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The genetic structure of the world’s first farmers

Iosif Lazaridis, Dani Nadel, Gary Rollefson, Deborah C. Merrett, Nadin Rohland, Swapan Mallick, Daniel Fernandes, Mario Novak, Beatriz Gamarra, Kendra Sirak, Sarah Connell, Kristin Stewardson, Eadaoin Harney, Qiaomei Fu, Gloria Gonzalez-Fortes, Songül Alpaslan Roodenberg, György Lengyel, Fanny Bocquentin, Boris Gasparian, Janet M. Monge, Michael Gregg, Vered Eshed, Ahuva-Sivan Mizrahi, Christopher Meiklejohn, Fokke Gerritsen, Luminita Bejenaru, Matthias Blueher, Archie Campbell, Gianpero Cavalleri, David Comas, Philippe Froguel, Edmund Gilbert, Shona M. Kerr, Peter Kovacs, Johannes Krause, Darren McGettigan, Michael Merrigan, D. Andrew Merriwether, Seamus O’Reilly, Martin B. Richards, Ornella Semino, Michel Shamoon-Pour, Gheorghe Stefanescu, Michael Stumvoll, Anke Tönjes, Antonio Torroni, James F. Wilson, Loic Yengo, Nelli A. Hovhannisyan, Nick Patterson, Ron Pinhasi, David Reich
doi: https://doi.org/10.1101/059311
Iosif Lazaridis
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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  • For correspondence: lazaridis{at}genetics.med.harvard.edu ron.pinhasi{at}ucd.ie reich{at}genetics.med.harvard.edu
Dani Nadel
3The Zinman Institute of Archaeology, University of Haifa, Haifa 3498838, Israel
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Gary Rollefson
4Dept. of Anthropology, Whitman College, Walla Walla, WA 99362, USA
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Deborah C. Merrett
5Dept. of Archaeology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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Nadin Rohland
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Swapan Mallick
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, Burkina Faso
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Daniel Fernandes
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
8CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
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Mario Novak
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
9Institute for Anthropological Research, Zagreb 10000, Croatia
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Beatriz Gamarra
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
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Kendra Sirak
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
10Dept. of Anthropology, Emory University, Atlanta, Georgia 30322, USA
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Sarah Connell
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
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Kristin Stewardson
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, Burkina Faso
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Eadaoin Harney
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, Burkina Faso
11Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge 02138, USA
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Qiaomei Fu
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
12Dept. of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
13Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
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Gloria Gonzalez-Fortes
14Dept. of Biology and Evolution, University of Ferrara, Ferrara I-44121, Italy
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Songül Alpaslan Roodenberg
15Independent Researcher, Santpoort-Noord, The Netherlands
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György Lengyel
16Department of Prehistory and Archaeology, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
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Fanny Bocquentin
17French National Centre for Scientific Research, UMR 7041, 92023 Nanterre Cedex, France
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Boris Gasparian
18Institute of Archaeology and Ethnology,National Academy of Sciences of the Republic of Armenia, 0025 Yerevan, Republic of Armenia
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Janet M. Monge
19University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
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Michael Gregg
19University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
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Vered Eshed
20Israel Antiquities Authority, Jerusalem 91710, Israel
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Ahuva-Sivan Mizrahi
20Israel Antiquities Authority, Jerusalem 91710, Israel
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Christopher Meiklejohn
21Dept. of Anthropology, University of Winnipeg, Winnipeg, Manitoba R3B 2E9, Canada
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Fokke Gerritsen
22Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyoğlu, Istanbul, Turkey
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Luminita Bejenaru
23Alexandru Ioan Cuza University of Iasi, Romania 700505, Romania
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Matthias Blueher
24Department of Internal Medicine and Dermatology, Clinic of Endocrinology and Nephrology, 04103 Leipzig, Germany
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Archie Campbell
25Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland
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Gianpero Cavalleri
26RCSI Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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David Comas
27Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Philippe Froguel
28Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199-EGID, F-59000 Lille, France
29Department of Genomics of common disease, London Hammersmith Hospital, London W12 0HS, UK
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Edmund Gilbert
26RCSI Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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Shona M. Kerr
25Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland
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Peter Kovacs
30Leipzig University Medical Center, IFB AdiposityDiseases, 04103 Leipzig, Germany
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Johannes Krause
31Max Planck Institute for the Science of Human History, 07745 Jena, Germany
32Institute for Archaeological Sciences, Archaeo-and Palaeogenetics, University of Tubingen, Tubingen, Germany
33Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72072 Tübingen, Germany
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Darren McGettigan
34Independent research, County Wicklow, Ireland
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Michael Merrigan
35Genealogical Society of Ireland, Dún Laoghaire, County Dublin, Ireland
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D. Andrew Merriwether
36Department of Anthropology, Binghamton University, New York 13902, USA
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Seamus O’Reilly
35Genealogical Society of Ireland, Dún Laoghaire, County Dublin, Ireland
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Martin B. Richards
37Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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Ornella Semino
38Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy
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Michel Shamoon-Pour
36Department of Anthropology, Binghamton University, New York 13902, USA
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Gheorghe Stefanescu
39Institutul de Cercetari Biologice, Iaşi 700505, Romania
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Michael Stumvoll
24Department of Internal Medicine and Dermatology, Clinic of Endocrinology and Nephrology, 04103 Leipzig, Germany
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Anke Tönjes
24Department of Internal Medicine and Dermatology, Clinic of Endocrinology and Nephrology, 04103 Leipzig, Germany
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Antonio Torroni
38Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy
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James F. Wilson
40Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH8 9AG, Scotland
41MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
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Loic Yengo
28Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199-EGID, F-59000 Lille, France
29Department of Genomics of common disease, London Hammersmith Hospital, London W12 0HS, UK
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Nelli A. Hovhannisyan
42Dept. of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Republic of Armenia
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Nick Patterson
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Ron Pinhasi
7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
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  • For correspondence: lazaridis{at}genetics.med.harvard.edu ron.pinhasi{at}ucd.ie reich{at}genetics.med.harvard.edu
David Reich
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, Burkina Faso
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  • For correspondence: lazaridis{at}genetics.med.harvard.edu ron.pinhasi{at}ucd.ie reich{at}genetics.med.harvard.edu
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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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  • ↵* Co-senior authors;

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The genetic structure of the world’s first farmers
Iosif Lazaridis, Dani Nadel, Gary Rollefson, Deborah C. Merrett, Nadin Rohland, Swapan Mallick, Daniel Fernandes, Mario Novak, Beatriz Gamarra, Kendra Sirak, Sarah Connell, Kristin Stewardson, Eadaoin Harney, Qiaomei Fu, Gloria Gonzalez-Fortes, Songül Alpaslan Roodenberg, György Lengyel, Fanny Bocquentin, Boris Gasparian, Janet M. Monge, Michael Gregg, Vered Eshed, Ahuva-Sivan Mizrahi, Christopher Meiklejohn, Fokke Gerritsen, Luminita Bejenaru, Matthias Blueher, Archie Campbell, Gianpero Cavalleri, David Comas, Philippe Froguel, Edmund Gilbert, Shona M. Kerr, Peter Kovacs, Johannes Krause, Darren McGettigan, Michael Merrigan, D. Andrew Merriwether, Seamus O’Reilly, Martin B. Richards, Ornella Semino, Michel Shamoon-Pour, Gheorghe Stefanescu, Michael Stumvoll, Anke Tönjes, Antonio Torroni, James F. Wilson, Loic Yengo, Nelli A. Hovhannisyan, Nick Patterson, Ron Pinhasi, David Reich
bioRxiv 059311; doi: https://doi.org/10.1101/059311
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The genetic structure of the world’s first farmers
Iosif Lazaridis, Dani Nadel, Gary Rollefson, Deborah C. Merrett, Nadin Rohland, Swapan Mallick, Daniel Fernandes, Mario Novak, Beatriz Gamarra, Kendra Sirak, Sarah Connell, Kristin Stewardson, Eadaoin Harney, Qiaomei Fu, Gloria Gonzalez-Fortes, Songül Alpaslan Roodenberg, György Lengyel, Fanny Bocquentin, Boris Gasparian, Janet M. Monge, Michael Gregg, Vered Eshed, Ahuva-Sivan Mizrahi, Christopher Meiklejohn, Fokke Gerritsen, Luminita Bejenaru, Matthias Blueher, Archie Campbell, Gianpero Cavalleri, David Comas, Philippe Froguel, Edmund Gilbert, Shona M. Kerr, Peter Kovacs, Johannes Krause, Darren McGettigan, Michael Merrigan, D. Andrew Merriwether, Seamus O’Reilly, Martin B. Richards, Ornella Semino, Michel Shamoon-Pour, Gheorghe Stefanescu, Michael Stumvoll, Anke Tönjes, Antonio Torroni, James F. Wilson, Loic Yengo, Nelli A. Hovhannisyan, Nick Patterson, Ron Pinhasi, David Reich
bioRxiv 059311; doi: https://doi.org/10.1101/059311

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