Thesis | DNA Methylation of heat-stress genes in Redband Trout from contrasting thermal enviornments

Epigenetic variation is a potential pathway for rapid response to environmental change and may be able to influence local adaptation at the population level through population by environment interactions. The most well-understood mechanism of epigenetic variation is DNA-methylation, a form of gene regulation that acts in response to environmental stress. Previous lab studies have shown ecotypic variation in DNA-methylation, but few have attempted to quantify epigenetic variation in natural populations. I developed a study to compare levels of DNA-methylation in redband trout (Oncorhynchus mykiss gairdneri) from contrasting environments. I sampled trout populations from cold montane and warm desert streams at repeated intervals, collecting tissue samples that were used for epigenetic analysis. Levels of DNA-methylation (percent methylation) were quantified using targeted bisulfite sequencing of two stress-related genes (Heat Shock Protein 70 and 47). There were no differences among fish from contrasting ecotypes, indicating that seasonal changes in DNA methylation may occur at finer spatial scales than at the level of ecotype. However, there were significant differences in DNA methylation among populations for heat shock protein 70 and between two montane populations for heat shock protein 47. These findings suggest that DNA methylation may act as a source of plastic adaptive phenotypic variation in natural populations and could be an important component of thermal adaptation in coldwater fishes. Further research is needed to better inform how DNA methylation acts as a source of adaptive phenotypic variation, and more specifically, how population-level adaptation may influence epigenetic change in wild populations.