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Abstract
The evolutionary history of a species is held within its genome, and comparative genomics and phylogenetics can be utilized to understand the forces that contribute to variation within and between species. This dissertation investigates the phylogenetic and genomic relationships across taxonomic scales of mushroom-feeding Drosophila. The immigrans-tripunctata radiation of Drosophila contains a suite of trait variation, but the phylogenetic relationships among these species have been poorly understood. To address this, I first resolve phylogenetic inconsistencies along the species tree. Of interest is the evolution of toxin tolerance among many mushroom-feeding species in this radiation. I expand the number of species that are tolerant for toxins, and I infer the ancestral state of toxin tolerance, where results suggest it evolved once in the radiation and has been lost multiple times. Within the immigrans-tripunctata radiation is the testacea species group, consisting of four species (D. testacea, D. orientacea, D. neotestacea, D. putrida), and the outgroup D. bizonata. I assemble genomes for these species and assess structural evolution, as well as genomic characteristics that could contribute to differences in size for the dot chromosome. I calculate phylogenetic discordance, where I discover that substantial introgression among species has occurred on Muller element E, and assess patterns of molecular evolution, where I find genes involved in immunity, fertility, and development under positive selection. Lastly, I evaluate the evolutionary genomics of Sex-Ratio (SR) meiotic drive in D. neotestacea, a selfish genetic element on the X-chromosome that causes males to only produce female offspring. I identify structural evolution along the SR X-chromosome and utilize population genomic methods to assess divergence from the non-driving chromosome. I evaluate differential expression across male and female genotypes and combine these data with the population genetic results to identify putative genes and mechanisms that could be implicated in SR drive in D. neotestacea. These results suggest nuclear import, piRNA synthesis, and cell division may play a role in the drive phenotype.