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Recent advances in DNA sequencing have revolutionized evolutionary biology by allowing for genome-scale studies of non-model organisms. We can now readily connect genotype with phenotype, i.e., identify the genetic basis of particular traits, a key goal in the study of evolution. In addition, genome-scale sequence analysis has shifted our understanding of the frequency and magnitude of gene flow in nature. Once viewed as important only for its role preventing divergence, the common view now is that in many taxa gene flow occurs among many lineages in the early stages of divergence. My dissertation focuses on gene flow in bearded manakins (genus Manacus), which are notable for their intense tandem courtship display, high degree of reproductive skew among males, and bright male plumage. In western Panama, yellow-collared M. vitellinus and white-collared M. candei interbreed in a narrow hybrid zone. Male vitellinus secondary sexual traits, including the yellow collar, have introgressed roughly 50 km west across the hybrid zone into candei populations and then stalled at the east bank of the Río Changuinola, the region’s largest river. Evidence from studies of male-male interaction and female choice implicate positive sexual selection for yellow collars as a driver of introgression. For thirty years since this situation was first described in detail, several key issues have remained unresolved, including why introgression has not continued across the river and what gene or genes are responsible for yellow coloration. In the first chapter, I reviewed the current state of knowledge of the Manacus hybrid zone system and proposed new hypotheses for some of the patterns exhibited by these populations. In the second chapter, I used reduced-representation genome sequencing to investigate whether reduced gene flow across the Río Changuinola alone can explain stalled trait introgression. I found that, although advantageous plumage traits have not introgressed far beyond the rive

Males of many animal species perform specialized courtship behaviours to gain copulations with females. Identifying physiological and anatomical specializations underlying performance of these behaviours helps clarify mechanisms through which sexual selection promotes the evolution of elaborate courtship. Our knowledge about neuromuscular specializations that support elaborate displays is limited to a few model species. In this review, we focus on the physiological control of the courtship of a tropical bird, the golden-collared manakin, which has been the focus of our research for nearly 20 years. Male manakins perform physically elaborate courtship displays that are quick, accurate and powerful. Females seem to choose males based on their motor skills suggesting that neuromuscular specializations possessed by these males are driven by female choice. Male courtship is activated by androgens and androgen receptors are expressed in qualitatively and quantitatively unconventional ways in manakin brain, spinal cord and skeletal muscles. We propose that in some species, females select males based on their neuromuscular capabilities and acquired skills and that elaborate steroid-dependent courtship displays evolve to signal these traits.