Data from: Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.

东南亚复杂的气候与地质历史塑造了该区域极高的生物多样性。特别是更新世冰期循环伴随的海平面波动，既促进了种群间的连通性，同时也对其形成了限制。本研究利用2个线粒体标记与3个匿名核标记，旨在明确淡水/咸淡水生的青鳉（Aplocheilus panchax，Hamilton, 1822）能否帮助进一步阐明气候振荡及相关海平面波动如何塑造该区域生物类群的分布格局，以及这些格局是否显示出古流域盆地内存在隔离的证据。我们的分析在青鳉中发现了3个主要的线粒体支系。青鳉线粒体谱系的基础分化时间约为3.5百万年，而这些支系后续的分化时间始于更新世早期（约2.6百万年），并贯穿整个更新世。连续系统地理学分析显示，青鳉在东南亚地区经历了清晰的西向东扩散过程，随后发生快速辐射演化。分布于克拉地峡以北甲米（Krabi）地区的个体与印度支系亲缘关系更近，这为克拉地峡生物地理屏障处存在淡水动物区系间断提供了进一步证据。研究结果表明，位于华莱士线另一侧的苏拉威西岛（Sulawesi）是在相对较近的时期（约30千年前）被殖民的。核DNA的地理结构较弱，但曼特尔（Mantel）检验显示核遗传距离与地理距离呈显著相关。总体而言，这些结果表明，相较于历史隔离，近期的基因流是决定青鳉核遗传变异格局的关键因素，不过线粒体基因组中仍保留了部分历史隔离的信号。本研究进一步验证了克拉地峡存在重要生物地理边界，同时也证明了广布性淡水/咸淡水物种可应用于系统地理学研究，以及它们能够在相对较近的地质时期内跨越主要海洋屏障进行扩散。