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Thread: Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)

  1. #3001
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    The Genomic History of the Middle East

    The Genomic History of the Middle East
    Mohamed A. Almarri, Marc Haber, Reem A. Lootah, Pille Hallast, Saeed Al Turki, Hilary C Martin, Yali Xue, Chris Tyler-Smith
    Abstract
    The Middle East is an important region to understand human evolution and migrations, but is underrepresented in genetic studies. We generated and analysed 137 high-coverage physically-phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations, but find Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. A divergence in population size within the region starts before the Neolithic, when Levantines expanded while Arabians maintained small populations that could have derived ancestry from local epipaleolithic hunter-gatherers. All populations suffered a bottleneck overlapping the archaeologically-documented 4.2 kiloyear aridification of the area, while regional migrations increased genetic structure, and may have contributed to the spread of the Semitic languages. We identify new variants that show evidence of selection, some dating from the onset of the desert climate in the region. Our results thus provide detailed insights into the genomic and selective histories of the Middle East.

    *** sorry wrong forum, no new ancient samples in this paper ****
    A thread to discuss the paper:
    https://anthrogenica.com/showthread....he-Middle-East
    Last edited by pmokeefe; 10-19-2020 at 03:40 PM.
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  3. #3002
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    DNA testing sheds light on old Viking murder mystery

    DNA testing sheds light on old Viking murder mystery
    Almost 40 years after the famous ‘Gerdrupgraven’ discovery was made near Roskilde, archaeologists uncover key piece of evidence
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  5. #3003
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    Diet in Bronze Age pastoral communities from the S. Russian steppes, N. Caucasus

    Diet and subsistence in Bronze Age pastoral communities from the southern Russian steppes and the North Caucasus
    Corina Knipper ,Sabine Reinhold ,Julia Gresky,Nataliya Berezina,Claudia Gerling,Sandra L. Pichler,Alexandra P. Buzhilova,Anatoly R. Kantorovich,Vladimir E. Maslov,Vladimira G. Petrenko,Sergey V. Lyakhov,Alexey A. Kalmykov,Andrey B. Belinskiy,Svend Hansen ,Kurt W. Alt
    Abstract
    The flanks of the Caucasus Mountains and the steppe landscape to their north offered highly productive grasslands for Bronze Age herders and their flocks of sheep, goat, and cattle. While the archaeological evidence points to a largely pastoral lifestyle, knowledge regarding the general composition of human diets and their variation across landscapes and during the different phases of the Bronze Age is still restricted. Human and animal skeletal remains from the burial mounds that dominate the archaeological landscape and their stable isotope compositions are major sources of dietary information. Here, we present stable carbon and nitrogen isotope data of bone collagen of 105 human and 50 animal individuals from the 5th millennium BC to the Sarmatian period, with a strong focus on the Bronze Age and its cultural units including Maykop, Yamnaya, Novotitorovskaya, North Caucasian, Catacomb, post-Catacomb and late Bronze Age groups. The samples comprise all inhumations with sufficient bone preservation from five burial mound sites and a flat grave cemetery as well as subsamples from three further sites. They represent the Caucasus Mountains in the south, the piedmont zone and Kuban steppe with humid steppe and forest vegetation to its north, and more arid regions in the Caspian steppe. The stable isotope compositions of the bone collagen of humans and animals varied across the study area and reflect regional diversity in environmental conditions and diets. The data agree with meat, milk, and/or dairy products from domesticated herbivores, especially from sheep and goats having contributed substantially to human diets, as it is common for a largely pastoral economy. This observation is also in correspondence with the faunal remains observed in the graves and offerings of animals in the mound shells. In addition, foodstuffs with elevated carbon and nitrogen isotope values, such as meat of unweaned animals, fish, or plants, also contributed to human diets, especially among communities living in the more arid landscapes. The regional distinction of the animal and human data with few outliers points to mobility radii that were largely concentrated within the environmental zones in which the respective sites are located. In general, dietary variation among the cultural entities as well as regarding age, sex and archaeologically indicated social status is only weakly reflected. There is, however, some indication for a dietary shift during the Early Bronze Age Maykop period.

    S1 Table.
    A. Archaeological contexts as well as carbon and nitrogen stable isotope data of human remains. The table lists short descriptions of the grave features, burial inventory, archaeological cultural affiliation, radiocarbon and dendrochronological dates, sampled skeletal element, results of the elemental and stable isotope analysis, age and sex information as well as ancestry groups, mtDNA and Y-chromosome haplogroups according to Wang et al. [7] of each burial. B. Archaeological contexts as well as carbon and nitrogen stable isotope data of animal remains. The table lists the contextual information, animal species, archaeological cultural information, radiocarbon dates, skeletal element as well as the results of the elemental and stable isotope analysis of each analyzed specimen.

    https://doi.org/10.1371/journal.pone.0239861.s007
    (XLSX)

    NOTE: No new DNA samples included.
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  7. #3004
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    Isotopic & genomic evidence from Tell Atchana (Alalakh) during the 2nd millennium BC

    Human mobility at Tell Atchana (Alalakh) during the 2nd millennium BC: integration of isotopic and genomic evidence
    Tara Ingman, Stefanie Eisenmann, Eirini Skourtanioti, Murat Akar, Jana Ilgner, Guido Alberto Gnecchi Ruscone, Petrus le Roux, Rula Shafiq, Gunnar U. Neumann, Marcel Keller, Cäcilia Freund, Sara Marzo, Mary Lucas, Johannes Krause, Patrick Roberts, K. Aslıhan Yener, Philipp W. Stockhammer

    Abstract
    The Middle and Late Bronze Age Near East, a period roughly spanning the second millennium BC (ca. 2000-1200 BC), is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh), situated in the northern Levant, we explore the role of mobility at the capital of a regional kingdom. We generated strontium isotope data for 53 individuals, oxygen isotope data for 77 individuals, and added ancient DNA data from 9 new individuals to a recently published dataset of 28 individuals. A dataset like this, from a single site in the Near East, is thus far unparalleled in terms of both its breadth and depth, providing the opportunity to simultaneously obtain an in-depth view of individual mobility and also broader demographic insights into the resident population. The DNA data reveals a very homogeneous gene pool, with only one outlier. This picture of an overwhelmingly local ancestry is consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be ‘non-local’. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.
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  9. #3005
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    A systematic investigation of human DNA preservation in medieval skeletons

    Published: 26 October 2020

    Abstract
    Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.

    https://www.nature.com/articles/s41598-020-75163-w

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  11. #3006
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    A genomic and historical synthesis of plague in 18th century Eurasia

    A genomic and historical synthesis of plague in 18th century Eurasia
    Meriam Guellil, Oliver Kersten, Amine Namouchi, Stefania Luciani, Isolina Marota, Caroline A. Arcini, Elisabeth Iregren, Robert A. Lindemann, Gunnar Warfvinge, Lela Bakanidze, Lia Bitadze, Mauro Rubini, Paola Zaio, Monica Zaio, Damiano Neri, N. C. Stenseth, and Barbara Bramanti
    Significance
    The spread and evolution of plague have been under debate in the past few years. However, very little is known of the dynamics of the plague pathogen, Yersinia pestis, during the last phase of the Second Plague Pandemic in Europe (18th and 19th century). We present nine ancient Y. pestis genomes from the Second Plague Pandemic. CHE1 is the first Second Plague Pandemic genome from the Caucasus region, an area that houses plague wildlife reservoirs to this day, making it a key strain to help elucidate the origin of Medieval and Early Modern plague. Our study documents the importance of a noneurocentric approach to historical plague dynamics and proposes an origin of plague introductions outside of Europe.

    Abstract
    Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

    Plague18th.jpg
    Last edited by pmokeefe; 10-26-2020 at 08:32 PM.
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    A curated dataset of modern and ancient high-coverage shotgun human genomes.

    A curated dataset of modern and ancient high-coverage shotgun human genomes.
    Pierpaolo Maisano Delser, Eppie R Jones, Anahit Hovhannisyan, Lara Cassidy, Ron Pinhasi, Andrea Manica

    Abstract
    Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of capture SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain type of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 34 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 73,435,604 sites called across 18 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

    A curated dataset of modern and ancient high-coverage shotgun human genomes.png
    Figure 1: Geographic distribution of samples included in the dataset. Population
    acronyms are reported in Table 2.
    Last edited by pmokeefe; 10-27-2020 at 06:45 PM.
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  15. #3008
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    Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

    https://www.nature.com/articles/s415...75387-w#MOESM1

    Ruoyun Hui, Eugenia D’Atanasio, Lara M. Cassidy, Christiana L. Scheib & Toomas Kivisild

    Abstract
    Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05–1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes.

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  17. #3009
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    Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan

    Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau
    Zhang et al.

    A timeline of cave dwellers in sediment
    Two archaic lineages overlapped with modern humans outside of Africa: the well-studied Neanderthals and their more mysterious cousins, the Denisovans. Denisovan remains are rare, being limited to Denisovan Cave in Siberia and a putative, undated jaw from Tibet. However, there is evidence for multiple introgressions from Denisovans into modern-day humans, especially in Australasian populations. By examining the sediment of Baishiya Karst Cave located on a high plateau in Tibet, Zhang et al. identified ancient mitochondrial DNA from Denisovans indicating their presence at about 100 thousand, 60 thousand, and possibly 45 thousand years ago. This finding provides insight into the timing and distribution of Denisovans in Asia and extends the time of occupation of the Tibetan plateau by hominins.

    Abstract
    A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.


    Also published in the same issue of Science:
    Denisovan ancestry and population history of early East Asians
    the preprint has already been discussed here:
    https://anthrogenica.com/showthread....-from-Mongolia

    Overview of the two Denisovan papers in Science:
    Denisovan DNA found in cave on Tibetan Plateau
    Ann Gibbons
    Last edited by pmokeefe; 10-29-2020 at 06:55 PM.
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  19. #3010
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    Origins and genetic legacy of prehistoric dogs
    Bergström et al.
    --- also has extensive discussion of ancient human DNA and correlations with dogs

    Discussion thread for the paper here:
    https://anthrogenica.com/showthread....ehistoric-dogs
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