Data from: Ancient hybridization and genomic stabilization in a swordtail fish

A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to post-speciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human-Neandertal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.

日益增多的研究表明，不同物种的基因组往往具备杂交起源（hybrid ancestry）特征，其成因大概率为近缘物种在物种形成后发生的杂交（post-speciation hybridization）事件。尽管已报道的杂交起源案例数量持续增长，但学界对杂交后基因组的演化与稳定机制，以及杂交在功能层面的相关程度，仍缺乏足够认知。本研究以剑尾鱼属物种Xiphophorus nezahualcoyotl——一种硬骨鱼（teleost fish）——为研究对象，该物种的基因组呈现出显著的杂交起源特征。研究证实，该物种的杂交事件距今相对久远，且大概率并未持续发生。尤为值得注意的是，X. nezahualcoyotl的基因组在杂交后已基本完成稳定化，这使其区别于人类-尼安德特人杂交（human-Neandertal hybridization）这类典型案例。杂交起源的基因组区域与基因组其余区域存在显著差异，往往富集于进化约束减弱（reduced constraint）的基因组区域中。上述结果表明，自然选择在清除部分功能重要区域内的杂交起源序列方面发挥了关键作用。结合其他研究体系中的相关发现，本研究结果引出了诸多亟待解答的问题：包括基因组稳定化的具体过程，以及自然选择在塑造基因组杂交起源模式中所扮演的角色。