The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Swapan Mallick (), Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon, Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin Rohland, Gabriel Renaud, Yaniv Erlich, Thomas Willems, Carla Gallo, Jeffrey P. Spence, Yun S. Song, Giovanni Poletti, Francois Balloux, George van Driem, Peter de Knijff, Irene Gallego Romero, Aashish R. Jha, Doron M. Behar, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Andres Moreno-Estrada, Olga L. Posukh, Elena Balanovska, Oleg Balanovsky, Sena Karachanak-Yankova, Hovhannes Sahakyan, Draga Toncheva, Levon Yepiskoposyan, Chris Tyler-Smith, Yali Xue, M. Syafiq Abdullah, Andres Ruiz-Linares, Cynthia M. Beall, Anna Di Rienzo, Choongwon Jeong, Elena B. Starikovskaya, Ene Metspalu, Jüri Parik, Richard Villems, Brenna M. Henn, Ugur Hodoglugil, Robert Mahley, Antti Sajantila, George Stamatoyannopoulos, Joseph T. S. Wee, Rita Khusainova, Elza Khusnutdinova, Sergey Litvinov, George Ayodo, David Comas, Michael F. Hammer, Toomas Kivisild, William Klitz, Cheryl A. Winkler, Damian Labuda, Michael Bamshad, Lynn B. Jorde, Sarah A. Tishkoff, W. Scott Watkins, Mait Metspalu, Stanislav Dryomov, Rem Sukernik, Lalji Singh, Kumarasamy Thangaraj, Svante Pääbo, Janet Kelso, Nick Patterson and David Reich ()
Additional contact information
Swapan Mallick: Harvard Medical School
Heng Li: Broad Institute of Harvard and MIT
Mark Lipson: Harvard Medical School
Iain Mathieson: Harvard Medical School
Melissa Gymrek: Broad Institute of Harvard and MIT
Fernando Racimo: University of California
Mengyao Zhao: Harvard Medical School
Niru Chennagiri: Harvard Medical School
Susanne Nordenfelt: Harvard Medical School
Arti Tandon: Harvard Medical School
Pontus Skoglund: Harvard Medical School
Iosif Lazaridis: Harvard Medical School
Sriram Sankararaman: Harvard Medical School
Qiaomei Fu: Harvard Medical School
Nadin Rohland: Harvard Medical School
Gabriel Renaud: Max Planck Institute for Evolutionary Anthropology
Yaniv Erlich: New York Genome Center
Thomas Willems: New York Genome Center
Carla Gallo: Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
Jeffrey P. Spence: Computational Biology Graduate Group, University of California
Yun S. Song: University of California
Giovanni Poletti: Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
Francois Balloux: Genetics Institute, University College London
George van Driem: Institute of Linguistics, University of Bern
Peter de Knijff: Postzone S5-P, Leiden University Medical Center
Irene Gallego Romero: School of Biological Sciences, Nanyang Technological University
Aashish R. Jha: University of Chicago
Doron M. Behar: Estonian Biocentre, Evolutionary Biology group
Claudio M. Bravi: Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET La Plata/CIC Buenos Aires/Universidad Nacional de La Plata, La Plata B1906APO
Cristian Capelli: University of Oxford
Tor Hervig: University of Bergen
Andres Moreno-Estrada: National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV
Olga L. Posukh: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences
Elena Balanovska: Research Centre for Medical Genetics
Oleg Balanovsky: Research Centre for Medical Genetics
Sena Karachanak-Yankova: National Human Genome Center, Medical University Sofia
Hovhannes Sahakyan: Estonian Biocentre, Evolutionary Biology group
Draga Toncheva: National Human Genome Center, Medical University Sofia
Levon Yepiskoposyan: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia
Chris Tyler-Smith: The Wellcome Trust Sanger Institute, Wellcome Genome Campus
Yali Xue: The Wellcome Trust Sanger Institute, Wellcome Genome Campus
M. Syafiq Abdullah: RIPAS Hospital
Andres Ruiz-Linares: Evolution and Environment, University College London WC1E 6BT
Cynthia M. Beall: Case Western Reserve University
Anna Di Rienzo: University of Chicago
Choongwon Jeong: University of Chicago
Elena B. Starikovskaya: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences
Ene Metspalu: Estonian Biocentre, Evolutionary Biology group
Jüri Parik: Estonian Biocentre, Evolutionary Biology group
Richard Villems: Estonian Biocentre, Evolutionary Biology group
Brenna M. Henn: Stony Brook University
Ugur Hodoglugil: NextBio, Illumina, Santa Clara
Robert Mahley: Gladstone Institutes
Antti Sajantila: University of Helsinki
George Stamatoyannopoulos: University of Washington
Joseph T. S. Wee: National Cancer Centre Singapore
Rita Khusainova: Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences
Elza Khusnutdinova: Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences
Sergey Litvinov: Estonian Biocentre, Evolutionary Biology group
George Ayodo: Jaramogi Oginga Odinga University of Science and Technology
David Comas: Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra
Michael F. Hammer: University of Arizona
Toomas Kivisild: Estonian Biocentre, Evolutionary Biology group
William Klitz: New York Genome Center
Cheryl A. Winkler: Basic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory
Damian Labuda: CHU Sainte-Justine, Pediatrics Departement, Université de Montréal
Michael Bamshad: University of Washington
Lynn B. Jorde: University of Utah School of Medicine
Sarah A. Tishkoff: University of Pennsylvania
W. Scott Watkins: Eccles Institute of Human Genetics, University of Utah
Mait Metspalu: Estonian Biocentre, Evolutionary Biology group
Stanislav Dryomov: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences
Rem Sukernik: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences
Lalji Singh: CSIR-Centre for Cellular and Molecular Biology
Kumarasamy Thangaraj: CSIR-Centre for Cellular and Molecular Biology
Svante Pääbo: Max Planck Institute for Evolutionary Anthropology
Janet Kelso: Max Planck Institute for Evolutionary Anthropology
Nick Patterson: Broad Institute of Harvard and MIT
David Reich: Harvard Medical School

Nature, 2016, vol. 538, issue 7624, 201-206

Abstract: Abstract Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Date: 2016
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DOI: 10.1038/nature18964

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