Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using *BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for > 10 Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.

非洲以其生物多样性（biodiversity）与特有性（endemicity）闻名于世，但学界对塑造非洲大陆全域此类特征的影响因素仍知之甚少。非洲鬣蜥属（Agama）蜥蜴共计45个物种，其分布遍及整个非洲大陆，是开展生物地理学（biogeography）研究的理想模式类群。该属诸多物种演化出了显著的性二态特征，包括成年雄性艳丽的繁殖体色、更大的成年雄性体型，以及色彩艳丽物种与暗淡物种间社会系统的差异。本研究采用混合系统发育-系统基因组学方法（hybrid phylogenetic-phylogenomic approach），构建了鬣蜥属及其近缘类群的综合时间校准物种树（time-calibrated species tree）：该方法整合了来自57个物种（146份样本）5个基因位点的传统桑格测序数据（Sanger sequence data），以及23个物种215个核基因（nuclear genes）位点的锚定系统基因组学数据（anchored phylogenomic data）。研究基于溯祖理论（coalescent theory），使用*BEAST软件对桑格测序数据开展物种树推断（species tree inference），并以系统基因组学树作为骨架约束（backbone constraint），对得到的物种树后验分布（posterior distribution）进行优化校正。最终构建的时间校准物种树覆盖了95%的鬣蜥属已知物种，多数物种均有多个样本支持，主要支系（clades）与多数初始分化事件均得到了强力支持。鬣蜥属的分化演化（diversification）始于约2300万年前，非洲南部、东部、西部与北部的独立辐射演化（radiations）过程均已持续超过1000万年。研究发现一系列形态、体色与社会行为相关的性状紧密关联，且支系内部呈现出极高的形态差异度；伴随类群向新的生物地理区域扩散分化，趋同表型（convergent phenotypes）的后续演化成为显著特征。