Data from: Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)

Investigating variation in gene flow across the genome between closely related species is important to understand how reproductive barriers shape genome divergence before speciation is complete. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange between species, leading to heterogeneous genome divergence. In the present study, genome-wide divergence and introgression patterns were investigated between two sole species, Solea senegalensis and Solea aegyptiaca, using restriction-associated DNA sequencing (RAD-Seq) to analyse samples taken from a transect spanning the hybrid zone. An integrative approach combining geographic and genomic clines methods with an analysis of individual locus introgression accounting for the demographic history of divergence was conducted. Our results showed that the two sole species have come into secondary contact postglacially, after experiencing a prolonged period (ca. 1.1 to 1.8 Myrs) of allopatric separation. Secondary contact resulted in the formation of a tension zone characterized by strong reproductive isolation, allowing introgression in only a minor fraction of the genome. We found multiple evidence for a preferential direction of introgression in the S. aegyptiaca genetic background, indicating a possible recent or ongoing movement of the hybrid zone. Deviant introgression signals found in the opposite direction suggested that S. senegalensis could have possibly undergone adaptive introgression that has not yet spread throughout the entire species range. Our study thus illustrates the varied outcomes of genetic interactions between divergent gene pools that recently met after a long history of divergence.探究近缘物种间全基因组基因流的变异规律，对于理解物种形成完成前生殖隔离如何塑造基因组分化具有重要意义。表征差异化基因流的有效途径，是研究杂交带内发生的遗传互作如何选择性过滤物种间的基因交换，进而导致基因组分化呈现异质性。本研究以两种鳎属物种——塞内加尔鳎（Solea senegalensis）与埃及鳎（Solea aegyptiaca）为研究对象，利用限制性位点相关DNA测序（restriction-associated DNA sequencing，RAD-Seq）分析了横跨杂交带样带采集的样本，以解析二者的全基因组分化与基因渐渗模式。本研究采用整合分析策略，结合地理梯度与基因组梯度分析方法，并开展了纳入分化种群历史背景的单基因座渐渗分析。研究结果显示，这两种鳎属物种在经历了约110万至180万年的异域隔离阶段后，于冰期后发生了二次接触。二次接触形成了以强生殖隔离为特征的杂交张力区，仅允许极小部分基因组发生基因渐渗。本研究发现多项证据表明，基因渐渗存在偏向埃及鳎遗传背景的方向，这提示杂交带可能正处于近期或持续的移动过程中。反向检测到的异常渐渗信号则表明，塞内加尔鳎或许经历了尚未在整个物种分布范围内扩散的适应性渐渗事件。综上，本研究阐明了经历长期分化后再度相遇的趋异基因库之间，遗传互作所产生的多样演化结果。