Widespread genomic signatures of natural selection in hominid evolution.
Widespread genomic signatures of natural selection in hominid evolution.
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DOI：
10.1371/journal.pgen.1000471
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发表时间：
2009-05
期刊：
影响因子：
4.5
通讯作者：
Green P
中科院分区：
文献类型：
--
作者：
McVicker G;Gordon D;Davis C;Green P
作用于基因组功能元件的选择可以通过其对连锁中性位点上的群体多样性的间接影响来检测。为了阐明影响原始人进化的选择性力量，我们分析了人类多态的基因组分布和五个灵长类物种之间相对于保守序列特征位置的序列差异。人类和祖先种群的中性序列多样性在这些特征附近显著减少，由于常染色体上的选择19-26%和X染色体上的12-40%，导致惊人的基因组平均多样性减少。总体趋势与“背景选择”或搭便车的祖先种群的行动，以消除有害的变异大致一致。在外显子(蛋白质编码和非翻译)保守的特征上，平均选择比非外显子特征强得多。长期选择，而不是复杂的物种形成情景，解释了人类/黑猩猩分化的巨大基因组内差异。我们的分析揭示了选择在塑造基因组多样性和分化模式中的主导作用，阐明了原始人的进化，并为研究特定的选择性事件提供了基线。对人类和黑猩猩基因组的比较表明，这些物种之间的序列差异在整个基因组中的频率差异很大。之前提出的对这种变异的解释包括：大量的祖先种群，可变的突变率，或者是人类和黑猩猩最初分离，但随后在数百万年后重新杂交的复杂物种形成场景。在这里，我们考虑了另一种可能性；从种群中移除不太适合的功能变体的选择行动显著减少了附近位置的“中性”序列差异的频率。我们确定了可能受到自然选择影响的序列，因为它们在胎盘哺乳动物中高度保守，并表明在这些序列附近，五个灵长类物种之间的中性差异大大减少。应用理论进化模型，我们发现选择在塑造原始人基因组进化中发挥了比人们所认识到的更大的作用，并比其他假设更好地解释了序列差异的模式。
Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19–26% on the autosomes and 12–40% on the X chromosome. The overall trends are broadly consistent with “background selection” or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events. Comparisons of the human and chimpanzee genomes have revealed that the frequency of sequence differences between these species varies dramatically across the genome. Previously proposed explanations for this variation include a large ancestral population, variable mutation rates, or a complex speciation scenario in which humans and chimpanzees initially separated but then rehybridyzed several million years later. We consider, here, an alternate possibility; the action of selection to remove less-fit functional variants from a population has significantly reduced the frequency of “neutral” sequence differences at nearby sites. We identified sequences that are likely to be subject to natural selection because they are highly conserved across placental mammals and showed that neutral differences among five primate species are greatly depleted near such sequences. Applying a theoretical evolutionary model, we found that selection has played a greater role in shaping hominid genome evolution than has been appreciated and provides a better explanation for patterns of sequence differences than other hypotheses.
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DOI：
10.1098/rstb.2000.0716
发表时间：
2000-11-29
影响因子：
6.3
作者：
Barton, NH
通讯作者：
Barton, NH
影响因子：
9.8
作者：
Berglund, Jonas;Pollard, Katherine S.;Webster, Matthew T.
通讯作者：
Webster, Matthew T.
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
9.8
作者：
Eddy, SR
通讯作者：
Eddy, SR
影响因子：
7
作者：
Hardison, RC;Roskin, KM;Haussler, D
通讯作者：
Haussler, D