Data from: Demographic modeling with whole genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well-suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here we use genomic data and demographic modeling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.

物种形成的模式与机制，在年轻物种类群中最便于开展研究。对于演化年代较久的类群而言，区分物种形成过程中与物种形成后发生的事件，难度会随类群年龄增长而不断提升。维多利亚湖朴丽鱼属（Pundamilia）慈鲷，包含了一组年轻物种类群与多态种群复合体。其中该属的两个物种类群——P. pundamilia与P. nyererei——尤其适合用于物种形成研究。该湖内不同岩质岛屿中均存在同域分布（sympatry）种群对，且这些种群对在表型分化（phenotypic differentiation）与生殖隔离（reproductive isolation）程度上存在显著差异。同一名义物种的异域分布（allopatry）岛屿种群间的遗传距离，往往大于同域分布物种间的遗传距离。因此，学界至今尚未明确：P. nyererei与P. pundamilia的物种形成事件是否仅发生过一次，随后经历了地理范围扩张，并在局部同域区域发生了种间基因流（gene flow）；亦或是这一物种类群通过平行物种形成（parallel speciation）的方式多次独立起源。本研究利用基因组数据与种群动力学建模（demographic modeling），对这两种对立的演化假说进行验证。研究结果表明，基因流在塑造观测到的遗传相似性模式中发挥了关键作用，涵盖同域物种间的基因流、异域种群间的基因流，以及近期与早期的基因流事件。针对两座不同岛屿上的P. pundamilia与P. nyererei种群对，支持度最高的起源模型显示：物种形成事件共发生过两次，其中第二次物种形成事件，发生在从早期起源的异域P. nyererei种群渗入（introgression）基因之后不久。本研究结果支持这一假说：高度相似的物种可能会多次独立起源，而渗入的遗传变异或可推动这一过程。