Reconstructing squamate biogeography in Afro-Arabia reveals the influence of a complex and dynamic geologic past

The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian squamate communities an ideal system to investigate biogeographic patterns and their drivers. Here we reconstruct the phylogenetic relationships and the ancestral geographic distributions of several Afro-Arabian reptile clades (totaling 430 species) to estimate the number of dispersal, vicariance and range contraction events. We then compare the observed biogeographic history to a distribution of simulated biogeographic events based on the empirical phylogeny and the best-fit model. This allows us to identify periods in the past where the observed biogeographic history was likely shaped by forces beyond the ones included in the model. We find an increase in vicariance following the Oligocene, most likely caused by the fragmentation of the Afro-Arabian plate. In contrast, we did not find differences between observed and expected dispersal and range contraction levels. This is consistent with diversification enhanced by environmental processes and with the establishment of a dispersal corridor connecting Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show that our novel approach is useful to pinpoint events in the evolutionary history of lineages that might reflect external forces not predicted by the underlying biogeographic model.

Methods
Distribution data was collected manually from Reptile Database (https://reptile-database.reptarium.cz/), and the biogeographic analyses were entirely performed in the R framework.

生物多样性的地理分布是理解演化生物学的核心议题。古地理学与古气候学的历史通常有助于阐释生物地理格局随时间的演变过程。然而，此类格局同时受多种其他因素影响，例如类群分化，这类因素可能改变特定生物地理事件发生的概率。非洲-阿拉伯区（Afro-Arabia）拥有复杂且广为人知的地质与气候历史，加之该区域爬行动物分类学研究基础扎实，使其有鳞类（squamate）群落成为探究生物地理格局及其驱动因素的理想研究体系。本研究对多个非洲-阿拉伯区爬行动物演化支（clade），共计430个物种的系统发育关系与祖先地理分布进行重建，以估算扩散、隔离分化与分布区收缩事件的数量。随后，我们基于实证系统发育与最优拟合模型，将观测到的生物地理历史与模拟生物地理事件的分布进行对比。借此可识别出过往时期中，观测到的生物地理历史可能受到模型未涵盖的因素塑造的阶段。研究发现渐新世（Oligocene）后隔离分化事件增多，这大概率由非洲-阿拉伯板块的裂解所致。与之相对，观测到的扩散与分布区收缩水平与预期值并无显著差异。该结果与环境过程推动类群分化的假说，以及中新世（Miocene）中期以来非洲、阿拉伯与欧亚大陆之间扩散廊道建立的结论相一致。最后，本研究证明所提出的新方法可精准定位类群演化历史中可能反映底层生物地理模型未涵盖的外部作用力的事件。

研究方法
分布数据手动采集自爬行动物数据库（Reptile Database，https://reptile-database.reptarium.cz/），所有生物地理分析均基于R语言框架完成。