Chimpanzee genomic diversity reveals ancient admixture with bonobos

被引：178

作者：

de Manuel, Marc ^{[1
]}

Kuhlwilm, Martin ^{[1
]}

Frandsen, Peter ^{[2
,3
]}

Sousa, Vitor C. ^{[4
,5
]}

Desai, Tariq ^{[6
]}

Prado-Martinez, Javier ^{[1
,7
]}

Hernandez-Rodriguez, Jessica ^{[1
]}

Dupanloup, Isabelle ^{[4
,5
]}

Lao, Oscar ^{[8
,9
]}

Hallast, Pille ^{[7
,10
]}

Schmidt, Joshua M. ^{[11
]}

Maria Heredia-Genestar, Jose ^{[1
]}

Benazzo, Andrea ^{[12
]}

Barbujani, Guido ^{[12
]}

Peter, Benjamin M. ^{[13
]}

Kuderna, Lukas F. K. ^{[1
]}

Casals, Ferran ^{[1
]}

Angedakin, Samuel ^{[14
]}

Arandjelovic, Mimi ^{[14
]}

Boesch, Christophe ^{[14
]}

Kuehl, Hjalmar ^{[14
]}

Vigilant, Linda ^{[14
]}

Langergraber, Kevin ^{[15
,16
]}

Novembre, John ^{[13
]}

Gut, Marta ^{[8
]}

Gut, Ivo ^{[8
]}

Navarro, Arcadi ^{[1
,8
,17
]}

Carlsen, Frands ^{[3
]}

Andres, Aida M. ^{[11
]}

Siegismund, Hans. R. ^{[2
]}

Scally, Aylwyn ^{[6
]}

Excoffier, Laurent ^{[4
,5
]}

Tyler-Smith, Chris ^{[7
]}

Castellano, Sergi ^{[11
]}

Xue, Yali ^{[7
]}

Hvilsom, Christina ^{[3
]}

Marques-Bonet, Tomas ^{[1
,8
,17
]}

机构：

[1] Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Barcelona Biomed Res Pk,Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain

[2] Univ Copenhagen, Dept Biol, Sect Computat & RNA Biol, DK-2200 Copenhagen, Denmark

[3] Copenhagen Zoo, Ctr Zoo & Wild Anim Hlth, DK-2000 Frederiksberg, Denmark

[4] Univ Bern, Computat & Mol Populat Genet, Inst Ecol & Evolut, CH-3012 Bern, Switzerland

[5] Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[6] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

[7] Wellcome Trust Sanger Inst, Wellcome Genome Campus, Hinxton CB10 1SA, England

[8] Barcelona Inst Sci & Technol, Natl Ctr Genom Anal, Ctr Genom Regulat, Barcelona 08028, Spain

[9] Univ Pompeu Fabra, Barcelona 08003, Spain

[10] Univ Tartu, Inst Mol & Cell Biol, EE-51010 Tartu, Estonia

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

[12] Univ Ferrara, Dept Life Sci & Biotechnol, I-44121 Ferrara, Italy

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

[14] Max Planck Inst Evolutionary Anthropol, Dept Primatol, D-04103 Leipzig, Germany

[15] Arizona State Univ, Sch Human Evolut & Social Change, Tempe, AZ 85287 USA

[16] Arizona State Univ, Inst Human Origins, Tempe, AZ 85287 USA

[17] ICREA, Barcelona 08010, Catalonia, Spain

来源：

SCIENCE | 2016年 / 354卷 / 6311期

基金：

瑞士国家科学基金会; 英国惠康基金;

关键词：

POPULATION HISTORY; PAN-TROGLODYTES; NEANDERTHAL; SEQUENCE; HUMANS;

D O I：

10.1126/science.aag2602

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：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.

引用

页码：477 / 481

页数：6

共 24 条

[1]

A new approach to estimate parameters of speciation models with application to apes [J].

Becquet, Celine ;

Przeworski, Molly .

GENOME RESEARCH, 2007, 17 (10) :1505-1519

[2]

Genetic structure of chimpanzee populations [J].

Becquet, Celine ;

Patterson, Nick ;

Stone, Anne C. ;

Przeworski, Molly ;

Reich, David .

PLOS GENETICS, 2007, 3 (04) :0617-0626

[3]

Analysis of chimpanzee history based on genome sequence alignments [J].

Caswell, Jennifer L. ;

Mallick, Swapan ;

Richter, Daniel J. ;

Neubauer, Julie ;

Gnerre, Christine Schirmer Sante ;

Gnerre, Sante ;

Reich, David .

PLOS GENETICS, 2008, 4 (04)

[4]

Robust Demographic Inference from Genomic and SNP Data [J].

Excoffier, Laurent ;

Dupanloup, Isabelle ;

Huerta-Sanchez, Emilia ;

Sousa, Vitor C. ;

Foll, Matthieu .

PLOS GENETICS, 2013, 9 (10)

[5]

Bonobos Fall within the Genomic Variation of Chimpanzees [J].

Fischer, Anne ;

Pruefer, Kay ;

Good, Jeffrey M. ;

Halbwax, Michel ;

Wiebe, Victor ;

Andre, Claudine ;

Atencia, Rebeca ;

Mugisha, Lawrence ;

Ptak, Susan E. ;

Paeaebo, Svante .

PLOS ONE, 2011, 6 (06)

[6]

An early modern human from Romania with a recent Neanderthal ancestor [J].

Fu, Qiaomei ;

Hajdinjak, Mateja ;

Moldovan, Oana Teodora ;

Constantin, Silviu ;

Mallick, Swapan ;

Skoglund, Pontus ;

Patterson, Nick ;

Rohland, Nadin ;

Lazaridis, Iosif ;

Nickel, Birgit ;

Viola, Bence ;

Pruefer, Kay ;

Meyer, Matthias ;

Kelso, Janet ;

Reich, David ;

Paeaebo, Svante .

NATURE, 2015, 524 (7564) :216-+

[7]

The Sampling Scheme Matters: Pan troglodytes troglodytes and P-t. schweinfurthii Are Characterized by Clinal Genetic Variation Rather Than a Strong Subspecies Break [J].

Fuenfstueck, Tillmann ;

Arandjelovic, Mimi ;

Morgan, David B. ;

Sanz, Crickette ;

Reed, Patricia ;

Olson, Sarah H. ;

Cameron, Ken ;

Ondzie, Alain ;

Peeters, Martine ;

Vigilant, Linda .

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, 2015, 156 (02) :181-191

[8]

A Draft Sequence of the Neandertal Genome [J].

Green, Richard E. ;

Krause, Johannes ;

Briggs, Adrian W. ;

Maricic, Tomislav ;

Stenzel, Udo ;

Kircher, Martin ;

Patterson, Nick ;

Li, Heng ;

Zhai, Weiwei ;

Fritz, Markus Hsi-Yang ;

Hansen, Nancy F. ;

Durand, Eric Y. ;

Malaspinas, Anna-Sapfo ;

Jensen, Jeffrey D. ;

Marques-Bonet, Tomas ;

Alkan, Can ;

Pruefer, Kay ;

Meyer, Matthias ;

Burbano, Hernan A. ;

Good, Jeffrey M. ;

Schultz, Rigo ;

Aximu-Petri, Ayinuer ;

Butthof, Anne ;

Hoeber, Barbara ;

Hoeffner, Barbara ;

Siegemund, Madlen ;

Weihmann, Antje ;

Nusbaum, Chad ;

Lander, Eric S. ;

Russ, Carsten ;

Novod, Nathaniel ;

Affourtit, Jason ;

Egholm, Michael ;

Verna, Christine ;

Rudan, Pavao ;

Brajkovic, Dejana ;

Kucan, Zeljko ;

Gusic, Ivan ;

Doronichev, Vladimir B. ;

Golovanova, Liubov V. ;

Lalueza-Fox, Carles ;

de la Rasilla, Marco ;

Fortea, Javier ;

Rosas, Antonio ;

Schmitz, Ralf W. ;

Johnson, Philip L. F. ;

Eichler, Evan E. ;

Falush, Daniel ;

Birney, Ewan ;

Mullikin, James C. .

SCIENCE, 2010, 328 (5979) :710-722

[9]

Contrasting demographic histories of the neighboring bonobo and chimpanzee [J].

Hvilsom, Christina ;

Carlsen, Frands ;

Heller, Rasmus ;

Jaffre, Nina ;

Siegismund, Hans R. .

PRIMATES, 2014, 55 (01) :101-112

[10]

Ancient gene flow from early modern humans into Eastern Neanderthals [J].

Kuhlwilm, Martin ;

Gronau, Ilan ;

Hubisz, Melissa J. ;

de Filippo, Cesare ;

Prado-Martinez, Javier ;

Kircher, Martin ;

Fu, Qiaomei ;

Burbano, Hernan A. ;

Lalueza-Fox, Carles ;

de la Rasilla, Marco ;

Rosas, Antonio ;

Rudan, Pavao ;

Brajkovic, Dejana ;

Kucan, Zeljko ;

Gusic, Ivan ;

Marques-Bonet, Tomas ;

Andres, Aida M. ;

Viola, Bence ;

Paeaebo, Svante ;

Meyer, Matthias ;

Siepel, Adam ;

Castellano, Sergi .

NATURE, 2016, 530 (7591) :429-+

← 1 2 3 →