@article {pmid36933795,
year = {2023},
author = {Zhang, G and Cui, C and Wangdue, S and Lu, H and Chen, H and Xi, L and He, W and Yuan, H and Tsring, T and Chen, Z and Yang, F and Tsering, T and Li, S and Tashi, N and Yang, T and Tong, Y and Wu, X and Li, L and He, Y and Cao, P and Dai, Q and Liu, F and Feng, X and Wang, T and Yang, R and Ping, W and Zhang, M and Gao, X and Liu, Y and Wang, W and Fu, Q},
title = {Maternal genetic history of ancient Tibetans over the past 4000 years.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2023.03.007},
pmid = {36933795},
issn = {1673-8527},
abstract = {The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstructed a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show ancient Tibetans shared the most recent common ancestor (TMRCA) with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians varied over the past 4000 years, with a stronger matrilineal connection between the two during 4000-3000 BP, and a weakened connection after 3000 BP, that coincident with climate change, followed by a reinforced connection after the Tubo period (1400-1100 BP). Besides, an over 4000-year matrilineal continuity was observed in some of the maternal lineages. We also found the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that were dynamically shaped by geography, climate changes, as well as historical events.},
}

@article {pmid36930997,
year = {2023},
author = {Schats, R},
title = {Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {32-42},
doi = {10.1016/j.ijpp.2023.03.002},
pmid = {36930997},
issn = {1879-9825},
abstract = {OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.

MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.

METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.

RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.

CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.

SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.

LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.

More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.},
}

@article {pmid36930529,
year = {2023},
author = {de-Dios, T and Scheib, CL and Houldcroft, CJ},
title = {An adagio for viruses, played out on ancient DNA.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad047},
pmid = {36930529},
issn = {1759-6653},
abstract = {Studies of ancient DNA have transformed our understanding of human evolution. Palaeogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic and pandemic pathogens. Viruses - and in particular those with single or double-stranded DNA genomes - are an important part of the palaeogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly-evolving viruses which cause disease. In this review, we will revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We will look at how palaeogenomics works for viral pathogens, such as the need for careful precautions against modern contamination, and robust computational pipelines to identify and analyse authenticated viral sequences. We will discuss the insights into virus evolution which have been gained through palaeogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.},
}

@article {pmid36922577,
year = {2023},
author = {Kerner, G and Choin, J and Quintana-Murci, L},
title = {Ancient DNA as a tool for medical research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {36922577},
issn = {1546-170X},
}

@article {pmid36919783,
year = {2023},
author = {Motti, JMB and Pauro, M and Scabuzzo, C and García, A and Aldazábal, V and Vecchi, R and Bayón, C and Pastor, N and Demarchi, DA and Bravi, CM and Reich, D and Cabana, GS and Nores, R},
title = {Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24727},
pmid = {36919783},
issn = {2692-7691},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.

MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.

RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.},
}

@article {pmid36918761,
year = {2023},
author = {Marsh, WA and Brace, S and Barnes, I},
title = {Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {111},
pmid = {36918761},
issn = {1471-2164},
abstract = {BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material.

RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors).

CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.},
}

@article {pmid36859677,
year = {2023},
author = {Callaway, E},
title = {Ancient genomes show how humans escaped Europe's deep freeze.},
journal = {Nature},
volume = {615},
number = {7951},
pages = {197-198},
pmid = {36859677},
issn = {1476-4687},
mesh = {Humans ; Europe ; *Genome, Human ; *DNA, Ancient/analysis ; *Human Migration/history ; Freezing ; *Cold Temperature ; History, Ancient ; },
}

Humans
Europe
*Genome, Human
*DNA, Ancient/analysis
*Human Migration/history
Freezing
*Cold Temperature
History, Ancient

@article {pmid36890036,
year = {2023},
author = {Johnson, OL and Tobler, R and Schmidt, JM and Huber, CD},
title = {Fluctuating selection and the determinants of genetic variation.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.02.004},
pmid = {36890036},
issn = {0168-9525},
abstract = {Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.},
}

@article {pmid36869137,
year = {2023},
author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M},
title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {240},
pmid = {36869137},
issn = {2399-3642},
abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.},
}

@article {pmid36862777,
year = {2023},
author = {Curry, A},
title = {Ancient DNA upends European prehistory.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6635},
pages = {865-866},
doi = {10.1126/science.adh3912},
pmid = {36862777},
issn = {1095-9203},
abstract = {Genes reveal striking diversity within similar ice age cultures.},
}

@article {pmid36855115,
year = {2023},
author = {Nyerki, E and Kalmár, T and Schütz, O and Lima, RM and Neparáczki, E and Török, T and Maróti, Z},
title = {correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {38},
pmid = {36855115},
issn = {1474-760X},
abstract = {Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.},
}

@article {pmid36458990,
year = {2023},
author = {Flohr, S},
title = {Canine dimensions for estimation of sex in adult and non-adult individuals with external validation by aDNA.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {80},
number = {2},
pages = {225-231},
doi = {10.1127/anthranz/2022/1653},
pmid = {36458990},
issn = {0003-5548},
mesh = {Humans ; Female ; *Tooth ; DNA, Ancient ; Discriminant Analysis ; Germany ; *Sex Determination by Skeleton/methods ; },
abstract = {Using discriminant functions obtained from canine dimensions for sex estimation in human skeletons has frequently been proposed as a promising approach within assemblages, even when used in non-adult individuals. However, applicability of this method to adult and non-adult individuals from other assemblages was rarely investigated, probably due to frequently observed inter-population differences in tooth dimensions. In the present study, discriminant functions obtained for permanent canine dimensions at the cemento-enamel junction in a previous study of the early medieval assemblage from Greding, were applied to individuals from a late medieval Jewish cemetery at Erfurt, Germany. The results were validated by aDNA analyses. Prior to the application of the functions, canine dimensions of the assemblages were compared. The comparison showed largely corresponding canine dimensions between the two assemblages. The application of the formulae obtained on the early medieval assemblage to the late medieval assemblage at Erfurt revealed a 100 % correct classification rate in the adult individuals. In non-adults, the correct classification rate was poorer, with 7 of 9 (77.8 %) individuals correctly classified. The study showed that the application of discriminant functions for sex estimation from canine measurements to assemblages other than those for which the functions were developed can lead to high correct classification rates in adults if the average canine dimensions are similar in the respective assemblages. An application to non-adult individuals should only be made with caution as canine dimensions in the "non-survivors" can lead to an over-estimation of the proportion of female non-adults.},
}

Humans
Female
*Tooth
DNA, Ancient
Discriminant Analysis
Germany
*Sex Determination by Skeleton/methods

@article {pmid33267568,
year = {2023},
author = {Gerussi, A and Halliday, N and Carbone, M and Invernizzi, P and Thorburn, D},
title = {Open challenges in the management of autoimmune hepatitis.},
journal = {Minerva gastroenterology},
volume = {69},
number = {1},
pages = {61-83},
doi = {10.23736/S2724-5895.20.02805-6},
pmid = {33267568},
issn = {2724-5365},
abstract = {Autoimmune hepatitis (AIH) is a rare autoimmune disease of the liver with many open questions as regards its etiopathogenesis, natural history and clinical management. The classical picture of AIH is chronic hepatitis with fluctuating elevation of serum transaminases and Immunoglobulin G levels, the presence of circulating autoantibodies and typical histological features. However, atypical presentations do occur and are not well captured by current diagnostic scores, with important consequences in terms of missed diagnoses and delayed treatments. AIH is treated with corticosteroids and immunosuppressive drugs but up to 40% of patients do not achieve full biochemical response and are at risk of progressing to cirrhosis and liver failure. Moreover, standard therapies are associated by significant side-effects which may impair the quality of life of patients living with AIH. However, advances in the understanding of the underlying immunology of AIH is raising the prospect of novel therapies and optimization of existing therapeutic approaches to reduce side-effect burdens and potentially restore immunological tolerance. In this review we outlined the clinical characteristics, etiopathogenesis and management of AIH and current challenges in the diagnosis and management of AIH and provided evidence underlying the evolution of diagnostic and clinical management protocols.},
}

@article {pmid36853456,
year = {2023},
author = {Ayling, C},
title = {TA Cloning Approaches to Cloning DNA with Damaged Ends DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {55-64},
pmid = {36853456},
issn = {1940-6029},
abstract = {DNA ends can become damaged for various reasons making them unsuitable for TA cloning techniques, the easiest and most common of the DNA cloning technologies. Examples of end-damaged DNA include ancient DNA and those produced by laboratory methods such as sonication. In this chapter, we discuss how to deal with end-damaged DNA prior to cloning with either the popular pGEM[®]-T Easy Vector Systems Kit and TOPO™ TA Cloning™ Kits.},
}

@article {pmid36853452,
year = {2023},
author = {Mikić, A and Alomari, A and Gowers, DM},
title = {Classical Recombinant DNA Cloning.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {1-24},
pmid = {36853452},
issn = {1940-6029},
abstract = {Traditional molecular cloning involves a series of linked experimental steps performed with the overall goal of isolating ("cloning") a specific DNA sequence-often a gene. The main purpose of cloning is to study either that DNA sequence or the RNA or protein product it encodes. Building on key enzymatic discoveries in the late 1960s, gene cloning was pioneered in the early 1970s. Since then, DNA cloning and manipulation have been used in every area of biological and biomedical research, from molecular genetics, structural biology, and developmental biology to neurobiology, ancient DNA studies, and immunology. It is a versatile technique that can be applied to a variety of starting DNA types and lengths, including cDNAs, genes, gene fragments, chromosomal regions, or shorter fragments such as PCR products and functional control regions such as enhancers or promoters. The starting DNA can originate from any cell, tissue, or organism. In this chapter we will cover traditional ("classic") molecular cloning strategy. This comprises six linked stages in which (1) PCR is used to amplify a DNA region of interest that is then (2) digested with restriction enzymes, alongside a selected vector, to produce complementary ends crucial for the two molecules to be (3) ligated by an ATP-dependent DNA ligase, creating a recombinant DNA molecule. The recombinant DNA is then (4) introduced into competent bacterial cells by transformation and (5) grown on a selective agar media, followed by (6) colony-PCR for screening purposes. We provide a worked example to demonstrate the cloning of an average-size gene (in this case the 2 kb DNA ligase A gene) from E. coli into a common plasmid expression vector. We have included six color figures and two tables to depict the key stages of a classical molecular cloning protocol. If you are cloning a segment of DNA or a gene, remember that each DNA cloning experiment is unique in terms of sequence, length, and experimental purpose. However, the principles of traditional cloning covered in this chapter are the same for any DNA sequence; we have included a detailed notes section, so you should easily be able to transfer them to your own work. Some of the following chapters in this volume will cover other, more recently developed, cloning protocols.},
}

@article {pmid36847465,
year = {2022},
author = {Hublin, JJ and Changeux, JP},
title = {Paleoanthropology of cognition: an overview on Hominins brain evolution.},
journal = {Comptes rendus biologies},
volume = {345},
number = {2},
pages = {57-75},
doi = {10.5802/crbiol.92},
pmid = {36847465},
issn = {1768-3238},
abstract = {Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.},
}

@article {pmid36821583,
year = {2023},
author = {Schmid, C and Schiffels, S},
title = {Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {9},
pages = {e2218375120},
doi = {10.1073/pnas.2218375120},
pmid = {36821583},
issn = {1091-6490},
mesh = {Humans ; History, Ancient ; *Genomics ; *DNA, Ancient/analysis ; Europe ; },
abstract = {The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility.},
}

Humans
History, Ancient
*Genomics
*DNA, Ancient/analysis
Europe

@article {pmid36841239,
year = {2023},
author = {Eaton, K and Sidhu, RK and Klunk, J and Gamble, JA and Boldsen, JL and Carmichael, AG and Varlık, N and Duchene, S and Featherstone, L and Grimes, V and Golding, GB and DeWitte, SN and Holmes, EC and Poinar, HN},
title = {Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.01.064},
pmid = {36841239},
issn = {1879-0445},
abstract = {The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.[1][,][2] A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.[3] Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.[4][,][5] To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.},
}

@article {pmid36834612,
year = {2023},
author = {Bruno, F and Abondio, P and Montesanto, A and Luiselli, D and Bruni, AC and Maletta, R},
title = {The Nerve Growth Factor Receptor (NGFR/p75[NTR]): A Major Player in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
doi = {10.3390/ijms24043200},
pmid = {36834612},
issn = {1422-0067},
abstract = {Alzheimer's disease (AD) represents the most prevalent type of dementia in elderly people, primarily characterized by brain accumulation of beta-amyloid (Aβ) peptides, derived from Amyloid Precursor Protein (APP), in the extracellular space (amyloid plaques) and intracellular deposits of the hyperphosphorylated form of the protein tau (p-tau; tangles or neurofibrillary aggregates). The Nerve growth factor receptor (NGFR/p75[NTR]) represents a low-affinity receptor for all known mammalians neurotrophins (i.e., proNGF, NGF, BDNF, NT-3 e NT-4/5) and it is involved in pathways that determine both survival and death of neurons. Interestingly, also Aβ peptides can blind to NGFR/p75[NTR] making it the "ideal" candidate in mediating Aβ-induced neuropathology. In addition to pathogenesis and neuropathology, several data indicated that NGFR/p75[NTR] could play a key role in AD also from a genetic perspective. Other studies suggested that NGFR/p75[NTR] could represent a good diagnostic tool, as well as a promising therapeutic target for AD. Here, we comprehensively summarize and review the current experimental evidence on this topic.},
}

@article {pmid36833406,
year = {2023},
author = {Dalal, V and Pasupuleti, N and Chaubey, G and Rai, N and Shinde, V},
title = {Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020479},
pmid = {36833406},
issn = {2073-4425},
abstract = {Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.},
}

@article {pmid36833230,
year = {2023},
author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA},
title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020303},
pmid = {36833230},
issn = {2073-4425},
abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.},
}

@article {pmid36819665,
year = {2023},
author = {Kerner, G and Neehus, AL and Philippot, Q and Bohlen, J and Rinchai, D and Kerrouche, N and Puel, A and Zhang, SY and Boisson-Dupuis, S and Abel, L and Casanova, JL and Patin, E and Laval, G and Quintana-Murci, L},
title = {Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe.},
journal = {Cell genomics},
volume = {3},
number = {2},
pages = {100248},
pmid = {36819665},
issn = {2666-979X},
abstract = {Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.},
}

@article {pmid36812666,
year = {2023},
author = {Bľandová, G and Patlevičová, A and Palkovičová, J and Pavlíková, Š and Beňuš, R and Repiská, V and Baldovič, M},
title = {Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {1-7},
doi = {10.1016/j.ijpp.2023.02.001},
pmid = {36812666},
issn = {1879-9825},
abstract = {OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains.

MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Devín (11th-12th century AD) and Cífer-Pác (8th-9th century AD).

METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917 + 326 C>T (rs4988235) associated with lactose intolerance.

RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917 + 326 C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion.

SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance.

LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out.

Genetic research based on larger sample sizes and in more diverse geographical regions.},
}

@article {pmid36812179,
year = {2023},
author = {Kalisher, R and Cradic, MS and Adams, MJ and Martin, MAS and Finkelstein, I},
title = {Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0281020},
doi = {10.1371/journal.pone.0281020},
pmid = {36812179},
issn = {1932-6203},
abstract = {Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death.},
}

@article {pmid36799477,
year = {2023},
author = {Cortez, AD and Lippert, D and Davis, JL and Nicholas, G and Malhi, RS and Weyrich, LS and Claw, KG and Bader, AC and Colwell, C},
title = {Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24714},
pmid = {36799477},
issn = {2692-7691},
abstract = {OBJECTIVES: The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process.

MATERIALS AND METHODS: We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews.

RESULTS: Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities.

DISCUSSION: This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.},
}

@article {pmid36796758,
year = {2023},
author = {Min-Shan Ko, A},
title = {The 2022 Nobel Prize in Physiology or Medicine awarded for the decoding of the complete ancient human genome.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2023.02.004},
pmid = {36796758},
issn = {2320-2890},
abstract = {Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.},
}

@article {pmid36790695,
year = {2022},
author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ},
title = {Metagenomic analysis of Ancient Egyptian canopic jars.},
journal = {American journal of biological anthropology},
volume = {179},
number = {2},
pages = {307-313},
doi = {10.1002/ajpa.24600},
pmid = {36790695},
issn = {2692-7691},
abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.

OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.

METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).

RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.

DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.},
}

@article {pmid36790664,
year = {2022},
author = {Vigeant, J and Ribot, I and Hélie, JF},
title = {Investigating individual migration life histories: An isotopic case study from 17th to 18th century Nouvelle France.},
journal = {American journal of biological anthropology},
volume = {177},
number = {2},
pages = {232-248},
doi = {10.1002/ajpa.24455},
pmid = {36790664},
issn = {2692-7691},
abstract = {OBJECTIVES: This isotopic study explores the mobility patterns of a growing urban population from Notre Dame's Catholic cemetery (1691-1796), located in Montreal (Canada). The site offers a unique opportunity to investigate early colonial settlement in Nouvelle France through individual life patterns.

MATERIALS AND METHODS: Stable oxygen isotopic compositions (δ[18]O) were measured on the enamel of 32 individuals from the Notre Dame collection. Premolars and third molars were selected, as they reflected the δ[18]O of the drinking water during childhood (2.5-5.5 years) and pre-adulthood (9.5-15.5 years). Firstly, premolars from three children (4-8 years of age) allowed us to provide a mean δ[18]O for the water consumed locally (22.7 ±  1.0 ‰ vs. VSMOW). Then, our δ[18]O were compared with published data from various geographical regions in North America (Eastern Canada and the United States) and Europe (France and the British Isles) to highlight mobility patterns of each individual.

RESULTS: Forty-eight percent of our sample (14 out of 29 individuals) did not reflect any long-distance mobility, as all their δ[18]O reflected Montreal's variation during their lifetime. The remaining (15 out of 29 individuals) experienced mobility within (n = 8) and outside (n = 7) North America and at different phases of their life (five at pre-adulthood, six at adulthood and four during both phases). Their migration patterns were analyzed according to age, sex, diet and possible ancestry in order to propose some "biographies."

DISCUSSION: This study highlights high population diversity in early colonial Montreal. Historians wrote that the city was growing, not only with the arrival of Europeans (e.g., young male workers, sailors), but also other groups (e.g., Indigenous people, slaves from North America). Additional analyses (e.g., ancient DNA) will be needed to explore further this phenomenon.},
}

@article {pmid36790637,
year = {2023},
author = {Balentine, CM and Alfonso-Durruty, M and Reynolds, AW and Vilar, M and Morello, F and Román, MS and Springs, LC and Smith, RWA and Archer, SM and Mata-Míguez, J and Wing, N and Bolnick, DA},
title = {Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.},
journal = {American journal of biological anthropology},
volume = {180},
number = {1},
pages = {144-161},
doi = {10.1002/ajpa.24638},
pmid = {36790637},
issn = {2692-7691},
abstract = {OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.

METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.

RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.

DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.},
}

@article {pmid36787794,
year = {2023},
author = {Baca, M and Popović, D and Agadzhanyan, AK and Baca, K and Conard, NJ and Fewlass, H and Filek, T and Golubiński, M and Horáček, I and Knul, MV and Krajcarz, M and Krokhaleva, M and Lebreton, L and Lemanik, A and Maul, LC and Nagel, D and Noiret, P and Primault, J and Rekovets, L and Rhodes, SE and Royer, A and Serdyuk, NV and Soressi, M and Stewart, JR and Strukova, T and Talamo, S and Wilczyński, J and Nadachowski, A},
title = {Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1993},
pages = {20222238},
doi = {10.1098/rspb.2022.2238},
pmid = {36787794},
issn = {1471-2954},
abstract = {The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.},
}

@article {pmid36787792,
year = {2022},
author = {Broccard, N and Silva, NM and Currat, M},
title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.},
journal = {American journal of biological anthropology},
volume = {177},
number = {1},
pages = {134-146},
doi = {10.1002/ajpa.24431},
pmid = {36787792},
issn = {2692-7691},
abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.

MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.

RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.

DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.},
}

@article {pmid36762361,
year = {2022},
author = {Riedel, A},
title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.},
journal = {ZooKeys},
volume = {1124},
number = {},
pages = {109-130},
pmid = {36762361},
issn = {1313-2989},
abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka & Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo & Riedel is chosen to prevail over T.tounaensis Narakusumo & Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.},
}

@article {pmid36760997,
year = {2023},
author = {Chang, X and Pamjav, H and Zhabagin, M and Wen, S},
title = {Editorial: The genetic history of human populations along the ancient silk road.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1130104},
pmid = {36760997},
issn = {1664-8021},
}

@article {pmid36755065,
year = {2021},
author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C},
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {66},
pmid = {36755065},
issn = {2730-6151},
abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.},
}

@article {pmid36750197,
year = {2023},
author = {Tiwari, J and Sur, S and Yadav, A and Kumar, R and Rai, N and Rani, S and Malik, S},
title = {Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1992},
pages = {20222374},
doi = {10.1098/rspb.2022.2374},
pmid = {36750197},
issn = {1471-2954},
abstract = {The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca[2+]/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca[2+] signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.},
}

@article {pmid36748324,
year = {2023},
author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L},
title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16859},
pmid = {36748324},
issn = {1365-294X},
abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.},
}

@article {pmid36747166,
year = {2023},
author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F},
title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {9},
pmid = {36747166},
issn = {1741-7007},
abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.},
}

@article {pmid36721228,
year = {2023},
author = {Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M and He, G},
title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.},
journal = {Human genomics},
volume = {17},
number = {1},
pages = {3},
doi = {10.1186/s40246-023-00452-0},
pmid = {36721228},
issn = {1479-7364},
abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.},
}

@article {pmid36714834,
year = {2022},
author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C},
title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac148},
pmid = {36714834},
issn = {2752-6542},
abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.},
}

@article {pmid36712342,
year = {2022},
author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG},
title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac209},
pmid = {36712342},
issn = {2752-6542},
abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.},
}

@article {pmid36691623,
year = {2023},
author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC},
title = {Genetic and functional odorant receptor variation in the Homo lineage.},
journal = {iScience},
volume = {26},
number = {1},
pages = {105908},
pmid = {36691623},
issn = {2589-0042},
abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.},
}

@article {pmid36672975,
year = {2023},
author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K},
title = {Methodological Changes in the Field of Paleogenetics.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010234},
pmid = {36672975},
issn = {2073-4425},
abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.},
}

@article {pmid36672874,
year = {2023},
author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A},
title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010133},
pmid = {36672874},
issn = {2073-4425},
abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.},
}

@article {pmid36672816,
year = {2022},
author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA},
title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010075},
pmid = {36672816},
issn = {2073-4425},
abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.},
}

@article {pmid36669262,
year = {2023},
author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J},
title = {Kinship analysis of skeletal remains from the Middle Ages.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102829},
doi = {10.1016/j.fsigen.2023.102829},
pmid = {36669262},
issn = {1878-0326},
abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.},
}

@article {pmid36661852,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA Data.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad008},
pmid = {36661852},
issn = {1537-1719},
abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies, and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat colouration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.},
}

@article {pmid36661298,
year = {2023},
author = {Henriksen, RA and Zhao, L and Korneliussen, TS},
title = {NGSNGS: Next generation simulator for next generation sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad041},
pmid = {36661298},
issn = {1367-4811},
abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data has become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here we present a multithreaded next-generation simulation tool for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform specific characteristics based on nucleotide quality score profiles, as well as including a post-mortem damage model which is relevant for simulating ancient DNA (aDNA). The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies, or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.

AVAILABILITY: The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid36658311,
year = {2023},
author = {Eaton, K and Featherstone, L and Duchene, S and Carmichael, AG and Varlık, N and Golding, GB and Holmes, EC and Poinar, HN},
title = {Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {23},
pmid = {36658311},
issn = {2399-3642},
abstract = {Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.},
}

@article {pmid36656838,
year = {2023},
author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE},
title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.},
journal = {PLoS genetics},
volume = {19},
number = {1},
pages = {e1010551},
doi = {10.1371/journal.pgen.1010551},
pmid = {36656838},
issn = {1553-7404},
abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.},
}

@article {pmid36653523,
year = {2023},
author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S},
title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {72},
pmid = {36653523},
issn = {2399-3642},
abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.},
}

@article {pmid36654346,
year = {2021},
author = {Liu, J and Zeng, W and Sun, B and Mao, X and Zhao, Y and Wang, F and Li, Z and Luan, F and Guo, J and Zhu, C and Wang, Z and Wei, C and Zhang, M and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Hou, W and Ping, W and Wu, X and Andrew Bennett, E and Liu, Y and Fu, Q},
title = {Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago.},
journal = {Science bulletin},
volume = {66},
number = {11},
pages = {1129-1135},
doi = {10.1016/j.scib.2021.01.029},
pmid = {36654346},
issn = {2095-9281},
abstract = {Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.},
}

@article {pmid36650598,
year = {2023},
author = {Popli, D and Peyrégne, S and Peter, BM},
title = {KIN: a method to infer relatedness from low-coverage ancient DNA.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {10},
pmid = {36650598},
issn = {1474-760X},
abstract = {Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.},
}

@article {pmid36649412,
year = {2023},
author = {Wang, X and Skourtanioti, E and Benz, M and Gresky, J and Ilgner, J and Lucas, M and Morsch, M and Peters, J and Pöllath, N and Ringbauer, H and le Roux, P and Schultz, M and Krause, J and Roberts, P and Stockhammer, PW},
title = {Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2210611120},
doi = {10.1073/pnas.2210611120},
pmid = {36649412},
issn = {1091-6490},
abstract = {Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ([87]Sr/[86]Sr), carbon, and oxygen (δ[18]O and δ[13]Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. [87]Sr/[86]Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.},
}

@article {pmid36649410,
year = {2023},
author = {Lewis, CM and Akinyi, MY and DeWitte, SN and Stone, AC},
title = {Ancient pathogens provide a window into health and well-being.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2209476119},
doi = {10.1073/pnas.2209476119},
pmid = {36649410},
issn = {1091-6490},
abstract = {This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.},
}

@article {pmid36646948,
year = {2023},
author = {Skourtanioti, E and Ringbauer, H and Gnecchi Ruscone, GA and Bianco, RA and Burri, M and Freund, C and Furtwängler, A and Gomes Martins, NF and Knolle, F and Neumann, GU and Tiliakou, A and Agelarakis, A and Andreadaki-Vlazaki, M and Betancourt, P and Hallager, BP and Jones, OA and Kakavogianni, O and Kanta, A and Karkanas, P and Kataki, E and Kissas, K and Koehl, R and Kvapil, L and Maran, J and McGeorge, PJP and Papadimitriou, A and Papathanasiou, A and Papazoglou-Manioudaki, L and Paschalidis, K and Polychronakou-Sgouritsa, N and Preve, S and Prevedorou, EA and Price, G and Protopapadaki, E and Schmidt-Schultz, T and Schultz, M and Shelton, K and Wiener, MH and Krause, J and Jeong, C and Stockhammer, PW},
title = {Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {36646948},
issn = {2397-334X},
abstract = {The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.},
}

@article {pmid36641836,
year = {2023},
author = {Barrenechea Angeles, I and Romero-Martínez, ML and Cavaliere, M and Varrella, S and Francescangeli, F and Piredda, R and Mazzocchi, MG and Montresor, M and Schirone, A and Delbono, I and Margiotta, F and Corinaldesi, C and Chiavarini, S and Montereali, MR and Rimauro, J and Parrella, L and Musco, L and Dell'Anno, A and Tangherlini, M and Pawlowski, J and Frontalini, F},
title = {Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.},
journal = {Environment international},
volume = {172},
number = {},
pages = {107738},
doi = {10.1016/j.envint.2023.107738},
pmid = {36641836},
issn = {1873-6750},
abstract = {The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.},
}

@article {pmid36638796,
year = {2022},
author = {Wang, K and Yu, H and Radzevičiūtė, R and Kiryushin, YF and Tishkin, AA and Frolov, YV and Stepanova, NF and Kiryushin, KY and Kungurov, AL and Shnaider, SV and Tur, SS and Tiunov, MP and Zubova, AV and Pevzner, M and Karimov, T and Buzhilova, A and Slon, V and Jeong, C and Krause, J and Posth, C},
title = {Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.062},
pmid = {36638796},
issn = {1879-0445},
abstract = {The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.},
}

@article {pmid36637197,
year = {2023},
author = {Neuenschwander, S and Cruz Dávalos, DI and Anchieri, L and Sousa da Mota, B and Bozzi, D and Rubinacci, S and Delaneau, O and Rasmussen, S and Malaspinas, AS},
title = {Mapache: a flexible pipeline to map ancient DNA.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad028},
pmid = {36637197},
issn = {1367-4811},
abstract = {SUMMARY: We introduce mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets-such as reference panels and multiple extracts and libraries per sample-to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.

AVAILABILITY: Mapache is freely available on GitHub (https://github.com/sneuensc/mapache).

SUPPLEMENTARY INFORMATION: The list of software (and their references) used in the pipeline and the benchmark results can be found in the Supplementary files. An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.},
}

@article {pmid36630487,
year = {2023},
author = {Kehlmaier, C and Graciá, E and Ali, JR and Campbell, PD and Chapman, SD and Deepak, V and Ihlow, F and Jalil, NE and Pierre-Huyet, L and Samonds, KE and Vences, M and Fritz, U},
title = {Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar.},
journal = {Science advances},
volume = {9},
number = {2},
pages = {eabq2574},
doi = {10.1126/sciadv.abq2574},
pmid = {36630487},
issn = {2375-2548},
abstract = {Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.},
}

@article {pmid36625884,
year = {2023},
author = {Xu, Y and Wang, N and Gao, S and Li, C and Ma, P and Yang, S and Jiang, H and Shi, S and Wu, Y and Zhang, Q and Cui, Y},
title = {Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {36625884},
issn = {1437-1596},
abstract = {Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.},
}

@article {pmid36625391,
year = {2023},
author = {Straiton, J},
title = {Ancient DNA sequencing: telling the tale of human history and evolution.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2022-0121},
pmid = {36625391},
issn = {1940-9818},
abstract = {Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].},
}

@article {pmid36623185,
year = {2023},
author = {Fleskes, RE and Cabana, GS and Gilmore, JK and Juarez, C and Karcher, E and Oubré, L and Mishoe, G and Ofunniyin, AA and Schurr, TG},
title = {Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {3},
pages = {e2201620120},
doi = {10.1073/pnas.2201620120},
pmid = {36623185},
issn = {1091-6490},
abstract = {In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.},
}

@article {pmid36620416,
year = {2023},
author = {Alfieri, JM and Johnson, T and Linderholm, A and Blackmon, H and Athrey, GN},
title = {Genomic investigation refutes record of most diverged avian hybrid.},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9689},
pmid = {36620416},
issn = {2045-7758},
abstract = {The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.},
}

@article {pmid36618122,
year = {2021},
author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP},
title = {The genomic origin of Zana of Abkhazia.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {2},
number = {2},
pages = {e10051},
pmid = {36618122},
issn = {2641-6573},
abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.},
}

@article {pmid36610858,
year = {2022},
author = {Miao, B and Liu, Y and Yang, R and Feng, X and Liu, F and Cao, P and Dai, Q and Ping, W and Liu, Y and Fu, Q},
title = {Assessment of contaminants associated with gold-standard ancient DNA protocols.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2022.12.027},
pmid = {36610858},
issn = {2095-9281},
}

@article {pmid36593352,
year = {2023},
author = {Montag, A},
title = {[The history of skin color is the history of mankind!].},
journal = {Dermatologie (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {36593352},
issn = {2731-7013},
abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.},
}

@article {pmid36582485,
year = {2022},
author = {Zhu, K and Du, P and Li, J and Zhang, J and Hu, X and Meng, H and Chen, L and Zhou, B and Yang, X and Xiong, J and Allen, E and Ren, X and Ding, Y and Xu, Y and Chang, X and Yu, Y and Han, S and Dong, G and Wang, CC and Wen, S},
title = {Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105636},
pmid = {36582485},
issn = {2589-0042},
abstract = {A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.},
}

@article {pmid36581666,
year = {2022},
author = {Changmai, P and Pinhasi, R and Pietrusewsky, M and Stark, MT and Ikehara-Quebral, RM and Reich, D and Flegontov, P},
title = {Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22507},
pmid = {36581666},
issn = {2045-2322},
abstract = {Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.},
}

@article {pmid36576953,
year = {2022},
author = {Nägele, K and Rivollat, M and Yu, H and Wang, K},
title = {Ancient genomic research - From broad strokes to nuanced reconstructions of the past.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10017},
pmid = {36576953},
issn = {2037-0644},
abstract = {Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past.},
}

@article {pmid36565457,
year = {2022},
author = {Vallini, L and Pagani, L},
title = {The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10013},
pmid = {36565457},
issn = {2037-0644},
abstract = {The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years.},
}

@article {pmid36555510,
year = {2022},
author = {Abondio, P and Bruno, F and Bruni, AC and Luiselli, D},
title = {Rare Amyloid Precursor Protein Point Mutations Recapitulate Worldwide Migration and Admixture in Healthy Individuals: Implications for the Study of Neurodegeneration.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
pmid = {36555510},
issn = {1422-0067},
abstract = {Genetic discoveries related to Alzheimer's disease and other dementias have been performed using either large cohorts of affected subjects or multiple individuals from the same pedigree, therefore disregarding mutations in the context of healthy groups. Moreover, a large portion of studies so far have been performed on individuals of European ancestry, with a remarkable lack of epidemiological and genomic data from underrepresented populations. In the present study, 70 single-point mutations on the APP gene in a publicly available genetic dataset that included 2504 healthy individuals from 26 populations were scanned, and their distribution was analyzed. Furthermore, after gametic phase reconstruction, a pairwise comparison of the segments surrounding the mutations was performed to reveal patterns of haplotype sharing that could point to specific cross-population and cross-ancestry admixture events. Eight mutations were detected in the worldwide dataset, with several of them being specific for a single individual, population, or macroarea. Patterns of segment sharing reflected recent historical events of migration and admixture possibly linked to colonization campaigns. These observations reveal the population dynamics of the considered APP mutations in worldwide human groups and support the development of ancestry-informed screening practices for the improvement of precision and personalized approaches to neurodegeneration and dementia.},
}

@article {pmid36553640,
year = {2022},
author = {Taufik, L and Teixeira, JC and Llamas, B and Sudoyo, H and Tobler, R and Purnomo, GA},
title = {Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/genes13122373},
pmid = {36553640},
issn = {2073-4425},
abstract = {Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.},
}

@article {pmid36546258,
year = {2022},
author = {Wang, Y},
title = {Ancient environmental DNA reveals Arctic ecosystem dynamics in last 50,000 years.},
journal = {Science bulletin},
volume = {67},
number = {13},
pages = {1304-1306},
doi = {10.1016/j.scib.2022.04.018},
pmid = {36546258},
issn = {2095-9281},
mesh = {*Ecosystem ; DNA, Ancient ; *DNA, Environmental ; Arctic Regions ; },
}

*Ecosystem
DNA, Ancient
*DNA, Environmental
Arctic Regions

@article {pmid36547255,
year = {2022},
author = {van der Kuyl, AC},
title = {Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {3},
number = {4},
pages = {443-464},
doi = {10.3390/epidemiologia3040034},
pmid = {36547255},
issn = {2673-3986},
abstract = {Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.},
}

@article {pmid36536113,
year = {2022},
author = {D'Agostino, A and Di Marco, G and Marvelli, S and Marchesini, M and Rizzoli, E and Rolfo, MF and Canini, A and Gismondi, A},
title = {Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1384},
pmid = {36536113},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Fruit ; Plants, Edible ; Pollen ; Poaceae ; Forests ; DNA, Ancient ; *Calculi ; },
abstract = {Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.},
}

Humans
Animals
*Fruit
Plants, Edible
Pollen
Poaceae
Forests
DNA, Ancient
*Calculi

@article {pmid36539480,
year = {2022},
author = {Young, JM and Liddicoat, C and van Dijk, KJ and Tabernero, P and Caillet, C and White, NJ and Linacre, A and Austin, JJ and Newton, PN},
title = {Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets-a pilot study of the pharmabiome.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {21997},
pmid = {36539480},
issn = {2045-2322},
support = {202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; },
abstract = {Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain diverse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven samples of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the 'pharmabiome' shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.},
}

@article {pmid36537881,
year = {2022},
author = {Muktupavela, RA and Petr, M and Ségurel, L and Korneliussen, T and Novembre, J and Racimo, F},
title = {Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.73767},
pmid = {36537881},
issn = {2050-084X},
support = {R01 GM132383/NH/NIH HHS/United States ; 951385/ERC_/European Research Council/International ; },
abstract = {Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.},
}

@article {pmid36531224,
year = {2022},
author = {Xiang, H and Wang, Z and Yang, L and Zhang, X and Zhao, X},
title = {Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1000123},
pmid = {36531224},
issn = {1664-8021},
abstract = {Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10[-3] ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.},
}

@article {pmid36525814,
year = {2022},
author = {Bardan, F and Higgins, D and Austin, JJ},
title = {A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102822},
doi = {10.1016/j.fsigen.2022.102822},
pmid = {36525814},
issn = {1878-0326},
abstract = {Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.},
}

@article {pmid36525576,
year = {2022},
author = {de Flamingh, A and Rivera-Colón, AG and Gnoske, TP and Kerbis Peterhans, JC and Catchen, J and Malhi, RS and Roca, AL},
title = {Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esac065},
pmid = {36525576},
issn = {1465-7333},
abstract = {Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.},
}

@article {pmid36476770,
year = {2022},
author = {Callaway, E},
title = {Oldest-ever DNA shows mastodons roamed Greenland 2 million years ago.},
journal = {Nature},
volume = {612},
number = {7940},
pages = {384},
pmid = {36476770},
issn = {1476-4687},
mesh = {Animals ; Fossils ; Greenland ; *Mastodons/genetics ; *DNA, Ancient/analysis ; History, Ancient ; },
}

Animals
Fossils
Greenland
*Mastodons/genetics
*DNA, Ancient/analysis
History, Ancient

@article {pmid36520391,
year = {2023},
author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T},
title = {Analysis of Ancient Microbial DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {103-131},
pmid = {36520391},
issn = {1940-6029},
abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.},
}

@article {pmid36518622,
year = {2022},
author = {Anderson, LA},
title = {Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.},
journal = {Ecology and evolution},
volume = {12},
number = {12},
pages = {e9518},
doi = {10.1002/ece3.9518},
pmid = {36518622},
issn = {2045-7758},
abstract = {Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.},
}

@article {pmid36517229,
year = {2022},
author = {Rohland, N and Mallick, S and Mah, M and Maier, R and Patterson, N and Reich, D},
title = {Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276728.122},
pmid = {36517229},
issn = {1549-5469},
abstract = {The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.},
}

@article {pmid36516232,
year = {2022},
author = {Söylev, A and Çokoglu, SS and Koptekin, D and Alkan, C and Somel, M},
title = {CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.},
journal = {PLoS computational biology},
volume = {18},
number = {12},
pages = {e1010788},
doi = {10.1371/journal.pcbi.1010788},
pmid = {36516232},
issn = {1553-7358},
abstract = {To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.},
}

@article {pmid36514938,
year = {2022},
author = {Rannamäe, E and Saarma, U and Kantanen, J and Bläuer, A},
title = {Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.},
journal = {Animal genetics},
volume = {},
number = {},
pages = {},
doi = {10.1111/age.13281},
pmid = {36514938},
issn = {1365-2052},
abstract = {Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.},
}

@article {pmid36513080,
year = {2022},
author = {Peltola, S and Majander, K and Makarov, N and Dobrovolskaya, M and Nordqvist, K and Salmela, E and Onkamo, P},
title = {Genetic admixture and language shift in the medieval Volga-Oka interfluve.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.036},
pmid = {36513080},
issn = {1879-0445},
abstract = {The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.[1][,][2][,][3] A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9[th] century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.[4][,][5][,][6] In the 10[th]-11[th] centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.[3] This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.},
}

@article {pmid36510283,
year = {2022},
author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B},
title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {250},
pmid = {36510283},
issn = {1474-760X},
support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.

RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.

CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.},
}

@article {pmid36494546,
year = {2022},
author = {Forshaw, R},
title = {Dental calculus - oral health, forensic studies and archaeology: a review.},
journal = {British dental journal},
volume = {233},
number = {11},
pages = {961-967},
doi = {10.1038/s41415-022-5266-7},
pmid = {36494546},
issn = {1476-5373},
abstract = {Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.},
}

@article {pmid36493775,
year = {2022},
author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M},
title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.034},
pmid = {36493775},
issn = {1879-0445},
abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.},
}

@article {pmid36493597,
year = {2022},
author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J},
title = {Reassessment of the human mandible from Banyoles (Girona, Spain).},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103291},
doi = {10.1016/j.jhevol.2022.103291},
pmid = {36493597},
issn = {1095-8606},
abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.},
}

@article {pmid36481947,
year = {2022},
author = {Bundell, S},
title = {Record-breaking ancient DNA found in frozen soil.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-04398-6},
pmid = {36481947},
issn = {1476-4687},
}

@article {pmid36481704,
year = {2022},
author = {Zhang, J and Shi, K and Paerl, HW and Rühland, KM and Yuan, Y and Wang, R and Chen, J and Ge, M and Zheng, L and Zhang, Z and Qin, B and Liu, J and Smol, JP},
title = {Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change.},
journal = {Water research},
volume = {229},
number = {},
pages = {119435},
doi = {10.1016/j.watres.2022.119435},
pmid = {36481704},
issn = {1879-2448},
abstract = {Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.},
}

@article {pmid36472532,
year = {2022},
author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K},
title = {Ecology, not host phylogeny, shapes the oral microbiome in closely related species.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac263},
pmid = {36472532},
issn = {1537-1719},
abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through dietary differences. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.},
}

@article {pmid36465121,
year = {2022},
author = {Ma, X and Xu, S},
title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105614},
pmid = {36465121},
issn = {2589-0042},
abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.},
}

@article {pmid36463384,
year = {2022},
author = {Wang, K and Bleasdale, M and Le Moyne, C and Freund, C and Krause, J and Boivin, N and Schiffels, S},
title = {4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20939},
pmid = {36463384},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient ; Africa, Eastern ; *Hair ; Sudan ; Body Remains ; },
abstract = {Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.},
}

Humans
*DNA, Ancient
Africa, Eastern
*Hair
Sudan
Body Remains

@article {pmid36455558,
year = {2022},
author = {Waldman, S and Backenroth, D and Harney, É and Flohr, S and Neff, NC and Buckley, GM and Fridman, H and Akbari, A and Rohland, N and Mallick, S and Olalde, I and Cooper, L and Lomes, A and Lipson, J and Cano Nistal, J and Yu, J and Barzilai, N and Peter, I and Atzmon, G and Ostrer, H and Lencz, T and Maruvka, YE and Lämmerhirt, M and Beider, A and Rutgers, LV and Renson, V and Prufer, KM and Schiffels, S and Ringbauer, H and Sczech, K and Carmi, S and Reich, D},
title = {Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14[th] century.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2022.11.002},
pmid = {36455558},
issn = {1097-4172},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14[th] century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14[th] century and highlight late medieval genetic heterogeneity no longer present in modern AJ.},
}

@article {pmid36454815,
year = {2022},
author = {Curry, A},
title = {Meeting the ancestors.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6623},
pages = {940-943},
doi = {10.1126/science.adg0308},
pmid = {36454815},
issn = {1095-9203},
mesh = {*Jews/genetics ; Population/genetics ; Germany ; Cemeteries/history ; DNA, Ancient ; Humans ; },
abstract = {DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.},
}

*Jews/genetics
Population/genetics
Germany
Cemeteries/history
DNA, Ancient
Humans

@article {pmid36450657,
year = {2022},
author = {Oh, CS and Kim, MJ and Kim, YS and Min, S and Oh, KT and Lee, SD and Shin, DH},
title = {Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.},
journal = {Anatomy & cell biology},
volume = {},
number = {},
pages = {},
doi = {10.5115/acb.22.178},
pmid = {36450657},
issn = {2093-3665},
abstract = {Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.},
}

@article {pmid36437963,
year = {2022},
author = {Charlier, P and Bourdin, V and Augias, A and Brun, L and Kenmogne, JB and Josue, E},
title = {Are museums the future of evolutionary medicine?.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1043702},
pmid = {36437963},
issn = {1664-8021},
}