Epigenetics in Salmonids: Impacts of Rearing Environment, Hybridization and Inbreeding

Epigenetic variation meets the requirements for evolution by natural selection: it is ubiquitous, controls the expression of adaptive traits, and may be inherited over generations. An epigenetic perspective also offers opportunities not entirely predicted by underlying genotypes. Here, we report on three studies that investigated environmental and genetic determinants of methylation variation and their possible fitness consequences. First, Venney et al. (2016) used a targeted multigene approach in Chinook Salmon to provide the first evidence of epigenetically-based inbreeding depression in vertebrates. They also showed that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. In the other two case studies from our group, we performed  genome-wide methylation profiles using RRBS to: i) document the effect of rearing environment in Coho Salmon and ii) investigate the impact of hybridization between two ecotypes for the Lake Whitefish differing in life history traits. Both studies showed that genomes were strongly methylated (~80%). No large scale difference of methylation levels were observed while differences in specific regions were associated with rearing habitats or ecotypes. In Coho, genomics variation was only explained by geographical location whereas epigenetic variation was equally explained by rearing environment and origin. For Whitefish, specific patterns of methylation were associated with ecotypes reared in a common environment, while hybrids were more similar to the dwarf ecotype. These studies highlight the relevance of integrating methylation monitoring for a better understanding of acclimation and adaptation of fish to either captive or natural environments.