Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP dataset, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations, and we found substantial evidence that genetic diversity of lizards differs along the two colonization routes.

We acquired tissue samples (toe or tail tissues) from 72 individuals of P. platyrhinos from 32 localities (1-5 samples/locality) across the species range spanning the Mojave, Sonoran, and Great Basin deserts. We then generated double-digest RADseq libraries for all samples using the protocol of Peterson et al. and processed sequence data with dDocent.

A README file that provides details on each script and data file is provided in the compressed directory.