4.2 Genetic diversity within demes
We find a strikingly lower level of genetic variation within Deme II
than Deme I for all variability measures (Tables 1, 2), and genomic data
from individual sequencing estimated much higher inbreeding levels in
Deme II than in Deme I (Figure 6a, b). Similar degrees of difference in
diversity appear rarely observed in sympatric salmonids
(Jorde et al., 2018).
Relatively few studies estimate inbreeding from whole-genome sequencing
data in natural populations. Those that do typically focus on extinct or
highly threatened populations such as woolly mammoth
(Palkopoulou et al., 2015), Scandinavian
wolves (Kardos et al., 2018), and
gorillas (van der Valk, 2019). In these
populations considerably longer (>2 Mb) runs of
homozygosity than ours were observed. We find only a few ROHs above 2 Mb
in our populations. Deme II individuals have the highest number with a
total of 14 ROHs > 2Mb (Table S7). This might imply that
recent inbreeding is not pronounced in any of the populations studied
here and that inbreeding is mainly due to deep historical shared
ancestors of parents. Similar observations with few long ROHs suggesting
limited recent inbreeding have been observed in wild Ficedulaflycatcher populations (Kardos et al.,
2017).
Our estimates of F ROH range from 0.032 in
individual 1 in Deme I in Lakes Bunnersjöarna to 0.405 in individual 1
in Deme II (Figure 6b). The samples from other lakes show values between
these extremes but all values for other lakes are aboveF ROH>0.09 with an average of 0.18
(Table S7). This appears high, and is above what has been estimated for
hatchery strains of rainbow trout where the highest observations were
typically around 0.1-0.2 (D’Ambrosio et
al., 2019). A large extent of this difference might be due to
differences in settings of ROH analyses: D´Ambrosia et al. (2019)
allowed a maximum of one heterozygous genotype per ROH while we allowed
three. For a low coverage data like ours, a maximum of three
heterozygous genotype is recommended (e.g.
Ceballos et al., 2018).