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（gene flow）会阻碍物种间生殖隔离屏障（reproductive isolating barriers）的演化。生殖强化（reinforcement）指因选择压力抑制代价高昂的杂交（costly hybridization），而在同域分布（sympatry）类群中演化出合子前生殖隔离（pre-zygotic reproductive isolation）的过程。已知过量的基因流会阻断生殖强化，但目前我们仍不清楚，在基因流存在的情况下合子前生殖隔离屏障演化的频率，以及生殖强化过程中可发生的基因流水平。德克萨斯本土野生植物福禄考（Phlox drummondii）的花色分化，是研究最为深入的生殖强化案例之一。本研究通过基因组分析，推断P. drummondii与其近缘同域物种P. cuspidata之间的基因流情况。我们对4种福禄考物种的转录组（transcriptomes）进行从头组装（de novo assembly），以明确这些物种间的系统发育关系（phylogenetic relationships），并发现不同基因的基因树拓扑结构（gene tree topologies）间存在广泛的不一致性。我们利用D统计量（D-statistic）检测到同域分布的P. drummondii与P. cuspidata之间存在基因渐渗（introgression），并通过系统发育分析推断了基因渐渗的主要方向。我们通过比较异域分布（allopatric）样本与同域分布样本间，携带不一致基因树的基因的相对分化程度，探究了基因流的地理变异。这些分析结果支持"同域分布的P. drummondii曾与P. cuspidata发生过基因流"这一假说。我们发现这两个物种间的基因流具有不对称性，这或许可以解释为何生殖强化仅导致其中一个同域物种发生了分化。结合该研究体系此前的相关成果，我们提出：尽管同域分布类群间存在基因流，但强大的选择压力可以解释本体系中生殖强化为何得以成功演化。