Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow.
Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow.
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DOI：
10.1093/molbev/mss118
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发表时间：
2012-10
影响因子：
10.7
通讯作者：
Tianqi Zhu;Ziheng Yang
中科院分区：
文献类型：
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作者：
Tianqi Zhu;Ziheng Yang
我们实现了三个物种的隔离和迁移模型，迁移发生在两个紧密相关的物种之间，而一个类群外的物种被用来提供关于基因树和模型参数的进一步信息。该模型是在用于分析多位点基因组序列比对的似然框架中实现的，从这三个物种中的每一个物种中都采集了一个序列。基因树拓扑结构和每个基因座上的分支长度的先验分布通过马尔科夫链描述合并和迁移的系谱过程来计算，该马尔科夫链解析地整合了迁移事件的历史。通过对基因树中的分支长度(合并时间)进行数值积分来计算似然函数。我们分析了该模型来研究基因树-物种树的错配概率和到最近共同祖先在一个基因座上的时间。该模型用于构建具有基因流的物种形成的似然比检验(LRT)。我们进行了计算机模拟来评估LRT，发现该测试总体上是保守的，假阳性率远低于显著水平。要使这项测试具有实质性的威力，需要数百个基因座。对人类-黑猩猩-大猩猩基因组数据集的测试表明，在人类和黑猩猩形成物种的时间周围，基因流动。
We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The prior distribution of gene tree topology and branch lengths at every locus is calculated using a Markov chain characterization of the genealogical process of coalescent and migration, which integrates over the histories of migration events analytically. The likelihood function is calculated by integrating over branch lengths in the gene trees (coalescent times) numerically. We analyze the model to study the gene tree-species tree mismatch probability and the time to the most recent common ancestor at a locus. The model is used to construct a likelihood ratio test (LRT) of speciation with gene flow. We conduct computer simulations to evaluate the LRT and found that the test is in general conservative, with the false positive rate well below the significance level. For the test to have substantial power, hundreds of loci are needed. Application of the test to a human-chimpanzee-gorilla genomic data set suggests gene flow around the time of speciation of the human and the chimpanzee.