New Results
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten I. Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George Busby, Francesco Cali, Mikhail Churnosov, David E. C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Hervig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platanov, Olga Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
doi: https://doi.org/10.1101/001552
Iosif Lazaridis
Department of Genetics, Harvard Medical School, Boston, MA, USA 02115Broad Institute of Harvard and MIT, Cambridge, MA, USA 02142
Nick Patterson
Department of Genetics, Harvard Medical School, Boston, MA, USA 02115Broad Institute of Harvard and MIT, Cambridge, MA, USA 02142
Alissa Mittnik
Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, Tübingen, Germany 72072
Gabriel Renaud
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Swapan Mallick
Department of Genetics, Harvard Medical School, Boston, MA, USA 02115Broad Institute of Harvard and MIT, Cambridge, MA, USA 02142
Peter H. Sudmant
Department of Genome Sciences, University of Washington, Seattle, WA, USA 98195
Joshua G. Schraiber
Department of Integrative Biology, University of California, Berkeley, CA 94720-3140
Sergi Castellano
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Karola Kirsanow
Johannes Gutenberg University Mainz, Institute of Anthropology, Mainz, Germany D-55128
Christos Economou
Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden 114 18
Ruth Bollongino
Johannes Gutenberg University Mainz, Institute of Anthropology, Mainz, Germany D-55128
Qiaomei Fu
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Kirsten I. Bos
Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, Tübingen, Germany 72072
Susanne Nordenfelt
Department of Genetics, Harvard Medical School, Boston, MA, USA 02115Broad Institute of Harvard and MIT, Cambridge, MA, USA 02142
Cesare de Filippo
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Kay Prüfer
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Susanna Sawyer
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Cosimo Posth
Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, Tübingen, Germany 72072
Wolfgang Haak
Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia SA 5005
Fredrik Hallgren
The Cultural Heritage Foundation, Västerås, Sweden 722 12
Elin Fornander
The Cultural Heritage Foundation, Västerås, Sweden 722 12
George Ayodo
Center for Global Health and Child Development, Kisumu, Kenya 40100
Hamza A. Babiker
Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK EH9 3JTBiochemistry Department, Faculty of Medicine, Sultan Qaboos University, Alkhod, Muscat, Oman 123
Elena Balanovska
Research Centre for Medical Genetics, Moscow, Russia 115478
Oleg Balanovsky
Research Centre for Medical Genetics, Moscow, Russia 115478Vavilov Institute for General Genetics, Moscow, Russia 119991
Haim Ben-Ami
Rambam Health Care Campus, Haifa 31096, Israel
Judit Bene
Department of Medical Genetics, and Szentagothai Research Center, University of Pécs, Pécs, Hungary 7624
Fouad Berrada
Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane, Morocco 53000
Francesca Brisighelli
Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy 00168
George Busby
Department of Zoology, University of Oxford, Oxford, UK OX1 3PSWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK OX3 7BN
Francesco Cali
Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina Italy 94018
Mikhail Churnosov
Belgorod State University, Belgorod, Russia
David E. C. Cole
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5
Larissa Damba
Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia 630089
Dominique Delsate
Luxembourg Natural History Museum, Luxembourg L-2160Centre National de Recherche Archéologique auprès du Musée National d’Histoire et d’Art, Luxembourg
George van Driem
Institute of Linguistics, University of Bern, Bern, Switzerland CH-3012
Stanislav Dryomov
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk, Russia 630090Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia 630090
Sardana A. Fedorova
Yakut Research Center of Complex Medical Problems and North-Eastern Federal University, Yakutsk, Russia, 677010
Michael Francken
Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany D-72070
Irene Gallego Romero
Department of Human Genetics, University of Chicago, Chicago, IL USA 60637
Marina Gubina
The Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia 630090
Jean-Michel Guinet
Luxembourg Natural History Museum, Luxembourg L-2160
Michael Hammer
ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA 85721
Brenna Henn
Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA 11794
Tor Hervig
Department of Clinical Science, University of Bergen, Bergen, Norway 5021
Ugur Hodoglugil
NextBio, part of Illumina, Santa Clara, CA, USA 95050
Aashish R. Jha
Department of Human Genetics, University of Chicago, Chicago, IL USA 60637
Rick Kittles
College of Medicine, University of Illinois at Chicago, Chicago, IL, USA 60607
Elza Khusnutdinova
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, Russia 450054Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia 450074
Toomas Kivisild
Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom CB2 1QH
Vaidutis Kučinskas
Department of Human and Medical Genetics, Vilnius University, Vilnius, Lithuania LT-08661
Rita Khusainova
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, Russia 450054Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia 450074
Alena Kushniarevich
Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia 51010
Leila Laredj
Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France 67404
Sergey Litvinov
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, Russia 450054Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia 450074Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia 51010
Robert W. Mahley
Robert W. Mahley, Gladstone Institutes, San Francisco, CA 94158
Béla Melegh
Department of Medical Genetics, and Szentagothai Research Center, University of Pécs, Pécs, Hungary 7624
Ene Metspalu
Department of Evolutionary Biology, University of Tartu, Tartu, Estonia 51010
Joanna Mountain
Research Department, 23andMe, Inc. Mountain View, CA, USA 94043
Thomas Nyambo
Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
Ludmila Osipova
The Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia 630090
Jüri Parik
Department of Evolutionary Biology, University of Tartu, Tartu, Estonia 51010
Fedor Platanov
Research Institute of Health, North-Eastern Federal University, Yakutsk, Russia 677000
Olga Posukh
The Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia 630090
Valentino Romano
Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy 90128
Igor Rudan
Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom EH8 9AG
Ruslan Ruizbakiev
Deceased: formerly of the Institute of Immunology, Academy of Science, Tashkent, Uzbekistan 70000
Hovhannes Sahakyan
Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia 51010Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia 0014
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, Spain 15872
Elena B. Starikovskaya
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk, Russia 630090Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia 630090
Ayele Tarekegn
Addis Ababa University and Center of Human Genetic Diversity, P.O. Box 1176, Addis Ababa, Ethiopia
Draga Toncheva
Shahlo Turdikulova
Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent, Uzbekistan 100125
Ingrida Uktveryte
Department of Human and Medical Genetics, Vilnius University, Vilnius, Lithuania LT-08661
Olga Utevska
Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, Kharkiv Ukraine 61077
Mikhail Voevoda
Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia 630089The Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia 630090
Joachim Wahl
State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz, Germany D-78467
Pierre Zalloua
Lebanese American University, School of Medicine, Beirut, Lebanon 13-5053Harvard School of Public Health, Boston, USA 02115
Levon Yepiskoposyan
Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia 0014
Tatijana Zemunik
Department of Medical Biology, University of Split, School of Medicine, Split, Croatia 21000
Alan Cooper
Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia SA 5005
Cristian Capelli
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK OX3 7BN
Mark G. Thomas
Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom WC1E 6BT
Sarah A. Tishkoff
Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA 19104
Lalji Singh
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500 007Present address: Banaras Hindu University, Varanasi, India 221 005
Kumarasamy Thangaraj
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500 007
Richard Villems
Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia 51010Department of Evolutionary Biology, University of Tartu, Tartu, Estonia 51010Estonian Academy of Sciences, Tallinn, Estonia 10130
David Comas
Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain 08003
Rem Sukernik
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk, Russia 630090Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia 630090
Mait Metspalu
Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia 51010
Matthias Meyer
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Evan E. Eichler
Department of Genome Sciences, University of Washington, Seattle, WA, USA 98195Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA 98195
Joachim Burger
Johannes Gutenberg University Mainz, Institute of Anthropology, Mainz, Germany D-55128
Montgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720-3140
Svante Pääbo
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
Janet Kelso
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
David Reich
Department of Genetics, Harvard Medical School, Boston, MA, USA 02115Broad Institute of Harvard and MIT, Cambridge, MA, USA 02142Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA 02115
Johannes Krause
Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, Tübingen, Germany 72072
Abstract
Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ∼7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ∼8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ∼8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ∼44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND Unported 3.0 license.
Posted December 23, 2013.
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten I. Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George Busby, Francesco Cali, Mikhail Churnosov, David E. C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Hervig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platanov, Olga Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
bioRxiv 001552; doi: https://doi.org/10.1101/001552
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten I. Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George Busby, Francesco Cali, Mikhail Churnosov, David E. C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Hervig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platanov, Olga Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
bioRxiv 001552; doi: https://doi.org/10.1101/001552
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