Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although
detecting gene flow between populations has been facilitated by new
analytical approaches, determining the timing and geography of
hybridization has remained difficult, particularly for historical gene
flow. A geographically explicit phylogenetic approach is needed to
determine the overlap of ancestral populations. In this study, we
performed population genetic analyses, species delimitation, simulations
and a recently developed approach of species tree diffusion to infer the
phylogeographic history, timing and geographic extent of gene flow in
lizards of the Sceloporus spinosus group. The two species in this group,
S. spinosus and S. horridus, are distributed in eastern and western
portions of Mexico, respectively, but populations of these species are
sympatric in the southern Mexican highlands. We generated data consisting
of three mitochondrial genes and eight nuclear loci for 148 and 68
individuals, respectively. We delimited six lineages in this group, but
found strong evidence of mito-nuclear discordance in sympatric populations
of S. spinosus and S. horridus owing to mitochondrial introgression. We
used coalescent simulations to differentiate ancestral gene flow from
secondary contact, but found mixed support for these two models. Bayesian
phylogeography indicated more than 60% range overlap between ancestral S.
spinosus and S. horridus populations since the time of their divergence.
Isolation–migration analyses, however, revealed near-zero levels of gene
flow between these ancestral populations. Interpreting results from both
simulations and empirical data indicate that despite a long history of
sympatry among these two species, gene flow in this group has only
recently occurred.