Data from: Spatiotemporal diversification of the true frogs (Genus Rana): a historical framework for a widely studied group of model organisms

True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29–18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci.蛙属（Rana）的真蛙类是发育生物学、遗传学、生理学、生态学、行为学以及进化生物学研究中广泛使用的模式生物。针对蛙属100余个物种的比较研究，有赖于对该类群进化历史与分化模式的深入认知。本研究基于多数蛙属物种的6个核基因位点（nuclear loci）与3个线粒体基因位点（mitochondrial loci）的序列数据，构建了分辨率优良且经时间校准的系统发育树（phylogeny），并依托该树阐明了该类群的分化模式与全球生物地理分布格局。分析结果一致支持"Out of Asia"的演化模式：蛙属类群曾通过白令陆桥（Beringian land bridges）从东亚向北美完成两次独立扩散事件。物种更为丰富的新大陆（New World）蛙属支系，在成功殖民新大陆后经历了快速辐射演化，尤其是在其扩张至墨西哥、中美洲及南美洲的山地与热带区域的过程中。与之形成鲜明对比的是，旧大陆（Old World）蛙属的分化轨迹截然不同：其分化进程初始阶段极为缓慢，直至约2900万至1800万年前（Ma），物种形成速率（speciation rate）才出现显著提升。净分化速率与环境变化紧密关联，尤其与渐新世（Oligocene）至中新世（Miocene）早期亚洲大陆边缘的强烈构造运动密切相关。本研究的系统发育分析进一步表明，过往的分类研究因受到形态趋同演化（morphological homoplasy）、祖征性体色模式（plesiomorphic color patterns）的误导，且过度依赖线粒体基因开展分类工作，从而出现了分类偏差。本研究基于多核基因与线粒体基因位点的整合分析结果，提出了一套全新的系统发育分类体系（phylogenetic taxonomy）。