My dissertation is now available. Please feel free to send me a request for the pdf. Population Structure of Island-Associated Pantropical Spotted Dolphins (*Stenella attenuata*) in Hawaiian Waters Chapter 1: Introduction to Population Genetics & Spotted Dolphins Chapter 2: Evidence of Multiple Populations of Pantropical Spotted Dolphins (*Stenella attenuata*) within Hawaiian Waters Chapter 3: Comparisons to Explore Potential Baselines for Biologically Significant Genetic Differentiation Levels: Population Structure of Pantropical Spotted Dolphins in the North Pacific Chapter 4: Are Small Sample Sizes and Use of Slow Evolving DNA Regions Hindering Resolution of the Phylogenetic Relationships among Delphinids: * Stenella* as an Example Genus Chapter 5: Conclusions The citation is: Courbis, S. 2011. Population Structure of Island-Associated Pantropical Spotted Dolphins (*Stenella attenuata*) in Hawaiian Waters. Ph.D. Dissertation. Portland State University. Portland, OR. 164pp. Abstract: Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of false killer whales (*Pseudorca crassidens*), spinner dolphins (*Stenella longirostris*), and common bottlenose dolphins (*Tursiops truncatus*), Hawaiian odontocete species are managed as single stocks within the U.S. Hawaiian Exclusive Economic Zone. These exceptions are a result of recent studies that have indicated that some species have populations that show fidelity to individual islands or groups of islands, resulting in genetic differentiation, often with management implications. The first part of my study (following the introductory chapter) focused on population structure of pantropical spotted dolphins (*Stenella attenuata*) near the Hawaiian Islands. Because of the level of human interaction, pantropical spotted dolphin populations need to be defined accurately to be managed in a way that will avoid local population losses, especially given that the commercial and recreational troll fisheries near the islands “fish on dolphins” to catch tuna. I analyzed genetic samples for mtDNA and microsatellite loci from four island regions: Hawai‘i, the 4-islands area, O‘ahu, and Kaua‘i/Ni‘ihau. My results support genetic differentiation among the regions of Hawai‘i, the 4-islands area, and O‘ahu and suggest that pantropical spotted dolphins near Kaua‘i/Ni‘ihau are likely transient and in very low numbers. There was no strong evidence to support sex-biased dispersal or group fidelity. Possibly, differentiation is mediated by behavior adapted to differing habitat types. From a management perspective, spinner and bottlenose dolphin populations near the Hawaiian Islands have been split into separate stocks for management based on levels of genetic differentiation similar to those found for pantropical spotted dolphins. These precedents suggest that comparable action should be taken to split pantropical spotted dolphin stocks near the Hawaiian Islands. Most population studies rely heavily upon fixation indices like *F*ST to determine whether populations are genetically differentiated. When *F*STvalues are low but significantly different from zero, it can be difficult to interpret the biological significance of these values. As part of my study, I suggest that one way to evaluate whether small *F*ST values indicate significant differentiation is to compare *F*ST values with other populations considered to be separate based on factors such as extreme distance or morphological differences. I examined pantropical spotted dolphins from the coastal and offshore Eastern Tropical Pacific (ETP), Hawaiian Islands, and China/Taiwan to examine the utility of comparing *F*STvalues across separate populations. Among Hawaiian Island regions, *F*ST values are significantly different from zero but small. The comparison of these *F*ST values with more distant populations in the ETP and China/Taiwan indicated that differences among Hawaiian Island regions were similar in magnitude to those found between the offshore and coastal ETP sub-species, but smaller than between the Hawaiian Island regions and the other regions examined. This suggests a level of reproductive isolation among the Hawaiian Islands regions that is comparable to that of offshore and coastal ETP populations, and supports the value of fixation index comparisons in evaluating differentiation among putative populations. My results suggest that assigning specific numerical baseline *F*ST values may not always be biologically meaningful but that determining whether related populations with geographic or other separation show a preponderance of similar, lower, or higher fixation index values can help evaluate whether genetic differences among sympatric or parapatric groups warrants designating them as separate populations for management. Lastly, I explore whether the fast evolving mtDNA control region may be more suited to phylogenetic comparisons among the *Stenella* than slower evolving gene regions and whether the small number of haplotypes generally used in phylogenetic analyses is adequate for defining relationships among dolphins. Usually, slow evolving regions, such as gene regions, are used in phylogenetic analyses because species and genera have been isolated long enough for variation to have accumulated in such regions but not so long that many reversals (*i.e.* a mutational change in sequence that later changes back to the original sequence) have occurred. The mtDNA control region is typically used for population genetic comparisons rather than phylogenetic comparisons because it is considered to be a fast evolving region. Historically, dolphin phylogeny has been examined using gene regions, which have resulted in ambiguous and unexpected relationships. However, the lack of variation in the mtDNA control region for pantropical spotted dolphin populations and the fact that recent studies have found that the mtDNA control region in cetaceans evolves at about one quarter the rate of other mammals, raises the question as to whether this region would be better suited to phylogenetic studies for the *Stenella *(and potentially other dolphin species). In comparing 346 haplotypes from five species of *Stenella* world-wide, I found that the mtDNA control region is probably not a good region to use for phylogenetic analyses, and that even faster evolving regions might perform better. The differences in the mtDNA control region were not sufficient to distinguish clear relationships among the *Stenella*. I also found that when subsets of haplotypes chosen at random were compared, the results differed among comparisons, suggesting that there is value in using more than the usual one or two haplotypes when making phylogenetic comparisons. Given the recent increases in sequence availability (*e.g*. GenBank) and computing power, researchers should strongly consider using many haplotypes from a variety of populations in their phylogenetic comparisons. Cheers, Sarah Sarah Courbis Operations Coordinator DLNR/Hawaiian Islands Humpback Whale National Marine Sanctuary sarahcourbis@gmail.com