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Nature. 2016 Oct 13;538(7624):201-206. doi: 10.1038/nature18964. Epub 2016 Sep 21.

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

Author information

1
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
2
Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
3
Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
4
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
5
Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA.
6
New York Genome Center, New York, New York 10013, USA.
7
Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
8
Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.
9
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
10
Department of Computer Science, Columbia University, New York, New York 10027, USA.
11
Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA.
12
Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
13
Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
14
Computational Biology Graduate Group, University of California, Berkeley, California 94720, USA.
15
Computer Science Division, University of California, Berkeley, California 94720, USA.
16
Department of Statistics, University of California, Berkeley, California 94720, USA.
17
Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
18
Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.
19
Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
20
Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
21
School of Biological Sciences, Nanyang Technological University, 637551 Singapore.
22
Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore.
23
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
24
Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
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.
26
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
27
Department of Clinical Science, University of Bergen, Bergen 5021, Norway.
28
National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
29
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
30
Novosibirsk State University, Novosibirsk 630090, Russia.
31
Research Centre for Medical Genetics, Moscow 115478, Russia.
32
Vavilov Institute for General Genetics, Moscow 119991, Russia.
33
Moscow Institute for Physics and Technology, Dolgoprudniy 141700, Russia.
34
Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
35
Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
36
The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
37
RIPAS Hospital, Bandar Seri Begawan, Brunei.
38
Department of Genetics, Evolution and Environment, University College London WC1E 6BT, UK.
39
Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA.
40
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
41
Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
42
Estonian Academy of Sciences, Tallinn 10130, Estonia.
43
Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA.
44
NextBio, Illumina, Santa Clara, California 95050, USA.
45
Gladstone Institutes, San Francisco, California 94158, USA.
46
Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland.
47
Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.
48
National Cancer Centre Singapore, 169610 Singapore.
49
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
50
Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
51
Jaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya.
52
Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
53
ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA.
54
Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
55
Basic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA.
56
CHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, Canada.
57
Department of Pediatrics, University of Washington, Seattle, Washington 98119, USA.
58
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
59
Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
60
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
61
Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
62
Altai State University, Barnaul 656000, Russia.
63
CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.

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.

PMID:
27654912
PMCID:
PMC5161557
DOI:
10.1038/nature18964
[Indexed for MEDLINE]
Free PMC Article

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