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.