Epigenetic mechanisms can alter gene expression and phenotypes in organisms responding to environmental changes. Within environmental parameters, temperature changes are notably the most pervasive abiotic factor for ectotherms, directly affecting organismal survival and fitness. The goal of this study was to investigate the scale of DNA methylation in populations of a cosmopolitan freshwater species occupying disparate thermal regimes. DNA methylation levels were compared among bluegill sunfish (Lepomis macrochirus) populations from an ambient temperature, temperate lake (Lake Mattoon), a nearby power plant-cooling lake (Lake Coffeen), and a tropical lake (Lake Lucchetti). We used epiRADseq to screen levels of DNA methylation at 105,811 loci among fish. We found levels of total DNA methylation increased among specimens as water temperature of lakes increased from the ambient temperature, temperate lake to the tropical lake. We identified loci with statistically significant differences in the frequency of DNA methylation among individuals between lakes: 654 loci between Lake Mattoon and Lake Lucchetti fish and 373 loci between Lake Coffeen and Lake Lucchetti fish. Considering that a previous study on the same power plant-cooling reservoirs showed a shorter lifespan, decrease in growth performance, and the populations skewed towards younger fish, this study observed DNA methylation pattern may be an important mechanism contributing to the observed phenotypic variations in bluegill from a anthropogenically-warmed lake compared to an ambient temperature lake. Our study suggests that epigenetic regulation of phenotypic plasticity in aquatic organisms may be a critical factor in understanding the organismal response to environmental stress.


We thank the NSF NSF-DUE Proposal No. 1504662, Georgia Southern University Armstrong Campus Department of Biology, College of Science and Technology, and STEP program for funding. We thank Dr. Frank Corotto and two reviewers for their valuable assistance to this manuscript. We also thank K. Adams, N. Ingebresten, A. Harder, J. Lee, K. Russel, and N. Schrey for assistance in this project. We will like to express our gratitude to the Puerto Rico Department of Natural and Environmental Resources, Division of Natural Protected Areas, for assisting with electrofishing sampling in Lake Lucchetti. Authors report no conflict of interests.