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、种群历史动态与自然选择可产生相似的基因组变异模式，厘清三者的效应是理解物种形成的关键。本研究通过评估转录组变异，解析红田蟋（Gryllus rubens）与德克萨斯田蟋（G. texensis）的演化历史——二者为交配行为高度分化的隐存田蟋物种。我们推断了它们的种群历史，并结合所推断的种群历史背景，在转录组中筛选自然选择的印记。研究结果强烈支持二者存在长期的双向基因流，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，这与其边缘成种的起源模式相符。值得注意的是，将观测到的固定指数（FST）分布与不同种群历史情景下的溯祖模拟结果进行比较后发现，不考虑选择的基因流极大地塑造了遗传分化模式。若未考虑种群历史，FST异常位点的遗传分化可能会被错误归因于自然选择。我们还鉴定出一批携带选择印记的位点，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，能够更全面地理解物种形成过程中的遗传分化机制。