Conclusions
We developed new genomic tools to examine two rare and recently diverged species of ground squirrels, identifying multiple sets of new loci with around 3000 SNPs each using minimally invasive sampling methods. Our results corroborate previous studies regarding the clear differentiation between NIDGS and SIDGS and provide further details regarding the differentiation of these two sister species at the adaptive level. We additionally analyzed the demographic and adaptive variation of each species independently and determined that local adaptation played a more prominent role in differentiation among NIDGS populations, while geographic barriers appear to be the largest determinant of genetic differentiation in SIDGS. The different demographic and adaptive groups within both species may require dedicated management strategies in order to protect both neutral (MUs) and adaptive (AUs) diversity. In this context, we are the first to identify adaptive loci that distinguish not only the two species, but also distinguish among populations within each species, and the associations of these adaptive loci with environmental variables. The differences we detected will potentially help inform management plans aiming to protect the evolutionary and adaptive capacity of populations. Our results suggest clear metapopulation structure in both species with strong isolation-by-distance and isolation-by-barriers, as well as evidence of recent local adaption within some of these small and isolated metapopulations.