Nature. 2014 Sep 18;513(7518):409-13. doi: 10.1038/nature13673.

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Lazaridis I¹, Patterson N², Mittnik A³, Renaud G⁴, Mallick S¹, Kirsanow K⁵, Sudmant PH⁶, Schraiber JG⁷, Castellano S⁴, Lipson M⁸, Berger B⁹, Economou C¹⁰, Bollongino R⁵, Fu Q¹¹, Bos KI³, Nordenfelt S¹, Li H¹, de Filippo C⁴, Prüfer K⁴, Sawyer S⁴, Posth C³, Haak W¹², Hallgren F¹³, Fornander E¹³, Rohland N¹, Delsate D¹⁴, Francken M¹⁵, Guinet JM¹⁶, Wahl J¹⁷, Ayodo G¹⁸, Babiker HA¹⁹, Bailliet G²⁰, Balanovska E²¹, Balanovsky O²², Barrantes R²³, Bedoya G²⁴, Ben-Ami H²⁵, Bene J²⁶, Berrada F²⁷, Bravi CM²⁰, Brisighelli F²⁸, Busby GB²⁹, Cali F³⁰, Churnosov M³¹, Cole DE³², Corach D³³, Damba L³⁴, van Driem G³⁵, Dryomov S³⁶, Dugoujon JM³⁷, Fedorova SA³⁸, Gallego Romero I³⁹, Gubina M³⁴, Hammer M⁴⁰, Henn BM⁴¹, Hervig T⁴², Hodoglugil U⁴³, Jha AR³⁹, Karachanak-Yankova S⁴⁴, Khusainova R⁴⁵, Khusnutdinova E⁴⁵, Kittles R⁴⁶, Kivisild T⁴⁷, Klitz W⁴⁸, Kučinskas V⁴⁹, Kushniarevich A⁵⁰, Laredj L⁵¹, Litvinov S⁵², Loukidis T⁵³, Mahley RW⁵⁴, Melegh B²⁶, Metspalu E⁵⁵, Molina J⁵⁶, Mountain J⁵⁷, Näkkäläjärvi K⁵⁸, Nesheva D⁴⁴, Nyambo T⁵⁹, Osipova L³⁴, Parik J⁵⁵, Platonov F⁶⁰, Posukh O³⁴, Romano V⁶¹, Rothhammer F⁶², Rudan I⁶³, Ruizbakiev R⁶⁴, Sahakyan H⁶⁵, Sajantila A⁶⁶, Salas A⁶⁷, Starikovskaya EB³⁶, Tarekegn A⁶⁸, Toncheva D⁴⁴, Turdikulova S⁶⁹, Uktveryte I⁴⁹, Utevska O⁷⁰, Vasquez R⁷¹, Villena M⁷¹, Voevoda M⁷², Winkler CA⁷³, Yepiskoposyan L⁷⁴, Zalloua P⁷⁵, Zemunik T⁷⁶, Cooper A¹², Capelli C⁷⁷, Thomas MG⁷⁸, Ruiz-Linares A⁷⁸, Tishkoff SA⁷⁹, Singh L⁸⁰, Thangaraj K⁸¹, Villems R⁸², Comas D⁸³, Sukernik R³⁶, Metspalu M⁵⁰, Meyer M⁴, Eichler EE⁸⁴, Burger J⁵, Slatkin M⁴⁸, Pääbo S⁴, Kelso J⁴, Reich D⁸⁵, Krause J⁸⁶.

Author information

1: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
2: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
3: Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany.
4: Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
5: Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany.
6: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
7: 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.
8: Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
9: 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.
10: Archaeological Research Laboratory, Stockholm University, 114 18, Sweden.
11: 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.
12: Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
13: The Cultural Heritage Foundation, Västerås 722 12, Sweden.
14: 1] National Museum of Natural History, L-2160, Luxembourg. [2] National Center of Archaeological Research, National Museum of History and Art, L-2345, Luxembourg.
15: Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen D-72070, Germany.
16: National Museum of Natural History, L-2160, Luxembourg.
17: State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz D-78467, Germany.
18: Center for Global Health and Child Development, Kisumu 40100, Kenya.
19: 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.
20: Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina.
21: Research Centre for Medical Genetics, Moscow 115478, Russia.
22: 1] Research Centre for Medical Genetics, Moscow 115478, Russia. [2] Vavilov Institute for General Genetics, Moscow 119991, Russia.
23: Escuela de Biología, Universidad de Costa Rica, San José 2060, Costa Rica.
24: Institute of Biology, Research group GENMOL, Universidad de Antioquia, Medellín, Colombia.
25: Rambam Health Care Campus, Haifa 31096, Israel.
26: Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs H-7624, Hungary.
27: Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane 53000, Morocco.
28: Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
29: 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.
30: Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina 94018, Italy.
31: Belgorod State University, Belgorod 308015, Russia.
32: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada.
33: Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, 1113 CABA, Argentina.
34: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
35: Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
36: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia.
37: Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse 31000, France.
38: North-Eastern Federal University and Yakut Research Center of Complex Medical Problems, Yakutsk 677013, Russia.
39: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
40: ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA.
41: Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA.
42: Department of Clinical Science, University of Bergen, Bergen 5021, Norway.
43: NextBio, Illumina, Santa Clara, California 95050, USA.
44: Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
45: 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.
46: College of Medicine, University of Arizona, Tucson, Arizona 85724, USA.
47: Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK.
48: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
49: Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania.
50: Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia.
51: Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.
52: 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.
53: 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.).
54: Gladstone Institutes, San Francisco, California 94158, USA.
55: Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
56: Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala.
57: Research Department, 23andMe, Mountain View, California 94043, USA.
58: Cultural Anthropology Program, University of Oulu, Oulu 90014, Finland.
59: Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam 65001, Tanzania.
60: Research Institute of Health, North-Eastern Federal University, Yakutsk 677000, Russia.
61: Dipartimento di Fisica e Chimica, Università di Palermo, Palermo 90128, Italy.
62: 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.
63: Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh EH8 9AG, UK.
64: 1] Institute of Immunology, Academy of Science, Tashkent 70000, Uzbekistan. [2].
65: 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.
66: 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.
67: 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.
68: Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK.
69: Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent 100125, Uzbekistan.
70: Department of Genetics and Cytology, V. N. Karazin Kharkiv National University, Kharkiv 61077, Ukraine.
71: 1] Instituto Boliviano de Biología de la Altura, Universidad Mayor de San Andrés, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomás Frías, Potosí, Bolivia.
72: 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.
73: Basic Research Laboratory, NCI, NIH, Frederick National Laboratory, Leidos Biomedical, Frederick, Maryland 21702, USA.
74: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
75: 1] Lebanese American University, School of Medicine, Beirut 13-5053, Lebanon. [2] Harvard School of Public Health, Boston, Massachusetts 02115, USA.
76: Department of Medical Biology, University of Split, School of Medicine, Split 21000, Croatia.
77: Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
78: Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
79: Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
80: 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.).
81: CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
82: 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.
83: Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
84: 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
85: 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.
86: 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.

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 analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.