The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. This richness can be explained by numerous hypotheses affecting divergence, which include biogeographic barriers, adaptation to climatic gradients across this region, and Pleistocene speciation in glacial refugia. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while one or more of these hypotheses may explain diversification, it is likely that taxa are forming within this region in species-specific ways. Here we generate a genomic dataset for the cornsnakes (P. guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous hypotheses are required to explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.

Included in the 'Assembled_rad_data' directory are assembled rad seq data from ipyrad in .loci, .phy, .ustr (unlinked structure input), and vcf formats, as well as a converted and subsampled nexus file for BFD* species delimitation with SNAPP.

In the 'ENM_locality_info' directory are the localities and museum species numbers of georeferenced specimens downloaded from VertNet and used for ENMs.

In the 'ENM_output_ascii' directory are the ENM ascii files from ENMs under different model parameters.

Lastly, in the 'fastsimcoal2_models' are all inputs for the two, four population models and all six, two population demographic models tested for the P. guttatus complex.

If the methods are followed from this paper these data set should allow users to reproduce our results and figures in this manuscript. Please feel free to contact the corresponding author with any questions.