UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard...

The Mexican Transition Zone is a biogeographic area where the Nearctic and Neotropical regions overlap, encompassing mountain ranges formed during different geological periods. Its complex geological and paleoclimatic history has promoted evolutionary processes such as introgression through hybridization, which can bias phylogenetic inferences and species delimitation. Here, we investigated evolutionary relationships among species of the endemic Mexican lizard genus Barisia using nuclear ultraconserved elements (UCEs). We analyzed samples largely overlapping with a previous study based on mitochondrial DNA (mtDNA) and compared topologies to evaluate mito-nuclear discordance. We also examined population structure, introgression, species boundaries, and biogeographic history of Barisia using molecular dating and ancestral area reconstruction. The strongly supported UCE phylogeny challenges the current species classification of the genus, revealing lineages structured by mountain ranges. Both UCE and previous mtDNA datasets revealed introgression between populations of B. imbricata and B. ciliaris in the southern Central Mexican Plateau and between B. imbricata and B. jonesi in the western Trans-Mexican Volcanic Belt (TMVB), which was further supported by structure and introgression analyses. Our results support the recognition of seven species within Barisia, with the reassignment of populations of B. imbricata, B. ciliaris, and B. jonesi. Overall, diversification within the genus was primarily driven by orogenic vicariance. This study highlights the utility of UCEs for reconstructing robust phylogenies, assessing species limits and genetic structure, as well as to inferring biogeographic patterns.