Hybrid zone analysis using coalescent-based estimates of introgression and migration in plateau fence lizards (Sceloporus tristichus)

Coalescent modeling of hybrid zones can provide novel insights into the historical demography of populations, including divergence times, population sizes, introgression proportions, migration rates, and the timing of hybrid zone formation. We used coalescent analysis to determine whether the hybrid zone between phylogeographic lineages of the Plateau Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to human-induced landscape changes, or if it originated during Pleistocene climatic shifts. Given the presence of mitochondrial DNA from another species in the hybrid zone (Southwestern Fence Lizard, S. cowlesi), we tested for the presence of S. cowlesi nuclear DNA in the hybrid zone as well as reassess the species boundary between S. tristichus and S. cowlesi. The data files supplied here include mtDNA sequences and nuclear DNA collected using ddRADseq for both study species. Files for phylogeographic and hybrid zone analysis are provided.

Methods
Mitochondrial DNA: The mitochondrial ND1 protein-coding gene (969 bp) was amplified and sequenced using standard PCR methods. New sequences were combined with previously published data, which included additional hybrid zone samples and broad-scale sampling of other species. Genbank numbers for each sample are listed in the supplemental table associated with the manuscript.

Nuclear DNA: The nuclear data was collected using double digestion restriction site associated DNA sequencing (ddRADseq). All samples collected from 2002, 2012, and 2022 were assembled together (335 hybrid zone samples). For the phylogeographic analysis, a total of 56 samples were used with species assignments determined using mtDNA-based phylogenetic placement.