Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model.
Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model.
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DOI：
10.1534/genetics.116.188060
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发表时间：
2017-04
期刊：
影响因子：
3.3
通讯作者：
Wilkinson-Herbots H
中科院分区：
文献类型：
--
作者：
Costa RJ;Wilkinson-Herbots H
迁移隔离（IM）模型通常用于利用多态性数据推断物种形成过程中的基因流。然而，据报道，通过拟合IM模型获得的参数估计值对模型的假设非常敏感，包括恒定基因流的假设。本文关注的是初始迁移隔离（IIM）模型，它恰恰放弃了这一假设。在IIM模型中，一个祖先种群分为两个后代亚种群，在这两个亚种群之间有一个初始的基因流动期和随后的隔离期。我们得到了一个非常快速的方法来拟合扩展版本的IIM模型，它也允许不对称的基因流和不平等的人口规模。这是一种最大似然法，适用于来自大量独立基因座的DNA序列对之间的分离位点数的数据。除了获得参数估计，我们的方法也可以用来，通过似然比检验，区分替代模型代表以下分歧的情况：（a）分歧与潜在的不对称基因流，直到现在，（B）分歧与潜在的不对称基因流，直到过去的某个点，并在隔离，因为那时起，（c）分歧完全隔离。我们举例说明的程序对果蝇序列从1030，000个座位。将模型的最复杂版本拟合到该数据集所需的计算时间仅为几分钟。适合IIM模型的R代码可以在本文的补充文件中找到。
The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, it has been reported that the parameter estimates obtained by fitting the IM model are very sensitive to the model’s assumptions—including the assumption of constant gene flow until the present. This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used, by means of likelihood-ratio tests, to distinguish between alternative models representing the following divergence scenarios: (a) divergence with potentially asymmetric gene flow until the present, (b) divergence with potentially asymmetric gene flow until some point in the past and in isolation since then, and (c) divergence in complete isolation. We illustrate the procedure on pairs of Drosophila sequences from ∼30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this article.