Discussion
We examined the genetic basis of adaptive divergence between two endemic and vulnerable sister species of Idaho ground squirrels and assessed the diversity and differentiation at both neutral and adaptive loci among populations of each species. As in previous studies (Garner et al. 2005; Hoisington 2007; Hoisington-Lopez et al. 2012), we observed a clear genetic separation between northern (NIDGS) and southern (SIDGS) Idaho ground squirrels. Within species, we identified different clustering of populations when considering neutral and adaptive variation separately, which suggests that local adaptation and demographic processes are both important in shaping genetic variation and both should be considered in management and conservation planning of these species.