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

Author

Listed:
  • Swapan Mallick

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute, 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
    Whitehead Institute for Biomedical Research
    MIT
    New York Genome Center)

  • Fernando Racimo

    (University of California)

  • Mengyao Zhao

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute, Harvard Medical School)

  • Niru Chennagiri

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute, Harvard Medical School)

  • Susanne Nordenfelt

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute, Harvard Medical School)

  • Arti Tandon

    (Harvard Medical School
    Broad Institute of Harvard and MIT)

  • Pontus Skoglund

    (Harvard Medical School
    Broad Institute of Harvard and MIT)

  • Iosif Lazaridis

    (Harvard Medical School
    Broad Institute of Harvard and MIT)

  • Sriram Sankararaman

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    †Present addresses: Department of Computer Science, University of California at Los Angeles, California 90095, USA and Department of Human Genetics Science, University of California at Los Angeles, California 90095, USA (S.S.); Genome Foundation, Hyderabad 500076, India (L.S).)

  • Qiaomei Fu

    (Harvard Medical School
    Broad Institute of Harvard and MIT
    Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS)

  • Nadin Rohland

    (Harvard Medical School
    Broad Institute of Harvard and MIT)

  • Gabriel Renaud

    (Max Planck Institute for Evolutionary Anthropology)

  • Yaniv Erlich

    (New York Genome Center
    Columbia University
    Center for Computational Biology and Bioinformatics, Columbia University)

  • Thomas Willems

    (New York Genome Center
    Computational and Systems Biology Program, Massachusetts Institute of Technology)

  • 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
    University of California
    University of Pennsylvania)

  • 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
    Lee Kong Chian School of Medicine, 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
    Novosibirsk State University)

  • Elena Balanovska

    (Research Centre for Medical Genetics)

  • Oleg Balanovsky

    (Research Centre for Medical Genetics
    Vavilov Institute for General Genetics
    Moscow Institute for Physics and Technology)

  • Sena Karachanak-Yankova

    (National Human Genome Center, Medical University Sofia)

  • Hovhannes Sahakyan

    (Estonian Biocentre, Evolutionary Biology group
    Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia)

  • 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
    University of Tartu)

  • Jüri Parik

    (Estonian Biocentre, Evolutionary Biology group)

  • Richard Villems

    (Estonian Biocentre, Evolutionary Biology group
    University of Tartu
    Estonian Academy of Sciences)

  • 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
    Bashkir State University)

  • Elza Khusnutdinova

    (Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences
    Bashkir State University)

  • Sergey Litvinov

    (Estonian Biocentre, Evolutionary Biology group
    Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences
    Bashkir State University)

  • 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
    University of Cambridge)

  • 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
    Institute of Archaeology and Ethnography, 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
    Altai State University)

  • Lalji Singh

    (CSIR-Centre for Cellular and Molecular Biology
    †Present addresses: Department of Computer Science, University of California at Los Angeles, California 90095, USA and Department of Human Genetics Science, University of California at Los Angeles, California 90095, USA (S.S.); Genome Foundation, Hyderabad 500076, India (L.S).)

  • 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
    Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute, Harvard Medical School)

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.

Suggested Citation

  • Swapan Mallick & Heng Li & Mark Lipson & Iain Mathieson & Melissa Gymrek & Fernando Racimo & Mengyao Zhao & Niru Chennagiri & Susanne Nordenfelt & Arti Tandon & Pontus Skoglund & Iosif Lazaridis & Sri, 2016. "The Simons Genome Diversity Project: 300 genomes from 142 diverse populations," Nature, Nature, vol. 538(7624), pages 201-206, October.
    • Handle: RePEc:nat:nature:v:538:y:2016:i:7624:d:10.1038_nature18964
    DOI: 10.1038/nature18964
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