UC San Diego

This dissertation provides empirical evidence for patterns of population structure – a necessary prerequisite for estimating abundance and ultimately conservation action - of two species of pelagic dolphins (spinner and spotted dolphins) that have been challenging to characterize using modern molecular genetics. I evaluated philosophies that could aid in accurate categorization of biological diversity for conservation and developed and employed novel techniques to collect genome-wide data in efforts to increase statistical power for testing hypotheses of genetic structure. For the former, I assessed the impacts of phylogenetic nomenclature (PN) on the efficacy of the Endangered Species Act (ESA). PN relies heavily on traditional nomenclature, and knowledge of evolutionary relationships is paramount for species protection, so I concluded that PN will have little impact the ESA. Using DNA capture and highly-parelleled sequencing, I collected whole mitochondrial genomes (mtDNA) and scores of nuclear loci (nuDNA) for population structure tests. MtDNA showed weak but significant differences between subspecies of spotted dolphins and the first mtDNA evidence for differentiation between ETP spinner dolphin subspecies. NuDNA supported subspecies of spotted dolphins, but not spinner dolphins. Strong differentiation was detected between whitebelly and eastern spinner stocks, but these data did not have statistical power to enable testing of population-level hypotheses needed for management, so I employed a genome-wide genotyping approach (RADseq) to collect >6,000 single nucleotide polymorphisms (SNPs) from regions throughout the genome associated with the restriction enzyme site PstI. Results supported the current subspecies for both species and indicate stock-level separation for Tres Marias spinner dolphins and two offshore spotted dolphin stocks the ETP. I also tested global taxonomic and phylogeographic hypotheses using RADseq and found deep divergence between Indo-Pacific and eastern tropical Pacific Ocean (ETP) spinner dolphins, but segregation between inshore and offshore ETP spotted dolphins. Australain dwarf spinner dolphins were genetically distant from conspecifics in Indonesia, but the dwarf spinner dolphin was monophyletic. Atlantic spinner dolphins were placed between a clade of Indo-Pacific Ocean populations and ETP population in our phylogeny, contrary to previous hypotheses. The eastern Pacific basin and the marine Wallace’s line are strong barriers for spinner dolphins despite high dispersal potential.