On the Mechanisms of Genomic and Phenotypic Evolution

During the process of adaptation, phenotypic variation present within a population provides the substrate on which selection may act. However, in light of epigenetic processes, the manner in which such variation is produced and the consequences of such variation is of central importance in understanding adaptive processes. In this dissertation, I consider two models of how this variation may arise, either through random, plastic means, or via a rapid recombination of pre-existing regulatory and protein-coding elements within the genome.While previous models of phenotypic plasticity have generally fallen into two classes of models, either considering adaptive or non-adaptive plasticity, I present a new unified model of phenotypic plasticity using stochastic differential equations and in silico selection. Though prior models have suggested that plasticity is deleterious during static conditions, I demonstrate how the relative evolvability of genic or epigenetic control of phenotype can determine whether plasticity will become maintained during stasis. Additionally, I analyze a model of new gene evolution via enhancer capture, where a new gene may adopt the expression patterns dictated by the regulatory environment into which the gene duplicates, evaluating and comparing it to other major models duplication-based evolution. By comparing the expression patterns of newly evolved essential and non-essential genes, I demonstrate that enhancer capture is likely a significant driver of the evolution of distally duplicated genes via enhancer capture. I then utilize genomic techniques, integrating RNA-seq, ChIP-seq, and Hi-C data, to show that a new essential gene, HP6/Umbrea, is one example of a gene that has evolved in this manner. Altogether, this dissertation encapsulates the breadth of methods used in evolutionary genetics, providing both a theoretical analysis of a novel model of phenotypic plasticity as well as an experimental validation of an old model of new gene neo-functionalization made possible only through nascent technological development, expanding our understanding of the methods and mechanisms by which phenotypic variation arises.