Speciation, or the process by which one population diverges into multiple populations that can no longer interbreed with each other, has brought about the incredible diversity of life. Mechanisms underlying this process can be more visible in the early stages of the speciation process. The mechanisms that restrict gene flow in highly mobile species with no absolute barriers to dispersal, especially marine species, are understudied. Similarly, human impacts are reshaping ecosystems globally, and we are only just beginning to understand the implications of these rapid changes on evolutionary processes. In this dissertation, I investigate patterns of speciation and evolution in two avian clades: a genus of widespread tropical seabirds (boobies, genus Sula), and two congeneric passerine species in an urban environment (cardinals, genus Cardinalis). First, I explore the prevalence of gene flow across land barriers within species and between sympatric species in boobies. I found widespread evidence of gene flow over all land barriers and between 3 species pairs. Next, I compared the effects of urbanization on the spatial distributions of two cardinal species, pyrrhuloxia (Cardinalis sinuatus) and northern cardinals (Cardinalis cardinalis), in Tucson, Arizona. I found that urbanization has different effects on the spatial distributions of two closely related species that share a similar environmental niche, and I identified environmental variables that might be driving this difference. Then I tested for effects of urbanization on color and size traits of these two cardinal species. In both of these species, urbanization has altered traits involved in signaling, heat tolerance, foraging, and maneuverability. Finally, I tested for evidence of selection on the urban populations of both cardinal species and found evidence of both parallel selection and introgression between the species, as well as selection on different genes in each species. The functions of the genes that experienced positive selection suggest that light at night, energetics, and air pollution may have acted as strong selective pressures on these species in the past. Overall, my dissertation emphasizes the role of introgression in the speciation process, identifies environmental stressors faced by wildlife in urban environments, and characterizes their evolutionary responses to those stressors.

Organisms regularly face the challenge of having to accumulate and allocate limited resources toward life-history traits. However, direct quantification of how resources are accumulated and allocated is rare. Carotenoids are among the best systems for investigating resource allocation, because they are diet-derived and multi-functional. Birds have been studied extensively with regard to carotenoid allocation towards life-history traits, but direct quantification of variation in carotenoid distribution on a whole-organism scale has yet to be done. Additionally, while we know that scavenger receptor B1 (SCARB1) is important for carotenoid absorption in birds, little is known about the factors that predict how SCARB1 is expressed in wild populations. For my dissertation, I first reviewed challenges associated with statistically analyzing tissue distributions of nutrients (nutrient profiles) and tested how tissue carotenoid distributions (carotenoid profiles) varied by sex, season, health state, and coloration in two bird species, house finches (Haemorhous mexicanus) and zebra finches (Taeniopygia guttata). Then, I investigated the relationship between dietary carotenoid availability, relative expression of SCARB1, and extent of carotenoid-based coloration in a comparative study of wood-warblers (Parulidae). In my review of studies analyzing nutrient profiles, I found that multivariate analyses were the most common, but studies rarely reported intercorrelations among nutrient types. In house finches, all tissue carotenoid profiles varied by sex, season, and coloration. For example, males during autumn (molt) had higher concentrations of 3-hydroxyechinenone (the major red carotenoid in sexually attractive male feathers) in most but not all tissues compared to other season and sex combinations. However, the relationship between color and carotenoid profiles depended on the color metric. In zebra finches, only muscle and spleen carotenoid profiles varied between immune-challenged and control birds. In wood-warblers, I found that capacity to absorb carotenoids was positively correlated with the evolution of carotenoid-based coloration but negatively associated with liver carotenoid accumulation. Altogether, my dissertation illustrates (a) the context-dependence of tissue carotenoid profile variation, (b) that carotenoid-based integumentary coloration is a reflection of tissue carotenoid profiles, and (c) that digestive physiology (e.g., carotenoid absorption) is an important consideration in the study of diet and coloration in wild birds.

The control, function, and evolution of sleep in animals has received little attention compared to many other fitness-relevant animal behaviors. Though natural selection has largely been thought of as the driving evolutionary force shaping sleep biology, sexual and social selection may also have transformative effects on sleep quantity and quality in animals. An overarching hypothesis is that increased levels of investment into inter-sexual choice and intra-sexual competition will reduce sleep. An alternative hypothesis is that sexual ornamentation (e.g. avian plumage coloration and song) may have evolved to communicate sleep health and may therefore be positively related to sleep investment. In this dissertation, I studied how sleep is related to components of sexual and social selection in animals (mostly in birds). I first reviewed the literature for empirical examples of how social and sexual selection drive animal sleep patterns and found support for this relationship in some common types of inter-individual interactions (e.g. mating, intra-sexual competition, parent-offspring interactions, group interactions); I also provided new ideas and hypotheses for future research. I then tested associations between sleep behavior with expression of ornaments (song and plumage coloration), using the house finch (Haemorhous mexicanus) as a model system. For both color and song, I found support for the hypothesis that individuals with exaggerated ornaments slept deeper and longer, suggesting that sleep is a critical resource for ornament elaboration and/or may be communicated by both types of sexual signal. Following this, I tested the phylogenetic association between sleep and social/sexual selection as well as other life-history traits across birds. I found that more territorial bird species sleep less, that polygynous birds sleep more than monogamous and polygynandrous birds, and that birds migrating longer distances sleep less and have less REM sleep. Finally, in the interest of applying basic knowledge about sleep biology to current global problems, I found support for the hypothesis that house finches from city environments have developed resilience to artificial light pollution at night. Altogether, I found that social, sexual, and life-history traits are indeed important and overlooked drivers of sleep behavior from multiple levels of analysis.