The Genomic Basis of Population and Adaptive Divergence in Buteo Sister Species Across Multiple Evolutionary and Geographic Scales

The genetic basis of adaptation and divergence has been at the forefront of evolutionary and ecological studies for many years. As environments change, it becomes increasingly important to understand the genetic basis and drivers of population and adaptive divergence to preserve local adaptation relevant to conservation, and to provide insight into the maintenance of species diversity. In this dissertation, I use whole-genome sequencing to answer questions related to adaptation on multiple scales from local adaptation to speciation in two closely related species of raptors. First, I characterized population divergence and local adaptation in a highly migratory species, the Swainson’s hawk (Buteo swainsoni), and find a clear distinction between the populations to the east and west of the continental divide, a pattern not yet documented in the Swainson’s hawk. I also identified patterns of genomic divergence between the slightly distinct Central Valley population and the rest of the populations in hopes of using this information to identify the genetic basis of multiple phenotypic traits. Next, I investigated the adaptive radiation of the Galapagos hawk (Buteo swainsoni), to assess patterns of diversity and diversification across islands as well as to investigate the genetic basis of both morphological and behavioral traits. The size distinct populations of the Galapagos hawk are significantly genetically divergent and have very low levels of genetic diversity. I also identified candidate loci and genes involved in the mating system of the Galapagos hawk as well as six morphometric traits and found that morphology differed significantly across islands independent of body size. Lastly, I assembled and annotated a high-quality draft genome for the Swainson’s hawk to be able to look at fine scale patterns of divergence between the Swainson’s hawk and the Galapagos hawk to better understand the genomic basis of allopatric speciation. The genome-wide patterns in both relative and absolute divergence support our hypothesis of founder speciation without secondary contact and represent an important step towards an understanding of the complex interactions between evolutionary processes that shape allopatric speciation at the genomic level. Overall, this work provides important insight into the evolutionary processes that shape genomic divergence in natural populations while also providing information imperative to the conservation of two, threatened species