Data from: Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modeling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis-based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of non refugial populations are corroborated with empirical data. In this study we focus on a montane-restricted cryophilic harvestman, <i>Sclerobunus robustus</i>, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau (SRMIP) of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double-digest RAD-seq data, and conducted population level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid-latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside of hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of <i>S. robustus</i>. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades predates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model-based coalescent approaches, we find support for post-divergence migration between clades from separate refugia.