Through common descent, closely-related taxa share many life history traits, some of which can influence extinction-proneness. Thus, examining historical and contemporary genetic patterns is valuable in accounting for evolutionary and ecological processes that may be critical to the successful conservation of threatened species. Unsustainable harvesting of monk seals (tribe Monachini) until the late nineteenth century caused the recent extinction of Caribbean monk seals (Neomonachus tropicalis) and critically low population sizes for Hawaiian and Mediterranean monk seals (Neomonachus schauinslandi and Monachus monachus, respectively). Having lost one branch of its evolutionary lineage, and with a second branch threatened by extinction, the genus Neomonachus can serve as a valuable case for examining evolutionary and ecological linkages that are sensitive to non-random anthropogenic selection pressure. An important foundation for such pursuits is the understanding of evolutionary sequences of speciation and diversification that gave rise to common traits shared by extinct and vulnerable species. Further consideration of the phylogenetic non-randomness of species vulnerability requires examination of genetic variation at the population level to infer the presence of fundamental processes (e.g., migration and reproduction) that directly influence population viability. This dissertation includes three individual studies that make use of molecular systematic and population genetic techniques to address these topics. First, a complete mitochondrial genome sequence of the extinct Caribbean monk seal (N. tropicalis) was assembled and used to resolve long-standing phylogenetic questions regarding the sequence of divergence among monk seal species and sister taxa. Second, novel microsatellite marker assays were developed and used to characterize the extent of population-level variation across 24 polymorphic microsatellite loci of 1192 endangered Hawaiian monk seals (N. schauinslandi) that were sampled during a longitudinal study spanning three decades. Third, resulting genotypes from a subset of individuals (N= 785) were integrated with previously reported genotypes consisting of 18 other loci for the largest ever population-level assessment of N. schauinslandi genetic diversity and population differentiation throughout the Hawaiian archipelago. The new microsatellite data will be of particular value for future individual-level assessment of parentage and relatedness in N. schauinslandi, which will help managers better infer the reproductive mechanisms that factor into population persistence and recovery. Results of this study expand understanding of the evolutionary and conservation genetic status of monk seals, as well as molecular genetic capacity, for future research regarding a unique and highly imperiled New World pinniped lineage.

<p>Infusing models for animal movement with more behavioral realism has been a goal of movement ecologists for several years. As ecologists have begun to collect more and more data on animal distribution and abundance, a clear need has arisen for more sophisticated analysis. Such analysis could include more realistic movement behavior, more information on the organism-environment interaction, and more ways to separate observation error from process error. Because landscape ecologists and behavioral ecologists typically study these same themes at very different scales, it has been proposed that their union could be productive for all (Lima and Zollner, 1996). </p><p>By understanding how animals interact with their land- and seascapes, we can better understand how species partition up resources are large spatial scales. Accordingly I begin this dissertation with a large spatial scale analysis of distribution data for marine mammals from Nova Scotia through the Gulf of Mexico. I analyzed these data in three separate regions, and in the two data-rich regions, find compelling separation between the different communities. In the northernmost region, this separation is broadly along diet based partitions. This research provides a baseline for future study of marine mammal systems, and more importantly highlights several gaps in current data collections.</p><p>In the last 6 years several movement ecologists have begun to imbue sophisticated statistical analyses with increasing amounts of movement behavior. This has changed the way movement ecologists think about movement data and movement processes. In this dissertation I focus my research on continuing this trend. I reviewed the state of movement modeling and then proposed a new Bayesian movement model that builds on three questions of: behavior; organism-environment interaction; and process-based inference with noisy data.</p><p>Application of this model to two different datasets, migrating right whales in the NW Atlantic, and foraging monk seals in the Northwest Hawaiian Islands, provides for the first time estimates of how moving animals make choices about the suitability of patches within their perceptual range. By estimating parameters governing this suitability I provide right whale managers a clear depiction of the gaps in their protection in this vulnerable and understudied migratory corridor. For monk seals I provide a behaviorally based view into how animals in different colonies and age and sex groups move throughout their range. This information is crucial for managers who translocate individuals to new habitat as it provides them a quantitative glimpse of how members of certain groups perceive their landscape.</p><p>This model provides critical information about the behaviorally based movement choices animals make. Results can be used to understand the ecology of these patterns, and can be used to help inform conservation actions. Finally this modeling framework provides a way to unite fields of movement ecology and graph theory.</p> / Dissertation