Book Description

"Epigenetic mechanisms, especially DNA methylation, have been typically studied in the domains of development and disease; however, recent studies have suggested that epigenetics may also play important roles in ecological and evolutionary processes. In this thesis, I examine the roles of DNA methylation in facilitating animals responding to environmental change. I begin my thesis with a chapter that provides a review of empirical and theoretical studies analysing the effects of epigenetics on phenotypic plasticity and evolution in animals. This forms the background knowledge for the dissertation, and also helps to reveal knowledge gaps to be filled by my other chapters. I found that epigenetic patterns can be shaped by the environment both within and across generations, and that epigenetic variation can play a role in local adaptation. I also evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation, and its transgenerational stability. During my literature review, I found that environmental effects on epigenetic variation have typically been assessed under laboratory conditions. Thus, to add to the limited but growing body of literature on epigenetics in natural populations of animals, I evaluate epigenetic responses to environmental conditions in three distinct empirical systems and ecological scenarios. In my second chapter, I investigate changes in genome-wide DNA methylation patterns of Trinidadian guppies (Poecilia reticulata) during the course of infection by the monogenean ectoparasite, Gyrodactylus turnbulli. I found an epigenetic signature of infection by ectoparasites, and identified unique methylation responses at distinct phases of infection. In my third chapter, I explore genome-wide DNA methylation variation of Anolis lizards (Anolis sagrei) during the early stage of colonization of new habitats. I found that the magnitude of epigenetic variation was dependent on the environmental shift between new and source habitats, and discovered a potential relationship between epigenetic variation and physiological changes in populations at the earliest stages of colonization of new environments. Together with previous work, results from the two chapters suggest that patterns of DNA methylation can rapidly respond to environmental change, and that these methylation changes are involved in the regulation of critical genes and pathways. Although these findings highlight the importance of environmentally-mediated methylation changes, most genomic methylation patterns are static across tissues and throughout life, and some are even stable across generations. Thus, in my last chapter, I use threespine stickleback (Gasterosteus aculeatus) to characterise the distribution and function of constitutive methylation, and assess the amount of heritable methylation. I found a clear pattern of epigenetic variation across generations that is likely to be shaped by genetic variation. In addition, I found that constitutive methylation mapped to genes with functions relevant to fish development, with distinct enrichment of genomic context (promoters or gene bodies) between constitutive hypo- and hypermethylation. Finally, I identified a small but significant amount of heritable methylation. Collectively, my thesis demonstrates the utility of epigenome-wide scans for identifying candidate loci associated with complex phenotypes, and represents a valuable contribution to our understanding of the involvement of epigenetics in ecological and evolutionary process. Consequently, this work helps to improve our ability to predict the capacity of organisms to respond to changing environments." --