3 | RESULTS
3.1 |
Genetic diversity and inbreeding
Fine-scale representations of the distribution of ROHs across the
longest scaffold analyzed suggest that such tracts are longer and more
abundant in threatened S. catenatus individuals relative to
non-threatened S. tergeminus individuals (Figure 1). Further
analyses confirmed that S. catenatus shows low genetic diversity
and high inbreeding levels with respect to S. tergeminus at the
genome-wide level (Figure 2). Specifically, when averaged across all
individuals, S. catenatus had a mean ΘW (scaled
to 103 hereafter) of 2.71 (SE = 0.01) andF ROH of 0.557 (SE = 0.013), while S.
tergeminus had a mean ΘW of 4.44 (SE = 0.02) andF ROH of 0.067 (SE = 0.001) (Figure 2a);
differences between species for both metrics were highly significant
(P < 0.001). These patterns are consistent with
repeated reductions in effective population size and higher levels of
inbreeding in S. catenatus compared to S. tergeminus .
A comparison of adjusted F ROH values across
studies suggests that S. catenatus is moderately inbred with
respect to other threatened and endangered species and subspecies (Table
S2 – see also Brüniche-Olsen et al., 2018). For these comparisons we
recalculated F ROH using data from our study to be
comparable with the different size criteria used in different studies
(see Table S2). We also recognize that such comparisons are problematic
because of varying criteria used to define ROH tracts (e.g., maximum
number of heterozygous genotypes allowed to account for sequencing
errors), However, based on these adjusted comparisons, S.
catenatus is half as inbred as Apennine brown bears (Ursus arctos
marsicanus ) that have existed in isolation for hundreds of years
(Bennazo et al., 2017), but shows similar levels of inbreeding to Alpine
ibex (Capra ibex ) that have recently undergone serial population
bottlenecks (Grossen et al., 2020) (Table S2). Our interpretation thatS. catenatus is moderately inbred is also consistent withF ROH values generated from 100 mammals
representing species with varying population sizes (van de Valk et al.,
2019). Based on a size criterion of ROH > 0.1 Mb,
the estimated F ROH value for S. catenatus(0.552) is in the upper third of values for species and subspecies
analyzed. On the other hand, F ROH values forS. tergeminus are always representative of an outbred species
that shows little inbreeding (Table S2).
In contrast, to species-level comparisons of ΘW andF ROH across the nine S. catenatuspopulations examined show few significant differences for both metrics
(Figures 2a and S1). Population-level values of ΘWranged from 2.58 (SE = 0.05) in ROME to 2.78 (SE = 0.01) in KPWA, with
only two pairwise comparisons among populations being significant
(P < 0.05; Figures 2a and S1). Likewise, values ofF ROH ranged from 0.513 (SE = 0.045) in PROF to
0.608 (SE = 0.033) in CEBO, with only three pairwise comparisons among
populations being significant (P < 0.05; Figures 2a and
S1). Overall, these results suggest a remarkable degree of uniformity
across S. catenatus populations with respect to their long-term
demographic trajectories.
S. catenatus genomes were also composed of a substantially
greater number of ROHs (N ROH = 364, SE = 10)
relative to S. tergeminus genomes (N ROH =
150, SE = 8) (P < 0.001; Figure 2b). This two-fold
increase in N ROH (combined with the eight-fold
increase in F ROH as above) is consistent with the
effects of recent bottlenecks leading to inbreeding in S.
catenatus populations, as it implies that ROH tracts have increased in
mean length (Figure 2b; also see Figure 1 in Ceballos et al.
[2018]).
We also found substantial variation among individuals for bothF ROH and N ROH metrics. For
example, there is a two-fold difference in F ROHand even greater variation in N ROH among
individuals from the SPVA population (Figure S2). Some of this variation
could be due to differences in the degree of relatedness among
individuals within single populations, since, unlike the only S.
tergeminus population analyzed, S. catenatus populations
presented small but perhaps significant (mean = 0.082, SE = 0.012)
proportions of close relatives (r xy> 0.125; Figure 3). These patterns are also consistent with
a recent onset of inbreeding in S. catenatus populations.