Phylogenetics and the Genomic Consequences of Divergence in a Radiation of Monkeyflowers

Understanding the forces that drive divergence, and the genomic consequences of this process, is a central goal in evolutionary biology. Evolutionary radiations provide excellent opportunities to study speciation, as taxa span a continuum of divergence. However, inherent features of radiations resulting from rapid diversification create challenges for inferring evolutionary history. In this thesis, I address outstanding questions relating to the process of divergence in a diverse radiation of monkeyflower, the Mimulus aurantiacus species complex. I first use reduced representation sequencing to infer evolutionary relationships, examine patterns of phenotypic evolution among taxa, and assess previous taxonomic treatments. I then employ whole genome sequencing of samples from across the radiation to examine phylogenetic discordance and to understand what forces shape patterns of genome-wide variation among taxa. This work furthers our understanding of factors that drive diversification and the genomic consequences of divergence. This thesis includes previously published and unpublished co-authored material