Data from: Genomic evidence of gene flow during reinforcement in Texas Phlox

Gene flow can impede the evolution of reproductive isolating barriers between species. Reinforcement is the process by which pre-zygotic reproductive isolation evolves in sympatry due to selection to decrease costly hybridization. It is known that reinforcement can be prevented by too much gene flow, but we still do not know how often have pre-zygotic barriers evolved in the presence of gene flow or how much gene flow can occur during reinforcement. Flower color divergence in the native Texas wildflower, Phlox drummondii, is one of the best-studied cases of reinforcement. Here we use genomic analyses to infer gene flow between P. drummondii and a closely related sympatric species, P. cuspidata. We de novo assemble transcriptomes of four Phlox species to determine the phylogenetic relationships between these species, and find extensive discordance among gene tree topologies across genes. We find evidence of introgression between sympatric P. drummondii and P. cuspidata using the D-statistic, and use phylogenetic analyses to infer the predominant direction of introgression. We investigate geographic variation in gene flow by comparing the relative divergence of genes displaying discordant gene trees between an allopatric and sympatric sample. These analyses support the hypothesis that sympatric P. drummondii has experienced gene flow with P. cuspidata. We find that gene flow between these species is asymmetrical, which could explain why reinforcement caused divergence in only one of the sympatric species. Given the previous research in this system, we suggest strong selection can explain how reinforcement successfully evolved in this system despite gene flow in sympatry.

基因流会阻碍物种间生殖隔离屏障的演化。强化选择（reinforcement）指因选择压力作用以降低代价高昂的杂交事件，最终在同域分布类群中演化出合子前生殖隔离的过程。已有研究表明，过高的基因流会阻碍强化选择的发生，但目前我们仍不清楚：在基因流存在的背景下，合子前生殖隔离屏障的演化频率究竟几何，或是在强化选择进程中可发生的基因流程度上限为何。德克萨斯州原生野生福禄考（Phlox drummondii）的花色分化现象，是目前研究最为深入的强化选择案例之一。本研究通过基因组分析手段，推断福禄考（P. drummondii）与其近缘同域物种尖叶福禄考（P. cuspidata）之间的基因流情况。我们对四种福禄考属物种的转录组进行从头组装，以明确这些物种间的系统发育关系，同时发现不同基因的基因树拓扑结构间存在广泛的拓扑冲突。我们借助D统计量（D-statistic），找到了同域分布的P. drummondii与P. cuspidata之间存在遗传渐渗的证据，并通过系统发育分析推断出该渐渗事件的主要方向。我们通过对比异域样本与同域样本间存在基因树拓扑冲突的基因的相对分化程度，探究了基因流的地理变异模式。上述分析结果支持了“同域分布的P. drummondii曾与P. cuspidata发生过基因交流”这一假说。我们发现这两个物种间的基因流具有不对称性，这一发现或可解释为何强化选择仅在其中一个同域物种中引发了分化。结合该研究体系此前的相关研究成果，我们提出：尽管同域分布类群间存在基因流，但强大的选择压力足以解释本研究体系中强化选择为何能够成功演化。