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.