Data from: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes

Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents. We estimate species trees inferred from phylogenomic scale data (304 loci) while exploring several strategies that consider topological error from each individual gene tree. With a dated species tree, we examine taxonomy and test previous hypotheses that suggest the ratsnakes originated in the Old World (OW) and dispersed to New World (NW). Furthermore, we determine if dispersal to the NW represented a source of ecological opportunity, which should show elevated rates of species diversification. We show that ratsnakes originated in the OW during the mid-Oligocene and subsequently dispersed to the NW by the mid-Miocene; diversification was also elevated in a subclade of NW taxa. Finally, the optimal biogeographic region-dependent speciation model shows that the uptick in ratsnake diversification was associated with colonization of the NW. We consider several alternative explanations that account for regionally distinct diversification rates.

全球广布的类群可能表现出区域特异性的物种分化速率：当生态机遇的时机与来源适配时，成种作用会被显著提升。然而对于多数生物类群而言，在所有研究区域实现基因组数据尺度下的近乎完整采样以降低拓扑结构误差，几乎无法达成，这进而阻碍了关于生物地理起源与物种分化速率相关结论的可靠性。本研究探讨了驱动全球鼠蛇类物种多样性形成的演化过程，并检验了多项与起源区域以及拓殖新大陆后物种分化加速相关的重要假说。我们以系统基因组学规模的数据（304个基因座）构建物种树，并探索了兼顾各单基因树拓扑结构误差的多种分析方案。基于定年物种树，我们对鼠蛇类的分类学问题进行了检视，并检验了此前提出的“鼠蛇类起源于旧世界（OW）并扩散至新世界（NW）”的假说。此外，我们还验证了向新世界的扩散是否构成了生态机遇的来源——若该假设成立，则新世界类群应表现出更高的物种分化速率。研究结果表明，鼠蛇类于渐新世中期起源于旧世界，并在中新世中期之前扩散至新世界；新世界类群的一个亚分支同样呈现出物种分化速率提升的特征。最终，最优的依赖生物地理区域的成种模型显示，鼠蛇类物种分化速率的跃升与新世界拓殖事件显著相关。我们还探讨了若干用以解释区域特异性物种分化速率的替代性假说。