The Genetic Basis of Defensive Structure Variation in Threespine Stickleback (Gasterosteus aculeatus)

72 pagesA longstanding goal in evolutionary biology is to link differences in traits among organisms with genetic variants in their genomes. Hybrid populations are excellent models for studies that aim to associate such phenotypic variation with regions of the genome. The Riverbend section of the McKenzie river in Oregon is home to a hybrid population of freshwater-like and ocean-like threespine stickleback (Gasterosteus aculeatus). Stickleback are small fish that live in a variety of aquatic habitats and appear highly armored in oceanic and brackish environments and often exhibit a loss of armor in freshwater systems. Previous work in this population demonstrated that variation in a handful of bony traits encompassed the differences observed between oceanic and freshwater types. I hypothesized I would see similar variation in the pelvic defensive structure–a group of bones that surround the fish and protects it from predation–and that by association mapping, I would identify genetic variants contributing to the diversity in this trait. For this thesis, I measured 12 aspects of the defensive structure in 192 fish and used 19,540 genetic markers to perform a genome-wide association analysis. Here, I show that the defensive structure and its components display abundant variation between individuals in this population. I describe the genetic architecture of this set of traits and report genetic regions of association, some of which overlap with previously discovered regions. In addition, I found novel regions of association for a subset of the traits and report candidate genes in these regions that may contribute to the phenotypic differences observed