Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of
endangered species can be assessed using estimates of neutral genetic
variation reflecting long-term impacts of genetic drift, yet this widely
used approach has been questioned in the genomics era. Here we leverage a
chromosome-level assembly and whole genome resequencing data (N=110
individuals) from an endangered rattlesnake (Sistrurus catenatus) to
evaluate the relationship between genome-wide neutral and functional
diversity over long- and short-term timescales. As predicted for
populations at long-term equilibrium, we found a positive correlation
between population-level estimates of neutral genetic diversity (π) and
the mean number of highly detrimental loss-of-function mutations, and a
negative relationship between neutral genetic diversity and an estimate of
genetic load. In contrast, we found only a weak, non-significant positive
correlation between levels of neutral and adaptive variation. Additional
analyses using estimates of drift at more recent time scales (> 100
generations) show expected correlations between both measures of genetic
load, but a lack of a significant correlation with levels of adaptive
variation. Individual-based demographic metrics that capture drift impacts
over recent time scales confirm these results. Broadly, our results
confirm that estimates of diversity and demography based on neutral
genetic variation provide an accurate measure of a key component of
genetic erosion – genetic load – in populations of a threatened
vertebrate. Our findings also provide nuance to the neutral-functional
diversity controversy by demonstrating that neutral genetic diversity is
useful in predicting some, but not all, components of functional genetic
diversity.