Data from: Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genus Dyscophus

Madagascar is a biodiversity hotspot with a unique fauna and flora largely endemic at the species level and highly threatened by habitat destruction. The processes underlying population-level differentiation in Madagascar's biota are poorly understood and have been proposed to be related to Pleistocene climatic cycles, yet the levels of genetic divergence observed are often suggestive of ancient events. We combined molecular markers of different variability to assess the phylogeography of Madagascar's emblematic tomato frogs (Dyscophus guineti and D. antongilii) and interpret the observed pattern as resulting from ancient and recent processes. Our results suggest that the initial divergence between these taxa is probably old as reflected by protein-coding nuclear genes and by a strong mitochondrial differentiation of the southernmost population. Dramatic changes in their demography appear to have been triggered by the end of the last glacial period and possibly by the short return of glacial conditions known as the 8K event. This dramatic change resulted in an approximately 50-fold reduction of the effective population size in various populations of both species. We hypothesize these species' current mitochondrial DNA diversity distribution reflects a swamping of the mitochondrial genetic diversity of D. guineti by that of D. antongilii previous to the populations' bottlenecks during the Holocene, and probably as a consequence of D. antongilii demographic expansion approximately 1 million years ago. Our data support the continued recognition of D. antongilii and D. guineti as separate species and flag D. guineti as the more vulnerable species to past and probably also future environmental changes.马达加斯加是全球生物多样性热点地区，拥有独特的动植物区系，其中多数物种为特有种，且其生存正遭受栖息地破坏的严重威胁。目前学界对马达加斯加生物群种群分化背后的演化机制尚不清楚，此前有研究提出该机制与更新世（Pleistocene）气候周期相关，但观测到的遗传分化水平往往暗示着更为古老的演化事件。本研究结合不同变异程度的分子标记，对马达加斯加标志性的番茄蛙（*Dyscophus guineti* 和 *D. antongilii*）的系统地理学开展评估，并将观测到的分布格局归因于古老与近期两类演化过程的共同作用。研究结果显示，这两个类群的初始分化时间可能较为久远，这一点可从编码蛋白质的核基因以及最南部种群显著的线粒体分化中得到印证。这两个类群的种群动态发生剧烈变化，其触发因素似乎是末次冰期的结束，也可能与被称为“8K事件”的短暂冰期环境回返有关。此次剧烈变化导致两个物种各群体的有效种群大小（effective population size）缩减约50倍。本研究提出假说：在全新世（Holocene）的种群瓶颈事件发生之前，安通吉尔湾番茄蛙（*D. antongilii*）的线粒体遗传多样性已淹没吉氏番茄蛙（*D. guineti*）的线粒体遗传多样性，这一现象正是当前两个物种线粒体DNA多样性分布格局的形成原因；而这一渗入过程可能源于约100万年前安通吉尔湾番茄蛙的种群扩张。本研究的数据支持将安通吉尔湾番茄蛙与吉氏番茄蛙仍作为两个独立物种进行分类，并指出吉氏番茄蛙相较于安通吉尔湾番茄蛙，对过去以及未来的环境变化更为脆弱。