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Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 2014; 513:409-13. [PMID: 25230663 PMCID: PMC4170574 DOI: 10.1038/nature13673] [Citation(s) in RCA: 737] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/11/2014] [Indexed: 12/19/2022]
Abstract
We sequenced the genomes of a ~7,000 year old farmer from Germany and eight
~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other
ancient genomes1–4 with 2,345 contemporary humans to show that most
present 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) related to Upper Paleolithic Siberians3, who 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 ~44% ancestry from a “Basal Eurasian”
population that split prior to the diversification of other non-African lineages.
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Affiliation(s)
- Iosif Lazaridis
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alissa Mittnik
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Gabriel Renaud
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Swapan Mallick
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Karola Kirsanow
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Joshua G Schraiber
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Sergi Castellano
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Lipson
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bonnie Berger
- 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [2] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christos Economou
- Archaeological Research Laboratory, Stockholm University, 114 18, Sweden
| | - Ruth Bollongino
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Qiaomei Fu
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. [3] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China
| | - Kirsten I Bos
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Susanne Nordenfelt
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Heng Li
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Susanna Sawyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Wolfgang Haak
- Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Elin Fornander
- The Cultural Heritage Foundation, Västerås 722 12, Sweden
| | - Nadin Rohland
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Dominique Delsate
- 1] National Museum of Natural History, L-2160, Luxembourg. [2] National Center of Archaeological Research, National Museum of History and Art, L-2345, Luxembourg
| | - Michael Francken
- Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen D-72070, Germany
| | | | - Joachim Wahl
- State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz D-78467, Germany
| | - George Ayodo
- Center for Global Health and Child Development, Kisumu 40100, Kenya
| | - Hamza A Babiker
- 1] Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. [2] Biochemistry Department, Faculty of Medicine, Sultan Qaboos University, Alkhod, Muscat 123, Oman
| | - Graciela Bailliet
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina
| | | | - Oleg Balanovsky
- 1] Research Centre for Medical Genetics, Moscow 115478, Russia. [2] Vavilov Institute for General Genetics, Moscow 119991, Russia
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José 2060, Costa Rica
| | - Gabriel Bedoya
- Institute of Biology, Research group GENMOL, Universidad de Antioquia, Medellín, Colombia
| | | | - Judit Bene
- Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Fouad Berrada
- Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane 53000, Morocco
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina
| | - Francesca Brisighelli
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - George B J Busby
- 1] Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Francesco Cali
- Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina 94018, Italy
| | | | - David E C Cole
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, 1113 CABA, Argentina
| | - Larissa Damba
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse 31000, France
| | - Sardana A Fedorova
- North-Eastern Federal University and Yakut Research Center of Complex Medical Problems, Yakutsk 677013, Russia
| | - Irene Gallego Romero
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Michael Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
| | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | | | - Aashish R Jha
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Rita Khusainova
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Elza Khusnutdinova
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Rick Kittles
- College of Medicine, University of Arizona, Tucson, Arizona 85724, USA
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - William Klitz
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania
| | | | - Leila Laredj
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Sergey Litvinov
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia. [3] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia
| | - Theologos Loukidis
- 1] Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.)
| | | | - Béla Melegh
- Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala
| | - Joanna Mountain
- Research Department, 23andMe, Mountain View, California 94043, USA
| | | | - Desislava Nesheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam 65001, Tanzania
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jüri Parik
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Fedor Platonov
- Research Institute of Health, North-Eastern Federal University, Yakutsk 677000, Russia
| | - Olga Posukh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo 90128, Italy
| | - Francisco Rothhammer
- 1] Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile. [2] Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile, Santiago 8320000, Chile. [3] Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh EH8 9AG, UK
| | - Ruslan Ruizbakiev
- 1] Institute of Immunology, Academy of Science, Tashkent 70000, Uzbekistan. [2]
| | - Hovhannes Sahakyan
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. [2] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Antti Sajantila
- 1] Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki 00014, Finland. [2] Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galcia 15872, Spain
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Ayele Tarekegn
- Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Shahlo Turdikulova
- Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Ingrida Uktveryte
- Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania
| | - Olga Utevska
- Department of Genetics and Cytology, V. N. Karazin Kharkiv National University, Kharkiv 61077, Ukraine
| | - René Vasquez
- 1] Instituto Boliviano de Biología de la Altura, Universidad Mayor de San Andrés, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomás Frías, Potosí, Bolivia
| | - Mercedes Villena
- 1] Instituto Boliviano de Biología de la Altura, Universidad Mayor de San Andrés, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomás Frías, Potosí, Bolivia
| | - Mikhail Voevoda
- 1] Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. [2] Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk 630089, Russia. [3] Novosibirsk State University, Novosibirsk 630090, Russia
| | - Cheryl A Winkler
- Basic Research Laboratory, NCI, NIH, Frederick National Laboratory, Leidos Biomedical, Frederick, Maryland 21702, USA
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Pierre Zalloua
- 1] Lebanese American University, School of Medicine, Beirut 13-5053, Lebanon. [2] Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split 21000, Croatia
| | - Alan Cooper
- Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Sarah A Tishkoff
- Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lalji Singh
- 1] CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.)
| | | | - Richard Villems
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. [3] Estonian Academy of Sciences, Tallinn 10130, Estonia
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - David Reich
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johannes Krause
- 1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany
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