Gene flow spans ecoregions in the Western Banded Gecko

Desert ecosystems of southwestern North America harbor high levels of endemism and genetic diversity. Previous studies have found strong selection and well-defined phylogeographic patterns correlated with desert regions, but did these lineages evolve in isolation or along geographic gradients with gene flow? In this study, we used genome wide SNP data to explore the genetic diversity of the gecko Coleonyx variegatus which spans the Sonora and Mojave deserts, and the entirety of the Baja California Peninsula. The broad geographic distribution of C. variegatus across these unique ecosystems provides an opportunity to determine whether populations are evolving within their distinctive desert ecoregions, or if genetic diversity is driven by other factors. We applied population structuring analyses to identify population boundaries and then use the MSC-M model to directly test for gene flow among populations. Further, we apply multispecies coalescent methods to infer a species tree, which informs novel relationships and divergence dates among populations of C. variegatus. These results add to the growing body of phylogeographic literature for taxa spanning the region of focus. Combining our results with those from multiple sympatric species can help inform shared patterns of diversification across the broad, diverse region of southwestern North America.