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