Tracing the processes of adaptation is a fundamental practice in the study of evolutionary biology. By combining multiple lines of evidence, we can elucidate the processes of diversification, speciation, and ultimately, evolution. For my doctoral dissertation, I studied the evolutionary history of a superorder of birds (Strisores) that have undergone a dramatic life history transition, the shift from a day-living (diurnal) to a night-living (nocturnal) lifestyle. Previous study found that the diurnal Apodiformes (swifts and hummingbirds) are nested deep within the clade of nocturnal or crepuscular Caprimulgiformes (nightbirds). However, resolution of the other major lineages eluded previous efforts, precluding analysis of the evolution of nocturnality in this group. To resolve the phylogeny of Strisores, I utilized a novel class of genome-scale markers, ultraconserved elements (UCEs). UCEs are operationally defined regions of extreme conservation between two or more genomes. I collected and sequenced ~4,000 UCEs from each of 191 species of birds representing every major extant lineage, plus two crocodilian outgroups—a greater number of elements than had ever been collected or studied before. With this data, I have resolved the phylogeny of the largest and oldest (Caprimulgidae and Nyctibiidae, respectively) lineages of nightbirds, as well as the superorder Strisores, and have shed light on best practices for the use of UCEs in phylogenomics. With a phylogeny representing the evolutionary history of Strisores I then ask when, and where, potential adaptations to nocturnality occurred. To this end, I have developed a molecular tool to efficiently enrich 47 genes comprising the phototransduction cascade, a network of genes that converts the absorption of a photon by an opsin into a neural signal. I demonstrated that this tool is effective in 33 bird species chosen to cover extant avian diversity. The data captured using this array will facilitate the identification of potential molecular adaptations to nocturnality, enable the improvement of models predicting opsin sensitivity from sequence data, and allow strong inference about the perception of color across birds and other vertebrates.