广义迁移隔离模型：多位点数据集的极大似然实现
The Generalised Isolation-With-Migration Model: a Maximum-Likelihood Implementation for Multilocus Data Sets
摘要：
物种形成过程的统计推断往往是基于隔离与迁移（IM）模型，特别是当研究的目的是了解存在或不存在的基因流在分歧。本文介绍的广义IM模型扩展了标准的两个人口IM模型和隔离与初始迁移（IIM）模型，并包括这两个模型的特殊情况。它可以被描述为一个两种群IM模型，其中迁移率和种群规模允许在过去的某个时间点发生变化。通过开发这个GIM模型的最大似然实现，我们能够推断两个密切相关的物种之间的基因流的历史和当代的速度。我们的方法依赖于合并生成矩阵的谱分解，并且适用于由大量独立位点中的每一个处的一对DNA序列之间的核苷酸差异的数目组成的数据集。
英文摘要：
Statistical inference about the speciation process has often been based on the isolation-with-migration (IM) model, especially when the research aim is to learn about the presence or absence of gene flow during divergence. The generalised IM model introduced in this paper extends both the standard two-population IM model and the isolation-with-initial-migration (IIM) model, and encompasses both these models as special cases. It can be described as a two-population IM model in which migration rates and population sizes are allowed to change at some point in the past. By developing a maximum-likelihood implementation of this GIM model, we enable inference on both historical and contemporary rates of gene flow between two closely related species. Our method relies on the spectral decomposition of the coalescent generator matrix and is applicable to data sets consisting of the numbers of nucleotide differences between one pair of DNA sequences at each of a large number of independent loci.
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