New Results
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Heng Li, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, Nadin Rohland, Dominique Delsate, Michael Francken, Jean-Michel Guinet, Joachim Wahl, George Ayodo, Hamza A. Babiker, Graciela Baillet, Elena Balanovska, Oleg Balanovsky, Ramiro Barrantes, Gabriel Bedoya, Haim Ben-Ami, Judit Bene, Fouad Berrada, Claudio M. Bravi, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Daniel Corach, Larissa Damba, George van Driem, Stanislav Dryomov, Jean-Michel Dugoujon, Sardana A. Fedorova, Irene Gallego Romero, Marina Gubina, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Sena Karachanak-Yankova, Rita Khusainova, Elza Khusnutdinova, Rick Kittles, Toomas Kivisild, William Klitz, Vaidutis Kučinskas, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Theologos Loukidis, Robert W. Mahley, Béla Melegh, Ene Metspalu, Julio Molina, Joanna Mountain, Klemetti Näkkäläjärvi, Desislava Nesheva, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Francisco Rothhammer, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antti Sajantila, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, René Vasquez, Mercedes Villena, Mikhail Voevoda, Cheryl Winkler, Levon Yepiskoposyan, Pierre Zalloua, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Andres Ruiz-Linares, 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 Pååbo, Janet Kelso, David Reich, Johannes Krause
doi: https://doi.org/10.1101/001552
Iosif Lazaridis
Department of Genetics, Harvard Medical School;
Nick Patterson
Broad Institute of Harvard and MIT;
Alissa Mittnik
Institute for Archaeological Sciences, University of Tübingen;
Gabriel Renaud
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Swapan Mallick
Department of Genetics, Harvard Medical School;
Karola Kirsanow
Johannes Gutenberg University Mainz, Institute of Anthropology, Mainz;
Peter H. Sudmant
Department of Genome Sciences, University of Washington, Seattle;
Joshua G. Schraiber
Department of Integrative Biology, University of California, Berkeley;
Sergi Castellano
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Mark Lipson
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, MIT;
Bonnie Berger
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, MIT;
Christos Economou
Archaeological Research Laboratory, Stockholm University;
Ruth Bollongino
Johannes Gutenberg University Mainz, Institute of Anthropology;
Qiaomei Fu
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Kirsten Bos
Institute for Archaeological Sciences, University of Tübingen;
Susanne Nordenfelt
Department of Genetics, Harvard Medical School;
Heng Li
Broad Institute of Harvard and MIT, Cambridge, MA;
Cesare de Filippo
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Kay Prüfer
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Susanna Sawyer
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Cosimo Posth
Institute for Archaeological Sciences, University of T&ubingen;
Wolfgang Haak
Australian Centre for Ancient DNA, University of Adelaide;
Fredrik Hallgren
The Cultural Heritage Foundation, Västerås;
Elin Fornander
The Cultural Heritage Foundation, Västerås;
Nadin Rohland
Department of Genetics, Harvard Medical School, Boston, MA;
Dominique Delsate
National Museum of Natural History, L-2160, Luxembourg;
Michael Francken
Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen;
Jean-Michel Guinet
Luxembourg Natural History Museum, L-2160, Luxembourg;
Joachim Wahl
State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz, Germany;
George Ayodo
Center for Global Health and Child Development, Kisumu, Kenya;
Hamza A. Babiker
Inst. of Evolution, Immunology and Infection Research, University of Edinburgh;
Graciela Baillet
Instituto Multidisciplinario de Biología Celular, CCT-CONICET & CICPBA, La Plata, Argentina;
Elena Balanovska
Research Centre for Medical Genetics, Moscow;
Oleg Balanovsky
Research Centre for Medical Genetics, Moscow;
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;
Haim Ben-Ami
Rambam Health Care Campus, Haifa;
Judit Bene
Department of Medical Genetics, and Szentagothai Research Center, University of Pécs;
Fouad Berrada
Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane;
Claudio M. Bravi
Instituto Multidisciplinario de Biología Celular, CCT-CONICET & CICPBA, La Plata, Argentina;
Francesca Brisighelli
Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome;
George B.J. Busby
Department of Zoology, University of Oxford;
Francesco Cali
Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina;
Mikhail Churnosov
Belgorod State University;
David E.C. Cole
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada;
Daniel Corach
School of Pharmacy and Biochemistry, Universidad de Buenos Aires, Argentina;
Larissa Damba
Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk;
George van Driem
Institute of Linguistics, University of Bern;
Stanislav Dryomov
Institute of Molecular and Cellular Biology, Russian Academy, Siberian Branch, Novosibirsk;
Jean-Michel Dugoujon
Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse;
Sardana A. Fedorova
Yakut Research Center of Complex Medical Problems and North-Eastern Federal University, Yakutsk;
Irene Gallego Romero
Department of Human Genetics, University of Chicago;
Marina Gubina
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk;
Michael Hammer
ARL Division of Biotechnology, University of Arizona;
Brenna Henn
Department of Ecology and Evolution, Stony Brook University;
Tor Helvig
Department of Clinical Science, University of Bergen;
Ugur Hodoglugil
NextBio;
Aashish R. Jha
Department of Human Genetics, University of Chicago;
Sena Karachanak-Yankova
Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia;
Rita Khusainova
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, 45005;
Elza Khusnutdinova
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, 45005;
Rick Kittles
College of Medicine, University of Illinois at Chicago;
Toomas Kivisild
Division of Biological Anthropology, University of Cambridge;
William Klitz
School of Public Health, University of California, Berkeley, CA, 94720, USA;
Vaidutis Kučinskas
Department of Human and Medical Genetics, Vilnius University;
Alena Kushniarevich
Estonian Biocentre, Evolutionary Biology group, Tartu;
Leila Laredj
Institut de Génétique et de Biologie Moléculaire et Cellulaire;
Sergey Litvinov
Inst. of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa;
Theologos Loukidis
Currently employed by AMGEN; 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece;
Robert W. Mahley
Gladstone Institutes, San Francisco;
Béla Melegh
Department of Medical Genetics, and Szentagothai Research Center, University of Pécs;
Ene Metspalu
Department of Evolutionary Biology, University of Tartu;
Julio Molina
Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala;
Joanna Mountain
Research Department, 23andMe, Inc.;
Klemetti Näkkäläjärvi
Cultural Anthropology Program, University of Oulu, Oulu, 90014, Finland;
Desislava Nesheva
Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Bulgaria;
Thomas Nyambo
Dept. of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam;
Ludmila Osipova
The Inst. of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk;
Jüri Parik
Department of Evolutionary Biology, University of Tartu;
Fedor Platonov
Research Institute of Health, North-Eastern Federal University, Yakutsk;
Olga L. Posukh
Inst. of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk;
Valentino Romano
Dipartimento di Fisica e Chimica, Università di Palermo;
Francisco Rothhammer
Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile;
Igor Rudan
Centre for Population Health Sciences, The University of Edinburgh Medical School;
Ruslan Ruizbakiev
Institute of Immunology, Academy of Science, Tashkent;
Hovhannes Sahakyan
Estonian Biocentre, Evolutionary Biology group, Tartu;
Antti Sajantila
Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, 00014, Finland;
Antonio Salas
Grupo de Medicina Xen&oacumica, Facultade de Medicina, Universidade de Santiago de Compostela;
Elena B. Starikovskaya
Inst. of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk;
Ayele Tarekegn
Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK;
Draga Toncheva
Dept. of Medical Genetics, National Human Genome Center, Medical University Sofia;
Shahlo Turdikulova
Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent;
Ingrida Uktveryte
Department of Human and Medical Genetics, Vilnius University;
Olga Utevska
Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, Kharkiv;
René Vasquez
Instituto Boliviano de Biología de la Altura, Universidad Autonoma Tomás Frías, Potosí, Bolivia;
Mercedes Villena
Instituto Boliviano de Biología de la Altura, Universidad Autonoma Tomás Frías, Potosí, Bolivia;
Mikhail Voevoda
Inst. of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk;
Cheryl Winkler
Frederick Natoinal Lab for Cancer Research, NCI, NIH, Frederick, MD;
Levon Yepiskoposyan
Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia;
Pierre Zalloua
Lebanese American University, School of Medicine, Beirut;
Tatijana Zemunik
Department of Medical Biology, University of Split, School of Medicine;
Alan Cooper
Australian Centre for Ancient DNA, School of Earth and Environmental Sciences,University of Adelaide;
Cristian Capelli
Department of Zoology, University of Oxford;
Mark G. Thomas
Research Department of Genetics, Evolution and Environment, University College London;
Andres Ruiz-Linares
Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK;
Sarah A. Tishkoff
Department of Biology and Genetics. University of Pennsylvania;
Lalji Singh
CSIR-Centre for Cellular and Molecular Biology, Hyderabad;
Kumarasamy Thangaraj
CSIR-Centre for Cellular and Molecular Biology, Hyderabad;
Richard Villems
Estonian Biocentre, Evolutionary Biology group, Tartu;
David Comas
Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra
Rem Sukernik
Inst. of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk;
Mait Metspalu
Estonian Biocentre, Evolutionary Biology group, Tartu;
Matthias Meyer
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Evan E. Eichler
Department of Genome Sciences, University of Washington, Seattle;
Joachim Burger
Johannes Gutenberg University Mainz, Institute of Anthropology;
Montgomery Slatkin
Department of Integrative Biology, University of California, Berkeley;
Svante Pååbo
Max Planck Institute for Evolutionary Anthropology, Leipzig;
Janet Kelso
Max Planck Institute for Evolutionary Anthropology, Leipzig;
David Reich
Department of Genetics, Harvard Medical School;
Johannes Krause
Institute for Archaeological Sciences, University of Tübingen;
Abstract
We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~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 ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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 4.0 International license.
- Posted April 5, 2014.
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Heng Li, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, Nadin Rohland, Dominique Delsate, Michael Francken, Jean-Michel Guinet, Joachim Wahl, George Ayodo, Hamza A. Babiker, Graciela Baillet, Elena Balanovska, Oleg Balanovsky, Ramiro Barrantes, Gabriel Bedoya, Haim Ben-Ami, Judit Bene, Fouad Berrada, Claudio M. Bravi, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Daniel Corach, Larissa Damba, George van Driem, Stanislav Dryomov, Jean-Michel Dugoujon, Sardana A. Fedorova, Irene Gallego Romero, Marina Gubina, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Sena Karachanak-Yankova, Rita Khusainova, Elza Khusnutdinova, Rick Kittles, Toomas Kivisild, William Klitz, Vaidutis Kučinskas, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Theologos Loukidis, Robert W. Mahley, Béla Melegh, Ene Metspalu, Julio Molina, Joanna Mountain, Klemetti Näkkäläjärvi, Desislava Nesheva, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Francisco Rothhammer, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antti Sajantila, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, René Vasquez, Mercedes Villena, Mikhail Voevoda, Cheryl Winkler, Levon Yepiskoposyan, Pierre Zalloua, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Andres Ruiz-Linares, 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 Pååbo, 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, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Heng Li, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, Nadin Rohland, Dominique Delsate, Michael Francken, Jean-Michel Guinet, Joachim Wahl, George Ayodo, Hamza A. Babiker, Graciela Baillet, Elena Balanovska, Oleg Balanovsky, Ramiro Barrantes, Gabriel Bedoya, Haim Ben-Ami, Judit Bene, Fouad Berrada, Claudio M. Bravi, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Daniel Corach, Larissa Damba, George van Driem, Stanislav Dryomov, Jean-Michel Dugoujon, Sardana A. Fedorova, Irene Gallego Romero, Marina Gubina, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Sena Karachanak-Yankova, Rita Khusainova, Elza Khusnutdinova, Rick Kittles, Toomas Kivisild, William Klitz, Vaidutis Kučinskas, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Theologos Loukidis, Robert W. Mahley, Béla Melegh, Ene Metspalu, Julio Molina, Joanna Mountain, Klemetti Näkkäläjärvi, Desislava Nesheva, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Francisco Rothhammer, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antti Sajantila, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, René Vasquez, Mercedes Villena, Mikhail Voevoda, Cheryl Winkler, Levon Yepiskoposyan, Pierre Zalloua, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Andres Ruiz-Linares, 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 Pååbo, Janet Kelso, David Reich, Johannes Krause
bioRxiv 001552; doi: https://doi.org/10.1101/001552
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