Adaptive associations with the environment
As we hypothesized, some populations within each species exhibited
signatures of adaptation to local environmental conditions. At the
interspecific level, SIDGS were generally more associated with grassland
and higher soil particle size, which is positively correlated with soil
temperature, while associations of NIDGS were varied and appeared to
vary mostly on a population basis (Figures 2 and S3A, Supporting
information). These differences are within our expectations of adaptive
differentiation between the two species, given that NIDGS and SIDGS
occur in high and low elevations, respectively (Hoisington-Lopezet al. 2012). These genomic signatures of adaptive differences
between NIDGS and SIDGS might also reflect associations with timing of
snow melt, or site productivity, which are related to difference in
hibernation (Hoisington-Lopez et al. 2012; Zero et al.2017; Goldberg, Conway, Mack, et al. 2020).
Intraspecific differences can quickly arise in populations that become
isolated and/or that are distributed across highly variable
environmental gradients (Doebeli & Dieckmann 2003; Smith et al.2019), and there is an important role of adaptive variants and their
specific adaptations in the maintenance of genetic diversity and the
long-term persistence of threatened species (Rubidge et al.2012). Small populations can naturally become locally adapted in the
process of isolation, resulting in a gradual increase in adaptive
differentiation from other populations, compared to neutral
differentiation (Doebeli & Dieckmann 2003; Holderegger et al.2006; Wood et al. 2016). In agreement with our initial hypothesis
(c), NIDGS showed a higher number of distinct populations both the
neutral and adaptive level, with Rocky Top and Lower Butter as the most
distinct populations and Tamarack to a lesser extent (Figures S11A and
S11B, Supporting information). None showed particularly low genetic
diversity or significantly lower H O thanH E (indicative of inbreeding), indicating that
these populations are unique but also demographically stable, despite
local bottlenecks (Assis et al. 2013). Rocky Top and Lower Butter
were mainly associated with environmental variables relating to
elevation (Figure 3), and they are the highest elevation populations
sampled in this study (around 1700 and 1600 m above sea level,
respectively). This suggests that these populations might have
particular adaptations to elevation compared to other NIDGS populations,
a pattern also observed in other North American ground squirrels
(Eastman et al. 2012). Tamarack is located on a west facing slope
which remains colder until later during the day, similarly to
populations at higher elevation sites. Tamarack was also found to be
associated with increased soil particle size (Figure 3), which is
positively correlated with soil temperature (Figure S3B, Supporting
information). Combined, Tamarack NIDGS may reflect an adaptation to the
colder temperatures despite living at ~1,275m
(relatively lower elevation for NIDGS total range). The highest adaptive
differentiation in SIDGS was observed for Paddock (PA), with patterns of
local adaptation particularly associated with grassland land cover
rather than shrub/scrubland, as well as increase Annual Mean Temperature
and Isothermality. Greater densities of SIDGS have been associated with
increased cover of perennial grasses and diversity of native perennial
plants (Lohr et al. 2013). Additionally, burrow density appears
to be influenced by the presence of native forbs typical of
shrub/scrubland, which was an environmental variable associated with
adaptive variation of the remaining SIDGS populations (Figure 6C). Forbs
have a large influence in protein intake for fat storage before
hibernation, and thus it is a strong predictor of overwintering survival
of all age classes, even when present at low densities (Barrett 2005).
The results of the GEA could indicate a particular adaptation of Paddock
to areas with lower forb density, but further sampling of other SIDGS
populations, as well as diet studies would be needed to confirm this
hypothesis.
We did not find particular Gene Ontology terms associated with putative
functions of genes in our analysis, which could be related to a lack of
annotations of the thirteen-lined ground squirrel genome, or also the
fact that no particular Gene Ontology term stands out as causative of
the differentiation of the two species (Szkiba et al. 2014).
Still, we found two non-synonymous substitutions in known genes
identified by the RDA, one of which was also identified bypcadapt , the NPR1. This gene has been found to be highly
expressed in brown adipose tissue of thirteen-lined ground squirrels
during hibernation, relating to heat production during periodic arousals
from hypothermic torpor (Hampton et al. 2013). Adaptations
relating to adipose tissue are common in high altitude adapted rodents
(Gossmann et al. 2019), and these associations suggest that there
are adaptive differences between NIDGS and SIDGS relating to their
hibernation patterns. In fact, one study on Columbian ground squirrel
(Urocitellus columbianus ) found that emergence timing was
heritable and hence, squirrels’ emergence date may also reflect local
adaptations (Lane et al. 2011). In accordance to our hypothesis
(d), altitude differences might have resulted in adaptive differences
between NIDGS and SIDGS in production and storage of fat, and increased
metabolism and oxygen transport at higher elevations, as seen in other
mammals (Faherty et al. 2018; Waterhouse et al. 2018;
Garcia-Elfring et al. 2019).