Abstract
Sexual selection is a major driver of rapid phenotypic evolution, often resulting in conspicuous and charismatic traits. How these traits and the preferences for them originate, and how they affect the evolution of an organism’s genome, remain largely unknown. This lack of knowledge is problematic because the evolution of complex traits is a vital mechanism that connects seemingly independent topics, such as behavior, genetic variation, reproduction, fitness, competition, and genome evolution allowing them to be incorporated into broader evolutionary theory. As modern methods offer new opportunities, we find ourselves better prepared to dive deep into these facets and provide a more accurate understanding of them. This dissertation aims to understand the role of sexual selection on complex trait and genome evolution. There are three specific areas of study for this dissertation: (1) the evolution of sexually selected traits in the African turquoise killifish (Nothobranchius furzeri), (2) the role of male pregnancy in genome and gonad transcriptome evolution, and (3) the role of sex-role-reversal and methodology in shaping our understanding of transcriptome-based analyses. The results from these studies have contributed to our understanding of female preferences in maintaining conspicuous male phenotypes, the role of sexual selection in genome and transcriptome evolution, and the degree to which bioinformatic analyses have greatly influence our understanding of biological processes.