Exploring Epigenomic Variation, Evolution, and the Implications for Long-term Population Viability

Abstract

This dissertation used genomics, epigenomics, and computational biology to explore the inheritance, temporal stability, and functional relevance of epigenetic marks in shaping genetic diversity and population persistence. I began with a quantitative summary and examination of existing literature and identified key questions in ecological epigenetics and conservation biology, with an emphasis on wild systems. This review motivated an empirical investigation of the epigenome in a wild mammal population to inform our understanding of epigenome variation in natural systems. My second chapter examined multigenerational patterns of DNA methylation in a population of banner-tailed kangaroo rats (Dipodomys spectabilis) in southwest Arizona, revealing partial but detectable epigenetic inheritance that declined with generational distance. Building on these findings, my third chapter evaluated environmentally induced methylation patterns in the same population and found consistent epigenomic responses to local environmental variation, suggesting potential mechanisms for plasticity-mediated adaptation. These empirical results highlight the need for broader taxonomic application of epigenome investigations as well as theoretical refinement of epigenome change expectations for wild systems. My fourth and fifth chapters addressed this need by developing a suite of theoretical and simulation-based models to extend insights beyond the constraints of field data. In chapter four, I modeled how the interaction of migration and population size influenced long-term viability in high‑extinction‑risk species with limited connectivity, and found that even minimal migration (e.g., one migrant per generation) significantly countered post‑crash declines by maintaining heterozygosity and altering population trajectories toward those of the migrant source—effects that were most pronounced in critically endangered scenarios. My fifth chapter considered how migration might influence epigenomes. I developed a set of recursive equations and agent-based simulations to evaluate how migration and the mode of epigenetic transmission (heritable vs. plastic) influenced population divergence, showing that both processes could generate elevated epigenetic differentiation under distinct evolutionary scenarios. Together, these models emphasized the importance of accounting for both genomic and epigenomic dynamics in conservation planning. Finally, in my sixth chapter, I considered the overall conclusions across studies, synthesizing insights from empirical and theoretical approaches to highlight how integrating epigenomic and genomic perspectives can improve predictions of population resilience and inform more effective conservation strategies. By incorporating epigenomic processes alongside traditional genetic measures, my work considers how we can predict population resilience and enhance the effectiveness of conservation strategies in a rapidly changing world.