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      Genomic insights into the origin of farming in the ancient Near East

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          Abstract

          We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

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          Most cited references33

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          The complete genome sequence of a Neandertal from the Altai Mountains

          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
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            A high-coverage genome sequence from an archaic Denisovan individual.

            We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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              Ancient human genomes suggest three ancestral populations for present-day Europeans

              We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                21 July 2016
                25 August 2016
                25 February 2017
                : 536
                : 7617
                : 419-424
                Affiliations
                [1 ] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [2 ] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
                [3 ] The Zinman Institute of Archaeology, University of Haifa, Haifa 3498838, Israel
                [4 ] Dept. of Anthropology, Whitman College, Walla Walla, WA 99362, USA
                [5 ] Dept. of Archaeology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
                [6 ] Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
                [7 ] School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
                [8 ] CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
                [9 ] Institute for Anthropological Research, 10000 Zagreb, Croatia
                [10 ] Dept. of Anthropology, Emory University, Atlanta, Georgia 30322, USA
                [11 ] Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge 02138, USA
                [12 ] Dept. of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
                [13 ] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
                [14 ] Dept. of Biology and Evolution, University of Ferrara, Ferrara I-44121, Italy
                [15 ] Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
                [16 ] Independent Researcher, Santpoort-Noord, The Netherlands
                [17 ] Department of Prehistory and Archaeology, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
                [18 ] French National Centre for Scientific Research, UMR 7041, 92023 Nanterre Cedex, France
                [19 ] Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, 0025 Yerevan, Republic of Armenia
                [20 ] University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
                [21 ] Israel Antiquities Authority, Jerusalem 91004, Israel
                [22 ] Dept. of Anthropology, University of Winnipeg, Winnipeg, Manitoba R3B 2E9, Canada
                [23 ] Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyoğlu, Istanbul, Turkey
                [24 ] Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Iasi 700505, Romania
                [25 ] Department of Internal Medicine and Dermatology, Clinic of Endocrinology and Nephrology, 04103 Leipzig, Germany
                [26 ] Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland
                [27 ] RCSI Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
                [28 ] Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
                [29 ] Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199 - EGID, F-59000 Lille, France
                [30 ] Department of Genomics of common disease, London Hammersmith Hospital, London W12 0HS, UK
                [31 ] Leipzig University Medical Center, IFB AdiposityDiseases, 04103 Leipzig, Germany
                [32 ] Max Planck Institute for the Science of Human History, 07745 Jena, Germany
                [33 ] Independent researcher, County Wicklow, Ireland
                [34 ] Genealogical Society of Ireland, Dún Laoghaire, County Dublin, Ireland
                [35 ] Department of Anthropology, Binghamton University, State University of New York, New York 13902, USA
                [36 ] Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
                [37 ] Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy
                [38 ] Institutul de Cercetari Biologice, Iaşi 700505, Romania
                [39 ] Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH8 9AG, Scotland
                [40 ] MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
                [41 ] Center of Excellence in Applied Biosciences, Yerevan State University, 0025 Yerevan, Republic of Armenia
                Author notes
                [*]

                Co-senior authors

                []Correspondence and requests for materials should be addressed to: I. L. ( lazaridis@ 123456genetics.med.harvard.edu ), R. P. ( ron.pinhasi@ 123456ucd.ie ), or D. R. ( reich@ 123456genetics.med.harvard.edu )
                Article
                NIHMS804247
                10.1038/nature19310
                5003663
                27459054
                fc73946a-037f-4958-81be-24330dace8f0

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