Interspecific neutral and adaptive divergence
Previous studies have found substantial differences in the ecological niches occupied by these two rare and endemic ground squirrels (Hoisington-Lopez et al. 2012; Zero et al. 2017), as well as distinct morphology and life history traits (Yensen 1991; Hoisington 2007), supporting the hypothesis that these two taxa have levels of divergence consistent with species level differences (Gill & Yensen 1992; Garner et al. 2005). Using the largest molecular dataset generated to date, we observed a clear genetic separation between northern (NIDGS) and southern (SIDGS) Idaho ground squirrels (Figures 2 and S2B, Supporting information). When we controlled for population structure to remove the variation associated with the interspecific differences, the resulting population structure was similar to that of the intraspecific pRDA analyses, indicating that this analysis was providing information regarding within-species variation (Figure 2). Therefore, we considered the RDA to produce more meaningful results than the pRDA results for interspecific comparisons of adaptive variation. This divergence was also clearly shown by F STvalues, which were significantly higher between species, than within species. As in line with previous microsatellite work (Garner et al. 2005; Hoisington-Lopez et al. 2012), SIDGS populations were generally less diverse than NIDGS and were more frequently found to have significantly lower H O thanH E, which suggests effects of inbreeding (Rousset & Raymond 1995).