Detection of population structure is critical to the management and conservation of wildlife populations. Cetacean populations are protected under US law, necessitating accurate information on population structure, yet identification of such structure is inherently difficult due to the highly pelagic and mobile nature of most cetacean species. The factors that lead to population divergence and eventual speciation are complex, and current cetacean population structure is the result of both evolutionary and ecological processes. This dissertation examines potential ecological mechanisms of divergence in order to improve detection of differences among conspecific populations. To understand the importance of population structure information in establishing marine mammal policy priorities and management plans, I examined both the policy process and the scientific data utilized in a global review of humpback whales under the US Endangered Species Act (ESA). The challenges in this review process highlighted the importance of population structure information and the utility of multiple lines of evidence in resolving structure at both demographic and evolutionary scales. Foraging ecology and prey selectivity may be possible drivers of ecological divergence between cetacean populations. Using stable isotope analysis, I examined the diet consistency of a single population of humpback whales in the California Current over decadal time scales. Diet varied significantly over the study period, suggesting that this population of humpback whales shows a high degree of foraging plasticity and that diet may not be a consistent marker of population identity for this species. Since future investigations of cetacean population foraging ecology and structure based on stable isotope methods require understanding of individual isotopic variability, I quantified individual variability in humpback whale tissue due to physiological processes and tissue preservation methods and found that individual variability was less than that associated with a trophic level shift and is not prohibitive for investigations of trophic differentiation in cetaceans. Lastly, since habitat specialization may also drive ecological divergence, the novel application of passive acoustics enabled me to better characterize and predict the habitat preferences of a poorly-described ceteacean species, Dall's porpoise. This predictive understanding allows for better estimation of population distribution, abundance and structur
