic evidence of M. leprae isolated from archaeological remains combined with systematic zooarchaeological and historical analysis would not only identify when and in what direction transmission occurred, but also key social behaviours and motivations that brought species together. In our opinion, this combination is crucial to understand the disease's zoonotic past and current potential.},
}
@article {pmid34743803,
year = {2021},
author = {Zilberman, U and Abramov, J and Smith, P},
title = {Supernumerary roots in maxillary deciduous canines: A rare anomaly with a long history.},
journal = {Archives of oral biology},
volume = {132},
number = {},
pages = {105292},
doi = {10.1016/j.archoralbio.2021.105292},
pmid = {34743803},
issn = {1879-1506},
mesh = {*Cuspid/diagnostic imaging ; Maxilla/diagnostic imaging ; Odontogenesis ; Tooth Crown ; *Tooth Root/diagnostic imaging ; Tooth, Deciduous ; },
abstract = {OBJECTIVE: To describe two maxillary deciduous bi-rooted canines, one archeological and one modern, and examine the possible etiology of this condition.<br><br>DESIGN: Two cases of bi-rooted canines were described and compared to published examples. Both specimens were radiographed and measured and compared to one-rooted samples. The archeological specimen was scanned using CBCT to facilitate detailed examination of the deciduous teeth. The extracted modern tooth was embedded in epoxy resin and two coronal sections were cut, one through the crown and one through the roots and examined with a light microscope.<br><br>RESULTS: The bi-rooted canines were larger than the control samples. They showed none of the features commonly associated with gemination. The radiographs and scans showed that the canine roots in the archeological case diverged mesio-distally like the buccal roots in the adjacent first deciduous molar. In the clinical case, the root trunk was elongated mesio-distally and the furcation was located very close to the apex with a C-shaped root canal.<br><br>CONCLUSIONS: Both variants of the condition described above are rare in deciduous canines. They do not seem to be associated with fusion or gemination. However, as the teeth are relatively flattened bucco-lingually and we tentatively propose that this form results from spatial constraints during the early stages of crown development that have contributed to the development of additional roots. The megadont dimension of the recent bi-rooted deciduous canine may affect root development and the necessity of two mesio-distally located roots for anchorage in the maxilla.},
}
@article {pmid34738712,
year = {2022},
author = {Fordham, DA and Brown, SC and Akçakaya, HR and Brook, BW and Haythorne, S and Manica, A and Shoemaker, KT and Austin, JJ and Blonder, B and Pilowsky, J and Rahbek, C and Nogues-Bravo, D},
title = {Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation.},
journal = {Ecology letters},
volume = {25},
number = {1},
pages = {125-137},
doi = {10.1111/ele.13911},
pmid = {34738712},
issn = {1461-0248},
mesh = {Animals ; Anthropogenic Effects ; Climate ; Extinction, Biological ; Fossils ; Humans ; *Mammoths/genetics ; },
abstract = {Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.},
}
@article {pmid34735939,
year = {2022},
author = {Emery, MV and Bolhofner, K and Ghafoor, S and Winingear, S and Buikstra, JE and Fulginiti, LC and Stone, AC},
title = {Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth.},
journal = {Forensic science international. Genetics},
volume = {56},
number = {},
pages = {102610},
doi = {10.1016/j.fsigen.2021.102610},
pmid = {34735939},
issn = {1878-0326},
mesh = {DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Tooth ; },
abstract = {The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.},
}
@article {pmid34731404,
year = {2022},
author = {Oh, CS and Hong, JH and Chai, JY and Song, MK and Jang, HJ and Seo, M and Shin, DH},
title = {Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea.},
journal = {Acta parasitologica},
volume = {67},
number = {1},
pages = {539-545},
pmid = {34731404},
issn = {1896-1851},
mesh = {Animals ; Body Remains ; DNA, Ancient ; *Heterophyidae/genetics ; Humans ; Phylogeny ; Republic of Korea ; *Trematode Infections/parasitology ; },
abstract = {PURPOSE: Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period.<br><br>METHODS: The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software.<br><br>RESULTS: Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai.<br><br>CONCLUSION: In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet.},
}
@article {pmid34721545,
year = {2021},
author = {Wang, L and Sheng, G and Preick, M and Hu, S and Deng, T and Taron, UH and Barlow, A and Hu, J and Xiao, B and Sun, G and Song, S and Hou, X and Lai, X and Hofreiter, M and Yuan, J},
title = {Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {759831},
pmid = {34721545},
issn = {1664-8021},
abstract = {Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unresolved. To address these questions, we retrieved three near-complete mitochondrial genomes from donkey specimens excavated from Gaoling County, Shaanxi Province, and Linxia Basin, Gansu Province, China, dated at 2,349-2,301, 469-311, and 2,160-2,004 cal. BP, respectively. Maximum-likelihood and Bayesian phylogenetic analyses reveal that the two older samples fall into the two different main lineages (i.e., clade Ⅰ and clade Ⅱ) of the domestic donkey, suggesting that the two donkey maternal lineages had been introduced into Midwestern China at least at the opening of Silk Road (approximately the first century BC). Bayesian analysis shows that the split of the two donkey maternal lineages is dated at 0.323 Ma (95% CI: 0.583-0.191 Ma) using root-tip dating calibrations based on near-complete mitogenomes, supporting the hypothesis that modern domestic donkeys go back to at least two independent domestication events. Moreover, Bayesian skyline plot analyses indicate an apparent female population increase between 5,000 and 2,500 years ago for clade I followed by a stable population size to the present day. In contrast, clade II keeps a relatively stable population size over the past 5,000 years. Overall, our study provides new insights into the early domestication history of Chinese domestic donkeys.},
}
@article {pmid34718543,
year = {2021},
author = {Colbran, LL and Johnson, MR and Mathieson, I and Capra, JA},
title = {Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment.},
journal = {Genome biology and evolution},
volume = {13},
number = {11},
pages = {},
pmid = {34718543},
issn = {1759-6653},
support = {T32 GM080178/GM/NIGMS NIH HHS/United States ; R35 GM133708/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Biological/genetics ; Adaptation, Physiological ; Biological Evolution ; DNA, Ancient ; *Genome, Human ; Humans ; Multifactorial Inheritance ; Selection, Genetic ; },
abstract = {As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.},
}
@article {pmid34712923,
year = {2021},
author = {Sinding, MS and Ciucani, MM and Ramos-Madrigal, J and Carmagnini, A and Rasmussen, JA and Feng, S and Chen, G and Vieira, FG and Mattiangeli, V and Ganjoo, RK and Larson, G and Sicheritz-Pontén, T and Petersen, B and Frantz, L and Gilbert, MTP and Bradley, DG},
title = {Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos.},
journal = {iScience},
volume = {24},
number = {11},
pages = {103226},
pmid = {34712923},
issn = {2589-0042},
abstract = {The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.},
}
@article {pmid34711884,
year = {2021},
author = {Fernandes, DM and Cheronet, O and Gelabert, P and Pinhasi, R},
title = {TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {21262},
pmid = {34711884},
issn = {2045-2322},
mesh = {Algorithms ; *Alleles ; Computational Biology/methods ; *DNA, Ancient ; Databases, Genetic ; Genetic Variation ; *Genome, Human ; *Genomics/methods ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide ; },
abstract = {Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1-1× minimum average genomic coverage per analysed pair of individuals. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026× average coverage, or around 18,000 SNPs from 1.3 million aligned reads per sample with average length of 62 bp-four times less data than 0.1× coverage at similar read lengths. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012×, or around 4000 SNPs from 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals that had been excluded from prior kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.},
}
@article {pmid34705496,
year = {2021},
author = {Moltke, I and Korneliussen, TS and Seguin-Orlando, A and Moreno-Mayar, JV and LaPointe, E and Billeck, W and Willerslev, E},
title = {Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull).},
journal = {Science advances},
volume = {7},
number = {44},
pages = {eabh2013},
pmid = {34705496},
issn = {2375-2548},
abstract = {A great-grandson of the legendary Lakota Sioux leader Sitting Bull (Tatanka Iyotake), Ernie LaPointe, wished to have their familial relationship confirmed via genetic analysis, in part, to help settle concerns over Sitting Bull’s final resting place. To address Ernie LaPointe’s claim of family relationship, we obtained minor amounts of genomic data from a small piece of hair from Sitting Bull’s scalp lock, which was repatriated in 2007. We then compared these data to genome-wide data from LaPointe and other Lakota Sioux using a new probabilistic approach and concluded that Ernie LaPointe is Sitting Bull’s great-grandson. To our knowledge, this is the first published example of a familial relationship between contemporary and a historical individual that has been confirmed using such limited amounts of ancient DNA across such distant relatives. Hence, this study opens the possibility for broadening genealogical research, even when only minor amounts of ancient genetic material are accessible.},
}
@article {pmid34702906,
year = {2021},
author = {Iadarola, B and Lavezzari, D and Modi, A and Degli Esposti, C and Beltrami, C and Rossato, M and Zaro, V and Napione, E and Latella, L and Lari, M and Caramelli, D and Salviati, A and Delledonne, M},
title = {Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 CE) indicates the first known case of late-onset Pompe disease.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {21070},
pmid = {34702906},
issn = {2045-2322},
mesh = {*DNA, Ancient ; Glycogen Storage Disease Type II/*genetics/history ; History, Medieval ; Humans ; Male ; *Mummies ; *Whole Exome Sequencing ; },
abstract = {Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard "clinical exome analysis" conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder.},
}
@article {pmid34679854,
year = {2021},
author = {Passamonti, MM and Somenzi, E and Barbato, M and Chillemi, G and Colli, L and Joost, S and Milanesi, M and Negrini, R and Santini, M and Vajana, E and Williams, JL and Ajmone-Marsan, P},
title = {The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {10},
pages = {},
pmid = {34679854},
issn = {2076-2615},
abstract = {Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.},
}
@article {pmid34674113,
year = {2021},
author = {Bonsu, DOM and Rodie, M and Higgins, D and Henry, J and Austin, JJ},
title = {Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces.},
journal = {Forensic science, medicine, and pathology},
volume = {17},
number = {4},
pages = {577-584},
pmid = {34674113},
issn = {1556-2891},
mesh = {Cellulose ; DNA ; *DNA Fingerprinting ; Humans ; Specimen Handling ; *Touch ; },
abstract = {A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 - 3.3 ng) compared to Rayon swabs (0.13 - 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.},
}
@article {pmid34672750,
year = {2021},
author = {Gibbons, A},
title = {Ancient DNA reveals long-sought homeland of modern horses.},
journal = {Science (New York, N.Y.)},
volume = {374},
number = {6566},
pages = {384-385},
doi = {10.1126/science.acx9390},
pmid = {34672750},
issn = {1095-9203},
mesh = {Animals ; *Animals, Domestic ; *DNA, Ancient ; *Domestication ; History, Ancient ; *Horses ; Mongolia ; },
}
@article {pmid34672105,
year = {2022},
author = {O'Grady, CJ and Dhandapani, V and Colbourne, JK and Frisch, D},
title = {Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs.},
journal = {Molecular ecology resources},
volume = {22},
number = {3},
pages = {946-961},
doi = {10.1111/1755-0998.13524},
pmid = {34672105},
issn = {1755-0998},
mesh = {Animals ; *Daphnia/genetics ; *Ecosystem ; Genomics/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing ; },
abstract = {Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.},
}
@article {pmid34671385,
year = {2021},
author = {Zhu, K and Du, P and Xiong, J and Ren, X and Sun, C and Tao, Y and Ding, Y and Xu, Y and Meng, H and Wang, CC and Wen, SQ},
title = {Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {745508},
pmid = {34671385},
issn = {1664-8021},
abstract = {The MGISEQ-2000 sequencer is widely used in various omics studies, but the performance of this platform for paleogenomics has not been evaluated. We here compare the performance of MGISEQ-2000 with the Illumina X-Ten on ancient human DNA using four samples from 1750BCE to 60CE. We found there were only slight differences between the two platforms in most parameters (duplication rate, sequencing bias, θ, δS, and λ). MGISEQ-2000 performed well on endogenous rate and library complexity although X-Ten had a higher average base quality and lower error rate. Our results suggest that MGISEQ-2000 and X-Ten have comparable performance, and MGISEQ-2000 can be an alternative platform for paleogenomics sequencing.},
}
@article {pmid34671162,
year = {2021},
author = {Librado, P and Khan, N and Fages, A and Kusliy, MA and Suchan, T and Tonasso-Calvière, L and Schiavinato, S and Alioglu, D and Fromentier, A and Perdereau, A and Aury, JM and Gaunitz, C and Chauvey, L and Seguin-Orlando, A and Der Sarkissian, C and Southon, J and Shapiro, B and Tishkin, AA and Kovalev, AA and Alquraishi, S and Alfarhan, AH and Al-Rasheid, KAS and Seregély, T and Klassen, L and Iversen, R and Bignon-Lau, O and Bodu, P and Olive, M and Castel, JC and Boudadi-Maligne, M and Alvarez, N and Germonpré, M and Moskal-Del Hoyo, M and Wilczyński, J and Pospuła, S and Lasota-Kuś, A and Tunia, K and Nowak, M and Rannamäe, E and Saarma, U and Boeskorov, G and Lōugas, L and Kyselý, R and Peške, L and Bălășescu, A and Dumitrașcu, V and Dobrescu, R and Gerber, D and Kiss, V and Szécsényi-Nagy, A and Mende, BG and Gallina, Z and Somogyi, K and Kulcsár, G and Gál, E and Bendrey, R and Allentoft, ME and Sirbu, G and Dergachev, V and Shephard, H and Tomadini, N and Grouard, S and Kasparov, A and Basilyan, AE and Anisimov, MA and Nikolskiy, PA and Pavlova, EY and Pitulko, V and Brem, G and Wallner, B and Schwall, C and Keller, M and Kitagawa, K and Bessudnov, AN and Bessudnov, A and Taylor, W and Magail, J and Gantulga, JO and Bayarsaikhan, J and Erdenebaatar, D and Tabaldiev, K and Mijiddorj, E and Boldgiv, B and Tsagaan, T and Pruvost, M and Olsen, S and Makarewicz, CA and Valenzuela Lamas, S and Albizuri Canadell, S and Nieto Espinet, A and Iborra, MP and Lira Garrido, J and Rodríguez González, E and Celestino, S and Olària, C and Arsuaga, JL and Kotova, N and Pryor, A and Crabtree, P and Zhumatayev, R and Toleubaev, A and Morgunova, NL and Kuznetsova, T and Lordkipanize, D and Marzullo, M and Prato, O and Bagnasco Gianni, G and Tecchiati, U and Clavel, B and Lepetz, S and Davoudi, H and Mashkour, M and Berezina, NY and Stockhammer, PW and Krause, J and Haak, W and Morales-Muñiz, A and Benecke, N and Hofreiter, M and Ludwig, A and Graphodatsky, AS and Peters, J and Kiryushin, KY and Iderkhangai, TO and Bokovenko, NA and Vasiliev, SK and Seregin, NN and Chugunov, KV and Plasteeva, NA and Baryshnikov, GF and Petrova, E and Sablin, M and Ananyevskaya, E and Logvin, A and Shevnina, I and Logvin, V and Kalieva, S and Loman, V and Kukushkin, I and Merz, I and Merz, V and Sakenov, S and Varfolomeyev, V and Usmanova, E and Zaibert, V and Arbuckle, B and Belinskiy, AB and Kalmykov, A and Reinhold, S and Hansen, S and Yudin, AI and Vybornov, AA and Epimakhov, A and Berezina, NS and Roslyakova, N and Kosintsev, PA and Kuznetsov, PF and Anthony, D and Kroonen, GJ and Kristiansen, K and Wincker, P and Outram, A and Orlando, L},
title = {The origins and spread of domestic horses from the Western Eurasian steppes.},
journal = {Nature},
volume = {598},
number = {7882},
pages = {634-640},
pmid = {34671162},
issn = {1476-4687},
mesh = {Animals ; Archaeology ; Asia ; DNA, Ancient ; *Domestication ; Europe ; *Genetics, Population ; Genome ; Grassland ; *Horses/genetics ; Phylogeny ; },
abstract = {Domestication of horses fundamentally transformed long-range mobility and warfare[1]. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling[2-4] at Botai, Central Asia around 3500 BC[3]. Other longstanding candidate regions for horse domestication, such as Iberia[5] and Anatolia[6], have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association[7] between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC[8,9] driving the spread of Indo-European languages[10]. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture[11,12].},
}
@article {pmid34671161,
year = {2021},
author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E},
title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.},
journal = {Nature},
volume = {600},
number = {7887},
pages = {86-92},
pmid = {34671161},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; },
abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood[1-8]. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistent