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Thread: New DNA Papers

  1. #1101
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    https://www.biorxiv.org/content/10.1101/694299v1

    West Asian sources of the Eurasian component in Ethiopians: a reassessment

    Ludovica Molinaro, Francesco Montinaro, Toomas Kivisild, Luca Pagani

    doi: https://doi.org/10.1101/694299

    Abstract

    Previous genome-scale studies of populations living today in Ethiopia have found evidence of recent gene flow from an Eurasian source, dating to the last 3,000 years. Haplotype and genotype data based analyses of modern and ancient data (aDNA) have considered Sardinia-like proxy, broadly Levantine or Neolithic Levantine populations as a range of possible sources for this gene flow. Given the ancient nature of this gene flow and the extent of population movements and replacements that affected West Asia in the last 3000 years, aDNA evidence would seem as the best proxy for determining the putative population source. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ~50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called NAF for Non African) and ancient and modern proxies area after having extracted NAF from Ethiopians through ancestry deconvolution, and unveil a genomic signature compatible with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization.

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  3. #1102
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    Mozambican genetic variation provides new insights into the Bantu expansion

    Mozambican genetic variation provides new insights into the Bantu expansion

    Armando Semo, Magdalena Gayà-Vidal, Cesar Fortes-Lima, Bérénice Alard, Sandra Oliveira, João Almeida, António Prista, Albertino Damasceno, Anne-Maria Fehn, Carina Schlebusch, Jorge Rocha

    Abstract
    The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ~1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a "late split" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.
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  5. #1103
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    Late Pleistocene exploration and settlement of the Americas by modern humans

    Late Pleistocene exploration and settlement of the Americas by modern humans in Science.
    Michael R. Waters

    Abstract
    North and South America were the last continents to be explored and settled by modern humans at the end of the Pleistocene. Genetic data, derived from contemporary populations and ancient individuals, show that the first Americans originated from Asia and after several population splits moved south of the continental ice sheets that covered Canada sometime between ~17.5 and ~14.6 thousand years (ka) ago. Archaeological evidence shows that geographically dispersed populations lived successfully, using biface, blade, and osseous technologies, in multiple places in North and South America between ~15.5 and ~14 ka ago. Regional archaeological complexes emerged by at least ~13 ka ago in North America and ~12.9 ka ago in South America. Current genetic and archaeological data do not support an earlier (pre–17.5 ka ago) occupation of the Americas.
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  7. #1104
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    Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent

    Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent in Science

    Abstract
    Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.
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  9. #1105
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    https://www.sciencedirect.com/scienc...72497319301097

    Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia

    Renata Jankova1, Maria Geppert2, Alja Videtic Paska3, Sascha Willuweit2, LutzRoewer2

    https://doi.org/10.1016/j.fsigen.2019.07.007

    Highlights

    • Three major ethno-linguistic groups in the Republic of North Macedonia were analyzed for 17 Y-SNPs and 27 Y-STRs
    • The haplogroup analysis revealed different dominant male ancestral lineages for the three subpopulations
    • The combined Y-SNP/Y-STR analyses place the North Macedonians in the genetic landscape of the Balkans and Southeastern Europe
    • This study adds high-resolution Y-STR profiles categorized by phylogenetic informative Y-SNPs from North Macedonia to the Y chromosome reference database (YHRD)

    Abstract

    A total of 314 individuals representing the three major ethno-linguistic groups (ethnic Macedonians, Albanians and Turks) in the Republic of North Macedonia were analyzed for Y-SNPs and Y-STRs using minisequencing and fragment analysis. The haplogroup composition differed remarkably between the three groups with dominance of haplogroup I2 in ethnic Macedonians (28.1%), E1b in Albanians (35.3%) and J2a (34.9%) in Turks, respectively. The haplotype analysis using the YFilerPlus kit disclosed a significant reduction in diversity values (DC, GD) for the Turkish subgroup compared to the Macedonian and Albanian speaking populations. The Y-STR based population analysis revealed a similarity of ethnic Macedonians with neighboring Serbians and Bulgarians. The same holds true for the Albanian speakers from Macedonia and Albania, whereas the Turkish minority in North Macedonia stands apart from the population in Turkey.

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  11. #1106
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    Genetics shifts in the Western Eurasian Steppe Associated with Scythian Dominance

    Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance


    NOTE: the preprint has been available for some time and already mentioned on this board. This is the published version. The full paper seems to be behind a paywall at the previous URL, but there's a pdf freely available here, looks like it might be the published version, but not completely sure about that.


    Highlights
    • 31 new ancient genomes help compare the Scythians to pre- and postdating cultures
    • Scythian dominance brought along an increase of eastern ancestry across the steppe
    • Results imply some demic diffusion in the spread of the Scythian culture
    • Genetic makeup agrees with the Gothic source of post-Scythian Chernyakhiv culture


    Summary
    The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1, 2, 3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.
    Last edited by pmokeefe; 07-17-2019 at 03:19 PM.
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  13. #1107
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    Population genomics of the Viking world

    Population genomics of the Viking world

    Ashot Margaryan, Daniel John Lawson, Martin Sikora, Fernando Racimo, Simon Rasmussen, Ida Moltke, Lara Cassidy, Emil Jorsboe, Andres Ingason, Mikkel Winther Pedersen, Thorfinn Sand Korneliussen, Helene Wilhelmson, Magdalena Maria Bus, Peter de Barros Damgaard, Rui Martiniano, Gabriel Renaud, Claude Bherer, J. Victor Moreno-Mayar, Anna Katerina Fotakis, Marie Allen, Martyna Molak, Enrico Cappellini, Gabriele Scorrano, Alexandra Buzhilova, Allison Mary Fox, Anders Albrechtsen, Berit Schutz, Birgitte Skar, Caroline Ahlstrom Arcini, Ceri G. Falys, Charlotte Hedenstierna-Jonson, Dariusz Blaszczyk, Denis Pezhemsky, Gordon Turner-Walker, Hildur Gestsdottir, Inge Lundstrom, Ingrid Gustin, Ingrid Mainland, Inna Potekhina, Italo Maria Muntoni, Jade Cheng, Jesper Stenderup, Jilong Ma, Julie Gibson, Jyri Peets, Jorgen Gustafsson, Katrine Hojholt Iversen, Linzi Simpson, Lisa Mariann Strand, Louise Katherine Loe, Maeve Sikora, Marek Florek, Maria Vretemark, Mark Redknap, Monika Bajka, Tamara Pushkina, Morten Sovso, Natalia Grigoreva, Tom Christensen, Ole Thirup Kastholm, Otto Christian Uldum, Pasquale Favia, Per Holck, Raili Allmae, Sabine Sten, Simun Vilhelm Arge, Sturla Ellingvag, Vayacheslav Moiseyev, Wieslaw Bogdanowicz, Yvonne Magnusson, Ludovic Orlando, Daniel G. Bradley, Marie Louise Schjellerup Jorkov, Jette Arneborg, Niels Lynnerup, Neil Price, M. Thomas Pius Gilbert, Morten E. Allentoft, Jan Bill, Soren Michael Sindbek, Lotte Hedeager, Kristian Kristiansen, Rasmus Nielsen, Thomas Werge, Eske Willerslev

    Abstract
    The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.
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