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      High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor

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          Abstract

          Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats ( Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.

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          Massive migration from the steppe was a source for Indo-European languages in Europe

          We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.
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            The formation of human populations in South and Central Asia

            By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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              Ancient DNA: do it right or not at all.

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                21 May 2020
                2020
                : 15
                : 5
                : e0233333
                Affiliations
                [1 ] Graduate School “Human Development in Landscapes”, Kiel University, Kiel, Germany
                [2 ] Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany
                [3 ] Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, United States of America
                [4 ] Archaeological Expertise, LLC, Almaty, Kazakhstan
                [5 ] International Institute for Central Asian Studies, Samarkand, Uzbekistan
                [6 ] Margulan Institute of Archaeology, Almaty, Kazakhstan
                [7 ] School of Humanities and Social Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
                [8 ] The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul, Russia
                [9 ] Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
                [10 ] Department of Archaeology, Vilnius University, Vilnius, Lithuania
                [11 ] National Museum of Mongolia, Ulaanbaatar, Mongolia
                [12 ] Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, United States of America
                [13 ] Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
                [14 ] Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
                University at Buffalo - The State University of New York, UNITED STATES
                Author notes

                Competing Interests: Author DV is affiliated with Archaeological Expertise, LLC, but this does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents or products in development at Archaeological Expertise, LLC that are relevant to this work

                [¤]

                Current address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany

                Author information
                http://orcid.org/0000-0002-8377-468X
                http://orcid.org/0000-0002-2010-9092
                http://orcid.org/0000-0001-9536-3856
                http://orcid.org/0000-0002-1649-336X
                Article
                PONE-D-19-29815
                10.1371/journal.pone.0233333
                7241827
                32437372
                5d4742ab-2fe8-4f56-a525-b5635d270878
                © 2020 Hermes et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 25 October 2019
                : 1 May 2020
                Page count
                Figures: 3, Tables: 3, Pages: 20
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, Graduate School "Human Development in Landscapes";
                Award ID: Deutsche Forschungsgemeinschaft GSC: 208
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100010663, H2020 European Research Council;
                Award ID: 772957
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004895, European Social Fund;
                Award ID: 09.3.3-LMT-K-712
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 0211431
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 0535341
                Award Recipient :
                Funded by: Western Kentucky University (US)
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 1132090
                Award Recipient :
                Funded by: Washington University in St. Louis
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100006769, Russian Science Foundation;
                Award ID: 16-18-10033
                Award Recipient :
                This research was supported by the doctoral fellowship of T.R.H. at the Graduate School “Human Development in Landscapes” (German Research Foundation: GSC 208). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant-772957/ASIAPAST held by C.A.M.). Archaeological research at Tasbas and Dali was funded by Washington University in St. Louis and the United States National Science Foundation (no. 1132090 held by P.N.D.D and M.D.F.). Archaeological research at Begash was funded by United States National Science Foundation (nos. 0211431 and 0535341 held by M.D.F.). Archaeological research at Uch-Kurbu was funded by the European Social Fund according to the activity “Improvement of researchers” qualification by implementing world-class R&D projects’ of Measure (no. 09.3.3-LMT-K-712 held by G.M.M.). Archaeological research at Zamiin-Utug was funded by Western Kentucky University (J-L.H.). This research was also supported by the Russian Science Foundation, project no. 16-18-10033 “Formation and Evolution of the Subsistence System of the Nomadic Societies of Altai and Adjacent Territories in Late Antiquity and the Middle Ages: Complex Reconstruction” held by A.A.T. Archaeological Expertise, LLC provided support in the form of salaries for author D.V., but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.
                Categories
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