Inference of Gene Flow between Species under Misspecified Models.
Inference of Gene Flow between Species under Misspecified Models.
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DOI：
10.1093/molbev/msac237
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发表时间：
2022-12-05
影响因子：
10.7
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
--
作者：
Huang, Jun;Thawornwattana, Yuttapong;Flouri, Tomas;Mallet, James;Yang, Ziheng
关键词：
基因组序列数据提供了有关物种分化和种间杂交或渐渗历史的丰富信息来源。尽管基因组学和统计学方法最近取得了进展，但推断基因流动仍然具有挑战性，因此，人们可能不得不在错误指定的模型下估计渗透率和时间。在这里，我们使用数学分析和计算机模拟来检查估计偏差和解释问题，当基因组数据集的分析中基因流动模型被错误指定时，例如，如果导入被分配到错误的谱系。在两个种群的情况下，我们建立了连续迁移模型中的迁移率与渗入模型中的渗入概率之间的对应关系。当基因流在时间上连续发生，但在分析中假设发生在固定的时间点时，物种分化时间等常见的进化参数被意外地准确地估计出来。然而，渐渗的时间倾向于估计到连续基因流动期的最近结束。当导入事件被错误地分配给父母或子代谱系时，导入时间倾向于崩溃到物种分化时间，而导入概率被低估。总体而言，我们的分析表明，简单的导入模型对于提取特定基因之间的流动和分化的信息是有用的，即使该模型可能被错误地指定。然而，为了可靠地推断基因流动，重要的是包括每个物种的多个样本，特别是来自杂交物种的样本。
Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species.
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