Rattlesnake genomics illustrate patterns of speciation, adaptation, and links between genome structure and function

Abstract

Understanding the origins of species and biological novelties that allow them to thrive in diverse environments is a key goal in evolutionary biology, and new genomic methods are constantly enabling research using non-model species to address important questions related to speciation and adaptation. Using phylogeographic, population genetic, and comparative genomic methods, I demonstrate that North American rattlesnakes are a uniquely enriched system for investigating patterns and processes at the intersection of adaptation and speciation. Specifically, this dissertation explores the evolution of biological novelty at multiple scales, including the origins of reproductive incompatibilities during the process of gene flow in secondary contact, evidence for links between genomic patterns of selection and locally adapted traits (e.g., venom and reproductive phenotypes), and cryptic genetic diversity in widely-distributed rattlesnake lineages. Detailed investigation of the high-quality prairie rattlesnake genome provides new perspectives into the evolution of genome structure in vertebrates, sex chromosome differentiation, the unique biology and significance of microchromosomes, and the origins of venom, one of the most distinctive features of rattlesnake biology. Collectively, this work serves as an example of the tremendous value that rattlesnakes hold for addressing important evolutionary questions in the age of genomics.