@article {pmid38040695,
year = {2023},
author = {Fournier, R and Tsangalidou, Z and Reich, D and Palamara, PF},
title = {Haplotype-based inference of recent effective population size in modern and ancient DNA samples.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7945},
pmid = {38040695},
issn = {2041-1723},
support = {850869//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 850869//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; R21-HG010748-01//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
abstract = {Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.},
}

@article {pmid38030719,
year = {2023},
author = {Fortes-Lima, CA and Burgarella, C and Hammarén, R and Eriksson, A and Vicente, M and Jolly, C and Semo, A and Gunnink, H and Pacchiarotti, S and Mundeke, L and Matonda, I and Muluwa, JK and Coutros, P and Nyambe, TS and Cikomola, JC and Coetzee, V and de Castro, M and Ebbesen, P and Delanghe, J and Stoneking, M and Barham, L and Lombard, M and Meyer, A and Steyn, M and Malmström, H and Rocha, J and Soodyall, H and Pakendorf, B and Bostoen, K and Schlebusch, CM},
title = {The genetic legacy of the expansion of Bantu-speaking peoples in Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38030719},
issn = {1476-4687},
abstract = {The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent[1-7]. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals[8]. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods[9] and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies[10] and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.},
}

@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},
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/ ; },
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 = {},
doi = {10.3390/genes14112036},
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/ ; },
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 = {},
doi = {10.7554/eLife.87749},
pmid = {37955570},
issn = {2050-084X},
support = {1836981//National Science Foundation/ ; },
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},
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 {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.},
}

*DNA, Ancient

@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},
doi = {10.1098/rsbl.2023.0343},
pmid = {37909055},
issn = {1744-957X},
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 {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&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.

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 & 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 = {},
doi = {10.3390/genes14101853},
pmid = {37895202},
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/ ; },
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 = {},
doi = {10.3390/microorganisms11102478},
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 {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//Universität Konstanz/ ; Centre of Excellence 2117 Centre for the Advanced Study of Collective Behaviour" ID: 422037984"//Deutsche Forschungsgemeinschaft/ ; Zukunftskolleg//Universität 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 für Bildung und Forschung/ ; bwHPC//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg/ ; 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 {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 {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 {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, Ö 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)/ ; },
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 {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 = {},
doi = {10.3390/plants12193452},
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 Förderung 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, İ 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},
doi = {10.1371/journal.pone.0292077},
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.

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},
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},
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},
doi = {10.1177/10732748231204755},
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.

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.

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.

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 {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 {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},
doi = {10.1098/rspb.2023.1349},
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 {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},
doi = {10.1126/sciadv.adh3822},
pmid = {37738339},
issn = {2375-2548},
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},
doi = {10.1016/j.xgen.2023.100377},
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 & 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},
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.

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.

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.

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.

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.

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.

LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed.

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 {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 & 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.},
}

*Biodiversity
*DNA, Ancient
Computational Biology
DNA Barcoding, Taxonomic

@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 {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},
doi = {10.6026/973206300181114},
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 {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},
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 {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 & 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.},
}

Mediterranean Region
Archaeology
*Human Migration/history
Humans
Principal Component Analysis
Human Genetics
*DNA, Ancient/analysis
Sequence Analysis, DNA
Burial
Anthropology
History, Ancient

@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 = {RGPIN-2019-04266//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
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 = {},
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 {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 & 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},
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},
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 = {},
doi = {10.3390/v15081631},
pmid = {37631973},
issn = {1999-4915},
support = {CA238592/NH/NIH HHS/United States ; P30CA013330/NH/NIH HHS/United States ; },
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 = {},
doi = {10.3390/genes14081523},
pmid = {37628575},
issn = {2073-4425},
support = {22-18-00470//Russian Science Foundation/ ; },
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/ ; },
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/ ; },
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},
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 {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 {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 {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 {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 {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, Á 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, BČ 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 Promoción Científica y Tecnológica/ ; //Fundación Científica Felipe Fiorellino/ ; //Fundación de Historia Natural Félix 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.

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.

RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥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.

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, É 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},
mesh = {Humans ; *Black or African American/genetics ; *Metagenomics ; DNA, Ancient ; },
abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.},
}

Humans
*Black or African American/genetics
*Metagenomics
DNA, Ancient

@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},
mesh = {Humans ; Animals ; Cattle/genetics ; *DNA, Ancient ; Phylogeny ; Americas ; Europe ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Haplotypes ; },
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.},
}

Humans
Animals
Cattle/genetics
*DNA, Ancient
Phylogeny
Americas
Europe
Caribbean Region
*DNA, Mitochondrial/genetics
Haplotypes

@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.},
}