The sky islands of southeastern Arizona (AZ) mark a major transition zone between tropical and temperate biota and are considered a neglected biodiversity hotspot. Dispersal ability and host plant specificity are thought to impact the history and diversity of insect populations across the sky islands. We aimed to investigate the population structure and phylogeography of two pine-feeding pierid butterflies, the pine white (Neophasia menapia) and the Mexican pine white (N. terlooii), restricted to these "islands" at this transition zone. Given their dependence on pines as the larval hosts, we hypothesized that habitat connectivity affects population structure and is at least in part responsible for their allopatry. We sampled DNA from freshly collected butterflies from 17 sites in the sky islands and adjacent high-elevation habitats and sequenced these samples using ddRADSeq. Up to 15,399 SNPs were discovered and analyzed in population genetic and phylogenetic contexts with Stacks and pyRAD pipelines. Low genetic differentiation in N. menapia suggests that it is panmictic. Conversely, there is strong evidence for population structure within N. terlooii. Each sky island likely contains a population of N. terlooii, and clustering is hierarchical, with populations on proximal mountains being more related to each other. The N. menapia habitat, which is largely contiguous, facilitates panmixia, while the N. terlooii habitat, restricted to the higher elevations on each sky island, creates distinct population structure. Phylogenetic results corroborate those from population genetic analyses. The historical climate-driven fluxes in forest habitat connectivity have implications for understanding the biodiversity of fragmented habitats.

• DNA was extracted from freshly-caught butterfly specimens
• A ddRADSeq library was prepared using the MseI and EcoRI restriction enzymes
• Library was sequenced using the Illumina platform
• Reads were demultiplexed, quality-filtered, and trimmed for downstream analyses
• SNPs were called using Stacks and pyRAD
• Structure and IQTree were used for population genetic and phylogeneitc analyses, respectively

The code_with_annotations.docx file provides the code used in all downstream processing and analyses. There are annotations in the code to explain each step.