High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analyzed reduced-representation bisulfite sequencing and whole-genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population) and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, although nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites that lost methylation, which instead have elevated nucleotide diversity in freshwater compared with marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. The results suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.