More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting.
More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting.
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DOI：
10.1111/evo.12118
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发表时间：
2013-08
期刊：
影响因子：
--
通讯作者：
Hahn MW
中科院分区：
文献类型：
--
作者：
Pease JB;Hahn MW
当物种形成事件发生在快速连续，不完全谱系排序（ILS）可能会导致个体基因树之间的分歧。ILS影响给定基因座的概率与其有效群体大小（Ne）直接相关，如果基因组中存在强选择，则有效群体大小（Ne）与重组率成比例。基于这些预期，我们假设基因组的低重组区域，以及性染色体和非重组染色体，应该表现出较低水平的ILS。我们在灵长类、黑腹果蝇进化枝和D.模拟进化枝在所有三种情况下，基因组中重组率低或没有重组的区域显示出对推定物种树的明显更强的支持，尽管X染色体的结果在分支之间存在差异。我们的研究结果表明，在这些低重组区域，经常性的选择，使目前的多样性水平也反映了过去的有效人口规模在这些相同的基因座减少。研究结果还表明，考虑基因树的基因组背景如何有助于更准确地确定真正的物种遗传，特别是在全基因组遗传似乎是一个无法解决的多分裂的情况下。
When speciation events occur in rapid succession, incomplete lineage sorting (ILS) can cause disagreement among individual gene trees. The probability that ILS affects a given locus is directly related to its effective population size (Ne), which in turn is proportional to the recombination rate if there is strong selection across the genome. Based on these expectations, we hypothesized that low-recombination regions of the genome, as well as sex chromosomes and non-recombining chromosomes, should exhibit lower levels of ILS. We tested this hypothesis in phylogenomic datasets from primates, the Drosophila melanogaster clade, and the D. simulans clade. In all three cases, regions of the genome with low or no recombination showed significantly stronger support for the putative species tree, although results from the X chromosome differed among clades. Our results suggest that recurrent selection is acting in these low-recombination regions, such that current levels of diversity also reflect past decreases in the effective population size at these same loci. The results also demonstrate how considering the genomic context of a gene tree can assist in more accurate determination of the true species phylogeny, especially in cases where a whole-genome phylogeny appears to be an unresolvable polytomy.
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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
影响因子：
4.5
作者：
Comeron JM;Ratnappan R;Bailin S
通讯作者：
Bailin S
影响因子：
12.3
作者：
Haddrill PR;Halligan DL;Tomaras D;Charlesworth B
通讯作者：
Charlesworth B
影响因子：
9.8
作者：
Chen, FC;Li, WH
通讯作者：
Li, WH
影响因子：
4.5
作者：
Cai, James J.;Macpherson, J. Michael;Sella, Guy;Petrov, Dmitri A.
通讯作者：
Petrov, Dmitri A.