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).