3.2 | Recent demographic history
The presence of distinct ROH size clusters represent time-stamps for
when population bottlenecks have occurred in the recent past (Bosse et
al., 2012; Pemberton et al., 2012). Analysis of the overall distribution
of ROH lengths in S. catenatus shows evidence for three size
classes: short (0.05−0.2 Mb), medium (0.2−0.7 Mb), and long (0.7−7.9 Mb)
(Figures S3 and S4). Assuming a recombination rate of 2.8 cM
Mb-1 and a generation time of 3 years (see Materials
and Methods), we estimated the following time-frames for the demographic
events responsible for each ROH size class: short (268−1071 years before
present [ybp]), medium (77−268 ybp), and long (7−77 ybp). The latter
two time-frames are consistent with possible anthropogenic impacts on
this species (Sovic et al., 2019).
The effects of these events can be assessed by comparing differences in
class N ROH between species. As such,N ROH for the three ROH size classes (i.e., short,
medium, long) was always greater in S. catenatus relative toS. tergeminus , which is consistent with a greater impact of
bottlenecks in S. catenatus during the recent past (Figure 4a).
Specifically, S. catenatus genomes had a greater number of short
(N ROH = 177, SE = 7), medium
(N ROH = 107, SE = 4), and long
(N ROH = 65, SE = 2) ROH tracts than S.
tergeminus genomes (N ROH [short] = 120, SE =
7; N ROH [medium] = 18, SE = 1;N ROH [long] = 6, SE < 1) (P< 0.05 in all cases; Figure 4a). Fold increases in each class
suggest that, in S. catenatus , ROH tract gains have been most
substantial lately (i.e., 7−77 ybp), followed by ROH tract gains 77−268
and 268−1071 ybp.
We can also use the relative proportion of each size class to measure
the relative impact of each event in a way that accounts for overall
differences in inbreeding between the species (Figure 4c). Using this
approach, small ROHs associated with the oldest bottleneck made up 93%
of all ROH segments in S. tergeminus as compared to 77% inS. catenatus (P < 0.05), whereas the relative
proportion of medium (S. catenatus : 17%; S. tergeminus :
5%; P < 0.001) and large (S. catenatus : 5%;S. tergeminus : 1%; P < 0.001) ROHs was
significantly greater in S. catenatus (Figure 4c). These
proportional increases indicate that more recent demographic events have
had a substantially greater impact on S. catenatus .
Finally, S. catenatus populations showed few differences, if any,
in class N ROH profiles (Figures 4b and S5a-c).
Overall, 14, 33, and 0% of N ROH pairwise
comparisons among populations were significant (P <
0.05) for short, medium, and long ROH tracts, respectively (Figures 4b
and S5a-c). We obtained similar species- and population-level results
using relative proportion metrics for each ROH size class (Figures 4d
and S5d-f). Broadly speaking, this suggests similar magnitudes of
population declines across different populations spanning the range of
the species.