Data from: Demographic modelling 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 modelling 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适于开展深入研究。对于演化年代较久的类群而言，区分物种形成过程与物种形成后发生的演化事件，难度愈发增大。维多利亚湖朴丽鱼属（Pundamilia）类群包含一系列年轻物种与多态种群。其中P. pundamilia与P. nyererei这一物种对，尤其适合用于物种形成研究：该湖不同岩礁岛屿的生境内，存在表型分化程度与生殖隔离水平各异的同域种群对。同一名义物种的异域岛屿种群间的遗传距离，往往高于同域分布物种间的遗传距离。因此，关于这两个物种的起源始终未有定论：究竟是单次物种形成事件后伴随地理范围扩张，并在局部同域环境中发生种间基因流，还是该物种类对通过平行物种形成多次独立起源？ 本研究利用基因组数据与种群人口建模（demographic modelling），检验这两种对立的演化假说。研究证实，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，既涵盖同域物种间的基因流，也包含异域种群间的基因流，同时涉及近期与早期的基因流事件。针对两座不同岛屿的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两次，其中第二次物种形成事件紧随来自早期分化的异域P. nyererei种群的渐渗事件之后发生。 本研究结果支持下述假说：高度相似的物种可多次独立起源，且渐渗获得的遗传变异或可促进这一演化过程。