Geography influences the evolutionary trajectory of species by mediating opportunities for hybridization, gene flow, demographic shifts and adaptation. We sought to understand how geography and introgression can generate species‐specific patterns of genetic diversity by examining phylogeographical relationships in the North American skink species Plestiodon multivirgatus and P. tetragrammus (Squamata: Scincidae). Using a multilocus dataset (three mitochondrial genes, four nuclear genes; a total of 3455 bp) we discovered mito‐nuclear discordance, consistent with mtDNA introgression. We further tested for evidence of species‐wide mtDNA introgression by using comparisons of genetic diversity, selection tests and extended Bayesian skyline analyses. Our findings suggest that P. multivirgatus acquired its mitochondrial genome from P. tetragrammus after their initial divergence. This putative species‐wide mitochondrial capture was further evidenced by statistically indistinguishable substitution rates between mtDNA and nDNA in P. multivirgatus. This rate discrepancy was observed in P. multivirgatus but not P. tetragrammus, which has important implications for studies that combine mtDNA and nDNA sequences when inferring time since divergence between taxa. Our findings suggest that by facilitating opportunities for interspecific introgression, geography can alter the course of molecular evolution between recently diverged lineages.

Spatial and demographic expansion can alter patterns of genetic variation and have predictable spatial and temporal consequences. Two-dimensional range expansion should result in genetic variation that is correlated with the geographical axis of expansion. Notably, populations across the range of a geographically widespread species may experience expansion and contraction events asynchronously. We tested for the genetic consequences of range expansion in the flat-headed snake, Tantilla gracilis, which inhabits the North American Great Plains and has few barriers to terrestrial dispersal. We sequenced mitochondrial DNA (mtDNA) and nuclear DNA from across the range of T. gracilis, inferred phylogenies and constructed haplotype networks. We observed multiple geographically circumscribed mtDNA clades that varied greatly in their spatial extent, but little range-wide variation in nuclear DNA. Mitochondrial sequence variation was negatively associated with latitude across their geographical range, the expected pattern of northward expansion. Finally, the three largest mtDNA clades exhibited varying demographic patterns, with only one being consistent with recent expansion. Despite substantial mtDNA cladogenesis, the predicted signature of northern range expansion was still detectable in T. gracilis. Our results bolster the notion that post-Pleistocene range expansion was a dominant force shaping the genetic diversity of vertebrates in central North America.