Data from: Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris

The Ponto-Caspian brackish-water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish-water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly) recolonized from the Caspian. Using microsatellite and mtDNA markers, we demonstrate deep among- and within-basin subdivisions in a widespread Ponto-Caspian mysid crustacean Paramysis lacustris. Five genetic clusters were identified, but their relationships did not reflect the geography of the region. The Azov cluster was the most distinct (4–5% COI divergence), despite its geographic position in the corridor between Black and Caspian seas, and may represent a new species. In the northern Black Sea area, the Dnieper cluster was closer to the Caspian cluster than to the neighbouring Danube–Dniester–Bug populations, suggesting separate colonizations of the Black Sea. Overall, the data implied a predominant gene flow from the east to the Black Sea and highlight the importance of Caspian Sea transgressions in facilitating dispersal. Yet, the presence of distinct lineages in the Black Sea points to the persistence of isolated refugial populations that have gained diagnostic differences under presumably high mutation rates and large population sizes. The unfavourable Pleistocene periods in the Black Sea therefore appear to have promoted diversification of the brackish-water lineages, rather than extirpated them.蓬蒂-里海咸水动物群（Ponto-Caspian brackish-water fauna）栖息于黑海、亚速海与里海的河口及河流生境，被高盐度水域与主要跨流域分水岭分割为孤立片段。该类群以极高的特有性水平、复杂的动物地理学演化历史，以及作为近期成功入侵物种的重要来源而广受关注。目前学界仍存在争议：黑海与亚速海的咸水种群究竟是在更新世恶劣气候下于多个独立避难所中存续下来，还是两海曾（反复）从里海获得重新定殖？本研究利用微卫星（microsatellite）标记与线粒体DNA（mtDNA），对广泛分布的蓬蒂-里海糠虾类甲壳动物湖柱突糠虾（Paramysis lacustris）开展遗传分析，揭示了该物种在盆地内与跨盆地间的深层遗传分化结构。研究共鉴定出5个遗传聚类（genetic cluster），但其演化亲缘关系并未与该区域的地理格局相匹配。其中亚速海聚类的分化程度最高（细胞色素氧化酶亚基I（COI）序列分歧率达4%–5%），尽管其地理上位于黑海与里海之间的生态廊道中，该聚类或代表一个全新的物种。在北黑海区域，第聂伯河聚类相较于邻近的多瑙河-德涅斯特河-布格河种群，与里海聚类的亲缘关系更为紧密，这表明黑海的咸水动物群存在独立的定殖事件。总体而言，研究数据显示存在以从东向西流向黑海为主的基因流（gene flow），凸显了里海海侵在促进物种扩散过程中的关键作用。然而，黑海区域存在独特演化支系这一现象表明，孤立的避难所种群得以长期存续，并在高突变率与大种群规模的背景下积累了诊断性遗传差异。因此，黑海地区更新世的恶劣环境非但没有导致咸水动物支系的灭绝，反而推动了其多样化演化进程。