4.2 | Genetic Load
Our ability to estimate genetic load in endangered species has been
transformed by applying novel analytical methods to infer the negative
impacts of variants detected in genomic datasets (van Oosterhout, 2020).
Our results show that the perspectives provided by mutations with
different evolutionary histories is significant for understanding
variation in genetic load at the species and populations levels.
Specifically, we estimated species level genetic load using derived
nonsynonymous variants at sites that were polymorphic in either one or
both species (Species level mutations). Using criterion to define sites
used for estimating species level load is important because incorporates
sites that reflect the almost two-fold difference in genome-wide
heterozygosity present between species which can substantially impact
estimates of load (Figure 6). Based on these sites we found that, on
average, the genomes of outbred S. tergeminus individuals had
significantly more deleterious mutations compared to more inbredS. catenaus individuals when genetic load was estimated in terms
of mean numbers of mutation or proportion of total mutations (Figure 6).
These results argue that based on absolute numbers of deleterious
mutations the inbred threatened species (S. catenatus ) has lower
levels of genetic load than the more outbred common species (S.
tergeminus ). This is contrary to the long-standing idea that small
inbred populations of threatened species will incur genetic erosion in
the form of increased genetic load (Frankham et al., 2017).
However, the impact of deleterious mutations is highly dependent the
genotypic segregation patterns of deleterious alleles and the assumed
dominance coefficients of mutations (Charlesworth, 2009). In particular,
empirical evidence suggests that many deleterious mutations are
recessive and are only expressed if they segregate in homozygous
genotypes (Agrawal & Whitlock, 2011). If this is the case then the
impact of mutation is lessened if they mainly found in heterozygote
genotypes. This is the case in outbred S. tergeminus :
heterozygotes containing deleterious mutations are from
~ 3 – 5-fold more common in S. tergeminus thanS. catenatus genomes (Figure 6). In addition, on a per site
basis, the frequency of deleterious mutations is between 40 – 68% less
in S. tergeminus (data not shown). Together these patterns argue
that although S. tergeminus has higher “Potential” genetic load
in the form of absolute numbers of deleterious mutations, the extent to
which the negative effects of these mutations (“Realized” load) is
blunted by the fact that proportionately more occur in presumably
unexpressed heterozygous genotypes and are also found at lower
frequencies on a per site basis (Mathur & DeWoody, 2021).
Recently, van der Valk et al. (2019) have argued that species level
differences in genetic load need to take into account the impact of long
term demographic patterns on levels of deleterious mutations.
Specifically, if threatened species have always persisted at low
effective sizes over evolutionary time-scales then selective purging of
deleterious mutations along with other types of variants due to
sustained genetic drift effects can explain reduced genetic load in
threatened species that currently exist in small populations. The long
and short term demographic differences documented here support this
explanation for the decreased genetic load shown in S. catenatuscompared to S. tergeminus. The ROH analyses shows that recent
population bottlenecks have occurred in both species with more recent
events having a greater impact on S. catenatus. In addition,
coalescent-based analyses demonstrate that S. catenatus has
consistently had a smaller effective size over the past 100,000 ybp.
These results argue that drift effects have been consistently stronger
in the species with lower absolute levels of genetic load which is
consistent with the explanation that lower load is due to more sustained
purging of mutations over short and long time-scales.
We also examined genetic load at the population level using a different
set of sites containing derived mutations were polymorphic found within
populations (Population level mutations). These variants capture a
different aspect of genetic load other than that due to differences in
long term genetic purging between species. In contrast to species level
patterns S. catenatus populations have, on average, higher
proportions of deleterious mutations on a per genome basis across all
impact classes and all classes of mutations are expressed at higher
levels in homozygote genotypes compared to S. tergeminus .
Finally, genetic load measured as proportion of deleterious mutations is
inversely related to short term effective population size. These
patterns mirror those found in other threatened species with small
populations (Grossen et al., 2020; Robinson et al., 2016; Robinson et
al., 2019) and reflect the negative impact of genetic drift on the
efficiency with which natural selection removes deleterious mutations
from small populations (Lohmueller, 2014).
These mechanisms extend to explaining the significant differences in
genetic load levels between S. catenatus populations that are
potentially responsible for population differences in negative genetic
effects such as inbreeding depression (Kardos et al., 2016). The inverse
correlation between contemporary effective size and genetic load signals
a strong impact of recent levels of genetic drift on observed levels of
load in S. catenatus populations. These effects are likely to
also have a historical component because contemporary and historical
effective sizes are positively correlated in this species (Ochoa et al.,
2020). This is relevant because allele frequency changes likely are the
result of processes that take place over longer timescale that the few
generations reflected in contemporary estimates of effective size.