Genomic analyses inform on migration events during the peopling of Eurasia

• Published in: Nature
• Main Authors: Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D., Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A. Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L., Järve, Mari, Karmin, Monika, Jacobs, Guy S., Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C., Lambert, David M., Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D., Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P., Barashkov, Nikolay A., Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A., Lichman, Daria V., Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph T. S., Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M., Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A., Osipova, Ludmila P., Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K., Metspalu, Ene, Thomas, Mark G., Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, Metspalu, Mait
• Other Authors: Biological and Environmental Sciences and Engineering (BESE) Division, Integrative Systems Biology Lab, Estonian Biocentre, Tartu, Estonia, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, Bologna, Italy, Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom, Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States, Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Estonian Genome Center, University of Tartu, Tartu, Estonia, Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France, Department of Psychology, University of Auckland, Auckland, New Zealand, Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand, Department of Biology, Pennsylvania State UniversityPA, United States, Institute for Human Genetics, University of California, San Francisco, CA, United States, MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Hills Road, Cambridge, United Kingdom, School of Life Sciences, Arizona State University, Tempe, AR, United States, Center for Evolution and Medicine, Biodesign Institute, Tempe, AR, United States, Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, Mathematical Sciences, University of Southampton, Southampton, United Kingdom, Institute for Complex Systems Simulation, University of Southampton, Southampton, United Kingdom, Division of Biological Sciences, University of Montana, Missoula, United States, Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom, Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russian Federation, Kuban State Medical University, Krasnodar, Russian Federation, Scientific Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, Georgia, Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark, Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia, Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics, Tirana, Albania, Center of High Technology, Academy of Sciences, Tashkent, Uzbekistan, Institute of Bioorganic Chemistry Academy of Science, Tashkent, Uzbekistan, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan, Centre for Advanced Research in Sciences, DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Bangladesh, Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States, Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, PA, United States, DNcode Laboratories, Moscow, Russian Federation, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia, Northern State Medical University, Arkhangelsk, Russian Federation, Royal Free Hospital, Pond Street, London, United Kingdom, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine, Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Toulouse, France, Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia, Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russian Federation, St. Catherine Specialty Hospital, Zagreb, Croatia, Eberly College of Science, Pennsylvania State UniversityPA, United States, University of Split, Medical School, Split, Croatia
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Springer Science and Business Media LLC 2016
• Subjects: Arctic; New Zealand
• Online Access: http://hdl.handle.net/10754/622409; https://doi.org/10.1038/nature19792

High-Coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago. © 2016 Macmillan Publishers Limited, part of Springer Nature. Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).