The spinner dolphin (Stenella longirostris) contains six groups (ecotypes) that exhibit striking differences in morphology, ecology, and mating system, but little genetic differentiation at neutral loci. This pattern raises questions regarding the evolutionary mechanisms which could allow dramatic phenotypic divergence in the presence of high or recent gene flow. A lack of correspondence between genotype and phenotype is generally attributed to “porous” genomic boundaries, in which neutral genetic loci move freely between phenotypic groups, but loci under selection do not. However, few studies have directly tested for the presence of porous genomic boundaries because techniques for identifying loci under selection have been expensive and time-consuming until only recently. We propose to use recently developed next-generation sequencing technologies to simultaneously identify and genotype thousands of single nucleotide polymorphisms (SNPs) across the genome for five spinner dolphin ecotypes to test for the presence of porous genomic boundaries between ecotypes. Adaptive loci will be identified based on their behavior as statistical outliers compared to the majority of the genome, and the function of these loci will be evaluated through mapping onto available mammalian genomes. Both adaptive and neutral variation will be compared with variation in phenotype and ecology to evaluate the relationships between these factors. We expect this study to provide insight into the genetic and ecological factors driving the evolution of phenotypic differentiation in the spinner dolphin, and to aid in the conservation of this species by revealing adaptive genetic variation and environmental parameters that are influential to the health of the species. Finally, this project will promote long-term research collaborations between the U.K., the U.S., and several Pacific Island nations.