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

被引：924

作者：

Mallick, Swapan ^{[1
,2
,3
]}

Li, Heng ^{[2
]}

Lipson, Mark ^{[1
]}

Mathieson, Iain ^{[1
]}

Gymrek, Melissa ^{[2
,4
,5
,6
]}

Racimo, Fernando ^{[7
]}

Zhao, Mengyao ^{[1
,2
,3
]}

Chennagiri, Niru ^{[1
,2
,3
]}

Nordenfelt, Susanne ^{[1
,2
,3
]}

Tandon, Arti ^{[1
,2
]}

Skoglund, Pontus ^{[1
,2
]}

Lazaridis, Iosif ^{[1
,2
]}

Sankararaman, Sriram ^{[1
,2
,64
,65
]}

Fu, Qiaomei ^{[1
,2
,8
]}

Rohland, Nadin ^{[1
,2
]}

Renaud, Gabriel ^{[9
]}

Erlich, Yaniv ^{[6
,10
,11
]}

Willems, Thomas ^{[6
,12
]}

Gallo, Carla ^{[13
]}

Spence, Jeffrey P. ^{[14
]}

Song, Yun S. ^{[15
,16
,17
,18
]}

Poletti, Giovanni ^{[13
]}

Balloux, Francois ^{[19
]}

van Driem, George

de Knijff, Peter ^{[20
]}

Romero, Irene Gallego ^{[21
,22
]}

Jha, Aashish R. ^{[23
]}

Behar, Doron M. ^{[24
]}

Bravi, Claudio M. ^{[25
]}

Capelli, Cristian ^{[26
]}

Hervig, Tor ^{[27
]}

Moreno-Estrada, Andres ^{[28
]}

Posukh, Olga L. ^{[29
,30
]}

Balanovska, Elena ^{[31
]}

Balanovsky, Oleg ^{[31
,32
,33
]}

Karachanak-Yankova, Sena ^{[34
]}

Sahakyan, Hovhannes ^{[24
,35
]}

Toncheva, Draga ^{[34
]}

Yepiskoposyan, Levon ^{[35
]}

Tyler-Smith, Chris ^{[36
]}

Xue, Yali ^{[36
]}

Abdullah, M. Syafiq ^{[37
]}

Ruiz-Linares, Andres ^{[38
]}

Beall, Cynthia M. ^{[39
]}

Di Rienzo, Anna ^{[23
]}

Jeong, Choongwon ^{[23
]}

Starikovskaya, Elena B. ^{[40
]}

Metspalu, Ene ^{[24
,41
]}

Parik, Juri ^{[24
]}

Villems, Richard ^{[24
,41
,42
]}

机构：

[1] Harvard Med Sch, Dept Genet, Boston, MA 02115 USA

[2] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[3] Harvard Med Sch, Howard Hughes Med Inst, Boston, MA 02115 USA

[4] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

[5] MIT, Harvard MIT Div Hlth Sci & Technol, Cambridge, MA USA

[6] New York Genome Ctr, New York, NY 10013 USA

[7] Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA

[8] Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins Chinese, IVPP, Beijing 100044, Peoples R China

[9] Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, D-04103 Leipzig, Germany

[10] Columbia Univ, Dept Comp Sci, New York, NY 10027 USA

[11] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA

[12] MIT, Computat & Syst Biol Program, Cambridge, MA 02139 USA

[13] Univ Peruana Cayetano Heredia, Fac Ciencias & Filosofia, Labs Invest & Desarrollo, Lima 15102, Peru

[14] Univ Calif Berkeley, Computat Biol Grad Grp, Berkeley, CA 94720 USA

[15] Univ Calif Berkeley, Div Comp Sci, Berkeley, CA 94720 USA

[16] Univ Penn, Dept Stat, Philadelphia, PA 19104 USA

[17] Univ Penn, Dept Math, Philadelphia, PA 19104 USA

[18] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

[19] UCL, Genet Inst, Gower St, London WC1E 6BT, England

[20] Leiden Univ, Med Ctr, Dept Human & Clin Genet, Postzone S5-P, NL-2333 ZA Leiden, Netherlands

[21] Nanyang Technol Univ, Sch Biol Sci, Singapore 637551, Singapore

[22] Nanyang Technol Univ, Lee Kong Chian Sch Med, Singapore 636921, Singapore

[23] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[24] Estonian Bioctr, Evolutionary Biol Grp, EE-51010 Tartu, Estonia

[25] Univ Nacl La Plata, Inst Multidisciplinario Biol Celular IMBICE, Lab Genet Mol Poblac, CCT CONICET La Plata,CIC Buenos Aires, B1906APO, La Plata, Buenos Aires, Argentina

[26] Univ Oxford, Dept Zool, Oxford OX1 3PS, England

[27] Univ Bergen, Dept Clin Sci, N-5021 Bergen, Norway

[28] CINVESTAV, Natl Lab Genom Biodivers LANGEBIO, Guanajuato 36821, Mexico

[29] Siberian Branch Russian Acad Sci, Inst Cytol & Genet, Novosibirsk 630090, Russia

[30] Novosibirsk State Univ, Novosibirsk 630090, Russia

[31] Med Genet Res Ctr, Moscow 115478, Russia

[32] Vavilov Inst Gen Genet, Moscow 119991, Russia

[33] Moscow Inst Phys & Technol, Dolgopruclniy 141700, Russia

[34] Med Univ Sofia, Dept Med Genet, Natl Human Genome Ctr, Sofia 1431, Bulgaria

[35] Natl Acad Sci Armenia, Inst Mol Biol, Lab Ethnogen, Yerevan 0014, Armenia

[36] Wellcome Trust Sanger Inst, Wellcome Genome Campus, Hinxton CB1O 1SA, Cambs, England

[37] RIPAS Hosp, Bandar Seri Begawan, Brunei

[38] UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

[39] Case Western Reserve Univ, Dept Anthropol, Cleveland, OH 44106 USA

[40] Russian Acad Sci, Siberian Branch, Inst Mol & Cellular Biol, Lab Human Mol Genet, Novosibirsk 630090, Russia

[41] Univ Tartu, Dept Evolutionary Biol, EE-51010 Tartu, Estonia

[42] Estonian Acad Sci, EE-10130 Tallinn, Estonia

[43] SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA

[44] NextBio, Santa Clara, CA 95050 USA

[45] Gladstone Inst, San Francisco, CA 94158 USA

[46] Univ Helsinki, Dept Forens Med, FIN-00014 Helsinki, Finland

[47] Univ Washington, Div Med Genet, Dept Med, Seattle, WA 98195 USA

[48] Natl Canc Ctr Singapore, Singapore 169610, Singapore

[49] Russian Acad Sci, Inst Biochem & Genet, Ufa Res Ctr, Ufa 450054, Russia

[50] Bashkir State Univ, Dept Genet & Fundamental Med, Ufa 450074, Russia

来源：

NATURE | 2016年 / 538卷 / 7624期

基金：

美国国家科学基金会; 英国生物技术与生命科学研究理事会; 瑞典研究理事会; 俄罗斯基础研究基金会; 加拿大自然科学与工程研究理事会; 俄罗斯科学基金会; 英国惠康基金;

关键词：

MODERN HUMANS; NEANDERTHAL; ANCESTRY; SEQUENCE; HISTORY; ADMIXTURE; DISPERSAL; INFERENCE; SELECTION; PLINK;

D O I：

10.1038/nature18964

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：201 / +

页数：14

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