Data from: Demography and selection shape transcriptomic divergence in field crickets

Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and G. texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, comparing the observed FST distribution with distributions from coalescent simulations under various demographic scenarios indicates that gene flow (without selection) strongly shaped patterns of genetic divergence. Genetic divergence at FST outlier loci could thus falsely be attributed to selection when not accounting for demographic history. We uncovered a subset of loci with signatures of selection, many of which are candidates for controlling variation in mating behavior. Our results underscore the importance of gene flow and demography in overall levels of genetic divergence and highlight that simultaneously examining demography and selection facilitates a more complete understanding of genetic divergence during speciation.基因流（gene flow）、种群历史动态（demography）与自然选择可产生高度相似的基因组变异模式，厘清三者的作用效应是理解物种形成（speciation）机制的关键所在。本研究通过解析转录组变异（transcriptomic variation），探究隐存田蟋物种红田蟋（Gryllus rubens）与得克萨斯田蟋（G. texensis）的演化历史，二者的交配行为存在显著分化。我们首先推断二者的种群历史动态，并基于该推断得到的种群背景，在其转录组中筛选自然选择印记（footprints of selection）。研究结果为二者存在长期双向基因流提供了强有力的支持，该基因流于更新世晚期终止；同时发现红田蟋存在种群瓶颈事件，与其边缘成种（peripatric origin）的起源假说相符。值得注意的是，将观测到的FST（固定化指数，Fixation Index）分布与不同种群历史情景下的溯祖模拟（coalescent simulations）结果进行对比后发现，未受选择影响的基因流强烈塑造了遗传分化模式。若未纳入种群历史动态的考量，FST异常位点（outlier loci）的遗传分化可能会被错误地归因于自然选择。我们还鉴定出一批带有选择印记的基因位点，其中多数为调控交配行为变异的候选基因。本研究结果强调了基因流与种群历史动态在整体遗传分化水平中的重要性，并表明同时考量种群历史与自然选择，有助于更全面地理解物种形成过程中的遗传分化机制。