Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

Aim: The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location: Mexico. Methods: We used target enrichment of ultraconserved elements (UCEs) to obtain sequence data from 58 skinks representing 11 of the 13 described species in the group. We estimated time-calibrated phylogenies using concatenated and multispecies coalescent phylogenetic approaches. We used these phylogenies to reconstruct ancestral geographic distributions. Results: The final dataset contained 3,282 UCEs from each skink. Samples of each putative species formed well-supported clades in phylogenetic trees. Time-calibrated phylogenies estimated using concatenated and multispecies coalescent methods were generally congruent, but differed in the placement of one basal relationship. Divergences in the P. brevirostris group were temporally and spatially congruent with the pre-Pleistocene formation of the Trans-Mexican Volcanic Belt. The group most likely colonized the Mexican highlands from east to west during the Late Miocene and Pliocene. Inferences about the early biogeographic history of the group were confounded by the unresolved placement of a key phylogenetic relationship deep in the phylogeny. Conclusions: Skinks in the P. brevirostris group represent another example of a widespread montane Mexican taxon with a long history of pre-Pleistocene diversification associated with the primary formation of the Trans-Mexican Volcanic Belt. This mountain range seems to have been both a cradle of diversification for P. brevirostris group species and a land bridge facilitating dispersal across the Mexican highlands. Our results highlight the probable existence of new species within the P. brevirostris complex and suggest that querying a large portion of the genome may be critically important for studying the biogeographic history of these skinks. However, inferred differences between the concatenated and multispecies coalescent phylogenies, and the different biogeographic histories of the P. brevirostris group reconstructed from these phylogenies, caution that methods of estimating phylogenetic trees used in biogeographic reconstructions need to be carefully considered.研究目的：本研究旨在基于系统基因组学数据生成的时间校准系统发育树，重建祖先地理分布，以解答关于短吻石龙子（Plestiodon brevirostris）类群生物地理学的三个核心问题：（1）生物地理模式是否与跨墨西哥火山带（Trans-Mexican Volcanic Belt）的形成相关？（2）不同的系统发育估计方法是否会产生不同的拓扑结构？若如此，（3）使用不同的系统发育树是否会对生物地理重建结果产生影响？研究区域：墨西哥。方法：我们采用超保守元件（ultraconserved elements, UCEs）靶向富集技术，从该类群13个已描述物种中的11个物种的58条石龙子样本中获取序列数据。我们分别采用串联法和多物种溯祖（multispecies coalescent）系统发育分析方法，估算时间校准系统发育树，并基于这些系统发育树重建祖先地理分布。结果：最终数据集包含每个石龙子样本对应的3282个超保守元件。所有推定物种的样本在系统发育树中均形成支持度良好的演化支。采用串联法与多物种溯祖法估算的时间校准系统发育树整体一致性较高，但在一处基部分支的拓扑结构上存在差异。短吻石龙子类群的分化事件在时间与空间上均与跨墨西哥火山带更新世前的形成过程相吻合。该类群最有可能在晚中新世至上新世期间，从东向西扩散至墨西哥高地。该类群早期生物地理历史的推论因系统发育深处一处关键分支的位置未被明确解析而受到干扰。结论：短吻石龙子类群是一类广泛分布于墨西哥山地的类群，其伴随跨墨西哥火山带主体形成的更新世前多样化历史具有悠久渊源，该案例进一步印证了相关规律。该山脉既是短吻石龙子类群物种的多样化摇篮，同时也是促进墨西哥高地间物种扩散的陆桥。我们的研究结果暗示，短吻石龙子复合类群中可能存在新的物种；同时提示，获取基因组的大片段序列信息，对于探究此类石龙子的生物地理历史至关重要。然而，串联法与多物种溯祖法得到的系统发育树之间存在推断差异，且基于二者重建的短吻石龙子类群生物地理历史也有所不同，这警示我们：在生物地理重建研究中，需审慎选择用于估算系统发育树的分析方法。