Article | Published:

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

Nature volume 538, pages 201206 (13 October 2016) | Download Citation

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.

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Accessions

Primary accessions

European Nucleotide Archive

Data deposits

Raw data for 279 genomes for which the informed consent documentation is consistent with fully public data release are available through the EBI European Nucleotide Archive under accession numbers PRJEB9586 and ERP010710. For the remaining 21 genomes (designated by code ‘Y’ in the seventh column of Supplementary Data Table 1), data are deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI and the CRG, under accession number EGAS00001001959. Data for these 21 genomes can be obtained by submitting to the EGA Data Access Committee a signed letter containing the following text: “(a) I will not distribute the data outside my collaboration; (b) I will not post the data publicly; (c) I will make no attempt to connect the genetic data to personal identifiers for the samples; and (d) I will not use the data for any commercial purposes.” Compact versions of the SGDP dataset and software for accessing it are available at (http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html). The short tandem repeat (STR) genotypes are available through dbVar under accession number nstd128 (http://www.ncbi.nlm.nih.gov/dbvar).

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Acknowledgements

We thank the volunteers who donated samples. We thank H. Blanche, N. Boivin, H. Cann (deceased), E. Eichler, H. Greely, M. Petraglia, K. Prüfer, A. Rogers, M. Steinrücken, U. Stenzel and P. Sudmant for comments, critiques, discussions, or advice on assembling samples. We thank S. Fan for uploading 21 genomes to the European Genome-phenome archive. The sequencing was funded by the Simons Foundation (SFARI 280376) and the US National Science Foundation (BCS-1032255). I.M. was supported by a Long Term Fellowship grant LT001095/2014 from the Human Frontier Science program. P.S. was supported by the Wenner-Gren foundation and the Swedish Research Council (VR grant 2014-453). T.W. and M.G. were supported by an NIJ grant 2014-DN-BX-K089. Y.E. was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and by NIJ grant 2014-DN-BX-K089. D.L. was supported by the Natural Sciences and Engineering Research Council of Canada. T.K. was supported by ERC Starting Investigator grant FP7 - 261213. R.S. received support from Russian Foundation for Basic Research (#15-04-02543). S.D. received support from the Russian Foundation for Basic Research (#16-34-00599). R.K., E.K. and S.L. were supported by the Russian Foundation for Basic Research (11-04-00725-a). E.B. was supported by the Russian Foundation for Basic Research (16-06-00303). O.B. was supported by the Russian Scientific Fund (14-04-00827) and by the Russian Foundation for Basic Research (16-04-00890). D.M.B., H.S., E.M., R.V. and M.M. were supported by Institutional Research Funding from the Estonian Research Council IUT24-1 and by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu. D.C. was supported by the Spanish MINECO grant CGL-44351-P. L.B.J. and W.S.W. were supported by NIH grant GM59290. S.A.T. was supported by NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01. C.T.-S. and Y.X. were supported by The Wellcome Trust grant 098051. C.M.B. was supported by NSF grants 0924726 and 1153911. K.T. was supported by CSIR Network Project grant (GENESIS: BSC0121). J.P.S. and Y.S.S. were supported in part by an NIH grant R01-GM094402, and a Packard Fellowship for Science and Engineering. G.R., J.K and S.P. were funded by the Max Planck Society. N.P. and D.R. were supported by NIH grant GM100233 and D.R. is a Howard Hughes Medical Institute investigator.

Author information

Author notes

    • Heng Li
    • , Mark Lipson
    •  & Iain Mathieson

    These authors contributed equally to this work.

    • Sriram Sankararaman
    •  & Lalji Singh

    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).

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    • , Mark Lipson
    • , Iain Mathieson
    • , Mengyao Zhao
    • , Niru Chennagiri
    • , Susanne Nordenfelt
    • , Arti Tandon
    • , Pontus Skoglund
    • , Iosif Lazaridis
    • , Sriram Sankararaman
    • , Qiaomei Fu
    • , Nadin Rohland
    •  & David Reich
  2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

    • Swapan Mallick
    • , Heng Li
    • , Melissa Gymrek
    • , Mengyao Zhao
    • , Niru Chennagiri
    • , Susanne Nordenfelt
    • , Arti Tandon
    • , Pontus Skoglund
    • , Iosif Lazaridis
    • , Sriram Sankararaman
    • , Qiaomei Fu
    • , Nadin Rohland
    • , Nick Patterson
    •  & David Reich
  3. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    • , Mengyao Zhao
    • , Niru Chennagiri
    • , Susanne Nordenfelt
    •  & David Reich
  4. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA

    • Melissa Gymrek
  5. Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA

    • Melissa Gymrek
  6. New York Genome Center, New York, New York 10013, USA

    • Melissa Gymrek
    • , Yaniv Erlich
    • , Thomas Willems
    •  & William Klitz
  7. Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA

    • Fernando Racimo
  8. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  9. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

    • Gabriel Renaud
    • , Svante Pääbo
    •  & Janet Kelso
  10. Department of Computer Science, Columbia University, New York, New York 10027, USA

    • Yaniv Erlich
  11. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA

    • Yaniv Erlich
  12. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Thomas Willems
  13. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú

    • Carla Gallo
    •  & Giovanni Poletti
  14. Computational Biology Graduate Group, University of California, Berkeley, California 94720, USA

    • Jeffrey P. Spence
  15. Computer Science Division, University of California, Berkeley, California 94720, USA

    • Yun S. Song
  16. Department of Statistics, University of California, Berkeley, California 94720, USA

    • Yun S. Song
  17. Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

    • Yun S. Song
  18. Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK

    • Francois Balloux
  19. Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland

    • George van Driem
  20. Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands

    • Peter de Knijff
  21. School of Biological Sciences, Nanyang Technological University, 637551 Singapore

    • Irene Gallego Romero
  22. Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore

    • Irene Gallego Romero
  23. Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA

    • Aashish R. Jha
    • , Anna Di Rienzo
    •  & Choongwon Jeong
  24. Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia

    • Doron M. Behar
    • , Hovhannes Sahakyan
    • , Ene Metspalu
    • , Jüri Parik
    • , Richard Villems
    • , Sergey Litvinov
    • , Toomas Kivisild
    •  & Mait Metspalu
  25. 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, Argentina

    • Claudio M. Bravi
  26. Department of Zoology, University of Oxford, Oxford OX1 3PS, UK

    • Cristian Capelli
  27. Department of Clinical Science, University of Bergen, Bergen 5021, Norway

    • Tor Hervig
  28. National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico

    • Andres Moreno-Estrada
  29. Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Olga L. Posukh
  30. Novosibirsk State University, Novosibirsk 630090, Russia

    • Olga L. Posukh
  31. Research Centre for Medical Genetics, Moscow 115478, Russia

    • Elena Balanovska
    •  & Oleg Balanovsky
  32. Vavilov Institute for General Genetics, Moscow 119991, Russia

    • Oleg Balanovsky
  33. Moscow Institute for Physics and Technology, Dolgoprudniy 141700, Russia

    • Oleg Balanovsky
  34. Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria

    • Sena Karachanak-Yankova
    •  & Draga Toncheva
  35. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia

    • Hovhannes Sahakyan
    •  & Levon Yepiskoposyan
  36. The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

    • Chris Tyler-Smith
    •  & Yali Xue
  37. RIPAS Hospital, Bandar Seri Begawan, Brunei

    • M. Syafiq Abdullah
  38. Department of Genetics, Evolution and Environment, University College London WC1E 6BT, UK

    • Andres Ruiz-Linares
  39. Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA

    • Cynthia M. Beall
  40. Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Elena B. Starikovskaya
    • , Stanislav Dryomov
    •  & Rem Sukernik
  41. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia

    • Ene Metspalu
    •  & Richard Villems
  42. Estonian Academy of Sciences, Tallinn 10130, Estonia

    • Richard Villems
  43. Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA

    • Brenna M. Henn
  44. NextBio, Illumina, Santa Clara, California 95050, USA

    • Ugur Hodoglugil
  45. Gladstone Institutes, San Francisco, California 94158, USA

    • Robert Mahley
  46. Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland

    • Antti Sajantila
  47. Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA

    • George Stamatoyannopoulos
  48. National Cancer Centre Singapore, 169610 Singapore

    • Joseph T. S. Wee
  49. Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia

    • Rita Khusainova
    • , Elza Khusnutdinova
    •  & Sergey Litvinov
  50. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia

    • Rita Khusainova
    • , Elza Khusnutdinova
    •  & Sergey Litvinov
  51. Jaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya

    • George Ayodo
  52. Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain

    • David Comas
  53. ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA

    • Michael F. Hammer
  54. Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK

    • Toomas Kivisild
  55. Basic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA

    • Cheryl A. Winkler
  56. CHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, Canada

    • Damian Labuda
  57. Department of Pediatrics, University of Washington, Seattle, Washington 98119, USA

    • Michael Bamshad
  58. Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Lynn B. Jorde
  59. Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

    • Sarah A. Tishkoff
  60. Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA

    • W. Scott Watkins
  61. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Stanislav Dryomov
  62. Altai State University, Barnaul 656000, Russia

    • Rem Sukernik
  63. CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India

    • Lalji Singh
    •  & Kumarasamy Thangaraj

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Contributions

S.M., Y.E., Y.S.S., S.P., J.K., N.P. and D.R. supervised the study. S.N., N.R., C.G., G.P., F.B., G.D., I.G.R., A.R.J., P.D., D.M.B., C.M.B., C.C., T.H., A.M.-E., O.L.P., E.B., O.B., S.K.-Y., H.S., D.T., L.Y., C.T.-S., Y.X., M.S.A., A.R.-L., C.B., A.D.R., C.J., E.B.S., E.M., J.P., R.V., B.M.H., U.H., R.W.M., A.S., G.S., J.T.S.W., R.K., E.K., S.L., G.A., D.C., M.H., T.K., W.K., C.A.W., D.L., M.B., L.B.J., S.A.T., W.S.W., M.M., S.D., R.S., L.S., K.T. and D.R. assembled samples. S.M., H.L., M.L., I.M., M.G., F.R., J.P.S., M.Z., N.C., A.T., P.S., I.L., S.S., Q.F., G.R., Y.S., N.P. and D.R. performed analyses. S.M., H.L., M.L., I.M., M.G., F.R., M.Z., N.P. and D.R. wrote the manuscript with help from all co-authors.

Competing interests

U.H. is employed by NextBio, a division of Illumina Ltd.

Corresponding authors

Correspondence to Swapan Mallick or David Reich.

Reviewer Information Nature thanks P. Bellwood and S. Ramachandran and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

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    Supplementary Information

    This file contains Supplementary Text and Data, Supplementary Tables Supplementary Figures and additional references (see Contents for details).

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  1. 1.

    Supplementary Table 1

    This file shows the data by each sample studied.

  2. 2.

    Supplementary Table 2

    This table shows the top hits for 3P-CLR run.

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DOI

https://doi.org/10.1038/nature18964

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