Data from: Interpreting the estimated timing of migration events between hybridizing species

The question of whether speciation can occur in the presence of gene flow has long been a contentious one. However, measuring the amount and timing of gene flow remains challenging. The computer program IMA2 allows researchers to estimate the timing of migration events for each locus during analyses, and these estimates have been used to infer the timing of introgression and mode of speciation. We use simulated datasets to examine the degree to which gene flow timing estimates can be used for these purposes, and what demographic conditions and datasets may be most amenable to gene flow timing estimation. We find that the 90% highest posterior density (HPD) interval of gene flow timing is almost always substantially wider than the actual window of gene flow, and increasing the information content of the dataset in terms of number of loci, number of sequences sampled, or locus length (and thus number of variable sites) has little impact on the posterior distribution over the range of values we tested. Even when simulated gene flow only occurred over the most recent 0.01% of the species’ history, the HPD interval usually encompasses the inferred divergence time. Our results indicate that gene flow timing estimates made using the method currently implemented in IMA2 cannot reliably be used to make inferences about the timing of introgression between diverged species or to distinguish between speciation with gene flow and allopatric speciation followed by one or more episodes of gene flow.

物种形成（speciation）能否在基因流（gene flow）存在的前提下发生，长期以来都是一个极具争议的学术议题。然而，量化基因流的规模与发生时间始终是一项颇具挑战性的工作。计算机程序IMA2可支持研究人员在分析过程中，对每个基因座（locus）的迁移事件发生时间进行估算，此类估算手段已被用于推断基因渐渗（introgression）的发生时间与物种形成模式。本研究借助模拟数据集，考察基因流时间估算在上述研究场景中的适用性，以及哪些种群统计条件与数据集最适配基因流时间估算任务。研究结果显示：基因流时间的90%最高后验密度（HPD, highest posterior density）区间，几乎始终显著宽于实际的基因流发生窗口；且在我们测试的参数范围内，通过增加基因座数量、采样序列数或基因座长度（进而提升可变位点总数）来提高数据集的信息含量，对其后验分布几乎无显著影响。即便模拟的基因流仅发生在物种历史中最近的0.01%时段，其HPD区间通常也会覆盖推断得到的物种分化时间。本研究结果表明，依托IMA2当前实现的方法所得到的基因流时间估算值，无法可靠地用于推断分化物种间的基因渐渗时间，也无法区分存在基因流的物种形成模式，与先发生异域物种形成（allopatric speciation）、后续再出现一次或多次基因流事件的演化模式。