Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors.
Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors.
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DOI：
10.1093/molbev/mst125
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发表时间：
2013-09
影响因子：
10.7
通讯作者：
Goddard ME
中科院分区：
文献类型：
--
作者：
MacLeod IM;Larkin DM;Lewin HA;Hayes BJ;Goddard ME
全基因组序列可能是推断祖先人口统计学的最丰富的遗传数据来源。然而，全序列也提出了重大挑战，以充分利用这样的大数据集，并确保测序错误不会引入偏见到推断的人口。使用两个荷斯坦牛的全基因组序列数据，我们展示了一种新的方法来纠正隐藏的错误所造成的偏见，然后推断逐步变化的祖先人口统计到目前为止。如果不对数据应用校正方法，则近期有效人口规模（Ne）的估计值存在强烈的向上偏差，无论是对于我们的方法还是Li和Durbin（从个体全基因组序列推断人类人口历史。Nature 475：493 - 496）成对顺序马尔可夫结合方法。为了推断人口统计学，我们使用了一个分析预测的多位点连锁不平衡（LD）的基础上一个简单的合并模型，允许在Ne的变化。LD统计量总结了任何给定人口统计学的纯合性运行的分布。我们推断出一个最佳拟合的人口统计学，预测与所观察到的分布在校正的序列数据中的纯合性运行的匹配。我们使用多位点LD，因为它可能比成对LD包含更多关于祖先人口统计学的信息。推测的人口统计学表明，大约在17万年前，Ne的数量大幅减少，这可能与非洲和欧洲的牛的分化有关。随后，随着牛的驯化，Ne进一步减少，在3，500和6，000之间。最近的减少Ne约100荷斯坦牛品种同意以及估计从系谱。我们的方法可以应用于任何二倍体物种的全基因组序列，并可以扩大到使用多个个体的序列。
Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant challenges to fully utilize such large data sets and to ensure that sequencing errors do not introduce bias into the inferred demography. Using whole-genome sequence data from two Holstein cattle, we demonstrate a new method to correct for bias caused by hidden errors and then infer stepwise changes in ancestral demography up to present. There was a strong upward bias in estimates of recent effective population size (Ne) if the correction method was not applied to the data, both for our method and the Li and Durbin (Inference of human population history from individual whole-genome sequences. Nature 475:493–496) pairwise sequentially Markovian coalescent method. To infer demography, we use an analytical predictor of multiloci linkage disequilibrium (LD) based on a simple coalescent model that allows for changes in Ne. The LD statistic summarizes the distribution of runs of homozygosity for any given demography. We infer a best fit demography as one that predicts a match with the observed distribution of runs of homozygosity in the corrected sequence data. We use multiloci LD because it potentially holds more information about ancestral demography than pairwise LD. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago, possibly related to the divergence of African and European Bos taurus cattle. This is followed by a further reduction coinciding with the period of cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. Our approach can be applied to whole-genome sequence from any diploid species and can be scaled up to use sequence from multiple individuals.
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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
DOI：
10.1073/pnas.0509210103
发表时间：
2006-05-23
影响因子：
11.1
作者：
Beja-Pereira, Albano;Caramelli, David;Bertorelle, Giorgio
通讯作者：
Bertorelle, Giorgio
影响因子：
64.8
作者：
Li, Heng;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
10.7
作者：
Lynch, Michael
通讯作者：
Lynch, Michael
影响因子：
3.3
作者：
Lohmueller, Kirk E.;Bustamante, Carlos D.;Clark, Andrew G.
通讯作者：
Clark, Andrew G.