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.