A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.
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DOI：
10.1371/journal.pgen.1003125
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Schierup MH
中科院分区：
文献类型：
--
作者：
Mailund T;Halager AE;Westergaard M;Dutheil JY;Munch K;Andersen LN;Lunter G;Prüfer K;Scally A;Hobolth A;Schierup MH
我们提出了一个隐马尔可夫模型(HMM)来推断物种形成过程中两个种群之间的逐渐隔离，该模型被建模为一个受限制的基因流的时间间隔。隐马尔可夫模型描述了两个基因组序列中相邻核苷酸的历史，使得核苷酸可以通过重组而分离，可以在种群之间迁移，或者可以在不同的时间点聚合，所有这些都取决于模型的参数，即有效种群大小、分裂时间、重组率和迁移率。大量的仿真实验表明，隐马尔可夫模型能够准确地推断出除重组率外的所有参数，重组率是向下偏向的。推断对序列上的突变率和重组率的变化是健壮的，对基因组的未知阶段也是健壮的，除非它们是非常密切的联系。我们提供了一个关于分歧是渐进的还是瞬时的测试，并将该模型应用于大猩猩的三个关键的分歧过程：(A)矮黑猩猩和普通黑猩猩，(B)东部和西部的大猩猩，以及(C)苏门答腊岛和婆罗洲的猩猩。我们发现，矮黑猩猩和黑猩猩似乎经历了明显的分裂，而大猩猩和猩猩物种的分化过程发生了数十万年，基因流动最近停止。我们还将该模型应用于人/潘物种形成事件，发现最有可能的情况涉及物种形成过程中延长的基因流动时期。下一代测序技术使许多密切相关物种的全基因组数据得以产生。对于群体遗传推断，我们已经对许多基因座进行了测序，但只对少数几个个体进行了测序。我们提出了一种新的方法，该方法允许基于两个紧密相关的基因组来推断分歧过程，这两个基因组被建模为在带有迁移的隔离模型中逐渐隔离。这使得可以估计限制基因流动的初始时间、基因流动停止的时间以及种群大小、迁移率和重组率。模拟结果表明，该模型对全基因组数据的参数估计是准确的，并利用该模型解开了三组关系密切的类人猿物种：矮黑猩猩/黑猩猩、东部/西部大猩猩和苏门答腊/婆罗洲猩猩之间的分化过程。我们发现矮黑猩猩和黑猩猩是异地物种，而大猩猩和红毛猩猩是非异地物种。我们还考虑了人类和黑猩猩/矮黑猩猩之间的分裂，并找到了非异地物种形成的证据，类似于大猩猩和猩猩的物种形成。
We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation. Next-generation sequencing technology has enabled the generation of whole-genome data for many closely related species. For population genetic inference we have sequenced many loci, but only in a few individuals. We present a new method that allows inference of the divergence process based on two closely related genomes, modelled as gradual isolation in an isolation with migration model. This allows estimation of the initial time of restricted gene flow, the cessation of gene flow, as well as the population sizes, migration rates, and recombination rates. We show by simulations that the parameter estimation is accurate with genome-wide data and use the model to disentangle the divergence processes among three sets of closely related great ape species: bonobo/chimpanzee, eastern/western gorillas, and Sumatran/Bornean orang-utans. We find allopatric speciation for bonobo and chimpanzee and non-allopatric speciation for the gorillas and orang-utans. We also consider the split between humans and chimpanzees/bonobos and find evidence for non-allopatric speciation, similar to that within gorillas and orang-utans.
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影响因子：
64.8
作者：
Kong A;Frigge ML;Masson G;Besenbacher S;Sulem P;Magnusson G;Gudjonsson SA;Sigurdsson A;Jonasdottir A;Jonasdottir A;Wong WS;Sigurdsson G;Walters GB;Steinberg S;Helgason H;Thorleifsson G;Gudbjartsson DF;Helgason A;Magnusson OT;Thorsteinsdottir U;Stefansson K
通讯作者：
Stefansson K
影响因子：
4.5
作者：
Hobolth A;Christensen OF;Mailund T;Schierup MH
通讯作者：
Schierup MH
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W
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：
Hey, Jody
通讯作者：
Hey, Jody