Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
School of Biomedical Engineering, Capital Medical University, Beijing 100069, P.R. China.
Mol Biol Evol. 2023 Aug 3;40(8). doi: 10.1093/molbev/msad178.
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here, we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences from Heliconius butterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength.
基因组数据提供了关于物种分歧和种间基因流的历史信息，包括基因流的方向、时间和强度。然而，相反方向的基因流会在多位点序列数据中产生相似的模式，例如杂交物种之间的序列差异减小。因此，推断基因流的方向具有挑战性。在这里，我们使用基于似然的方法在多物种合并-基因渗入模型下研究基因组序列数据中关于基因流方向的信息。我们分析了两个物种的情况，并使用模拟来检验三个或四个物种的情况。我们发现，从一个小种群向一个大种群推断基因流比相反方向更容易，从一个外群物种向一个内群物种推断基因流（基因流从外群物种到内群物种）比从一个内群物种向一个外群物种推断基因流（基因流从内群物种到外群物种）更容易。如果在初始分歧和随后的基因渗入之间有更长的独立进化时间，推断基因流也更容易。如果假设基因渗入发生在错误的方向，那么基因渗入的时间往往会被正确估计，基因流的贝叶斯检验通常是显著的，而基因渗入概率的估计甚至可能大于真实概率。我们分析了来自 Heliconius 蝴蝶的基因组序列，以证明典型的基因组数据集提供了关于种间基因流的方向、时间和强度的信息。
