Genome Architecture And Phenotypic Evolution

Abstract

While investigating phenotypic change, evolutionary studies in non-model systems have mostlylooked at the first order genomic structure, which encompasses sequence level polymorphisms. In my dissertation, I reveal that the genetic architecture of phenotypic change can be embedded in several layers of genomic information, hereafter referred to as primary (sequence-level), secondary (epigenetic modifications of DNA base pairs) and tertiary (chromatin architecture) levels. In my first chapter, I report primary sequence level polymorphisms associated with breed behavioral profiles in dogs and track the demographic history of genomic regions associated with behavioral traits under selection. In my second chapter, I report epigenetic modifications that could allow a non-adapted low-land deer mouse population to dynamically modulate genes promoting tolerance to hypoxia, a feature of high attitudinal habits. In my third chapter, I bridge the gap between a high-effect non-coding variant implicated in canine hyper-sociability and its functional impacts on gene regulation, via investigating and incorporating information from 3D genome architecture at the tertiary level. I hope that my work provides a novel approach to look at evolutionarily imperative genetic changes as more than just a collection of base pairs, but a culmination of intermediate molecular processes along several levels of the genomic information.