DOI: 10.5061/dryad.21j0n
title: Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

description: 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.
description: Plestiodon BEAST data
 setNexus file with
 concatenated UCE sequences. See ReadMe file to match sample names with
 species and locality.plestiodonUCE.nexPlestiodon RAxML data setPhylip file with concatenated UCE sequences. UCE loci specified in partition file. See ReadMe file to match sample names with species and locality.plestiodonUCE.phyPlestiodon UCE loci partitions fileUCE loci partitions.plestiodonUCEpartitions.txt