Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armor and reduction of appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters.

栖息于古老湖泊、海洋岛屿及其他长期隔离生境的特有物种集群，常被视为适应性辐射的典型范例。然而，针对此类物种集群辐射过程中定向选择的分子证据却较为匮乏。本研究利用俄罗斯西伯利亚贝加尔湖特有端足类（amphipods）64个物种及2个非特有外群（outgroup）的部分转录组（transcriptome）数据，构建了该特有物种集群的修正系统发育树，并分析了特有支系内的正选择证据。本研究确认端足类曾两次独立入侵贝加尔湖，并证实贝加尔湖端足类的多项形态特征，如躯体装甲、附肢与感官器官退化等，在多个支系中平行演化。贝加尔湖端足类的辐射演化以系统发育分支较短、频繁出现正选择事件为典型特征；其中正选择在端足类第二次入侵贝加尔湖的早期（即物种多样性快速分化最剧烈的时期）发生频率更高。值得注意的是，编码参与电子传递链（electron transfer chain）与ATP合成（ATP synthesis）功能的线粒体膜蛋白（mitochondrial membrane proteins）基因中，正选择信号出现频率显著偏高。具体而言，浮游端足类物种Macrohectopus branickii的膜结合型与底物水平ATP合酶（ATP synthase）的亚基基因均呈现正选择信号，这可能反映其对活跃浮游生活方式的适应，以及对低温、高静水压（hydrostatic pressures，已知会影响膜功能环境下的生存适应性。其他在正选择候选基因所富集的功能类别还包括钙结合（Ca-binding）肌肉相关蛋白，这或反映其对贝加尔湖缺钙、低矿化度（mineralization）水体环境的适应性。