Browsing by Department "Marine Science and Conservation"

A vast range of theoretical and empirical studies now suggests that MPAs can conserve marine biodiversity and, under some circumstances, increase fishery yields. However, despite the importance of pelagic apex predators to ecosystem function, the effectiveness of spatial management for the conservation of pelagic apex predator species is still unknown. I used fishery-dependent logbook and observer datasets to assess fishing effort and both the catch and size of pelagic apex predator species around five different MPAs. The US Hawaii-based deep-set or Atlantic pelagic longline fisheries fish the waters around these MPAs; both of these fisheries have experienced multiple management measures over time to protect species and maximize fishery yield. The MPAs selected for this study range in size, age, level of protection, and reason for establishment. I found that only two MPAs of the five appeared to be benefitting the pelagic apex predator species that I selected: the DeSoto Canyon and East Florida Coast MPAs, both in the Atlantic Ocean. The size of yellowfin tuna around the DeSoto Canyon MPA borders has increased over time, as has fishing effort. In contrast, the size of swordfish has decreased near the boundary of the East Florida Coast MPA, although the catch of swordfish has increased. The increase in catch of smaller swordfish was not a surprise because the East Florida Coast MPA was established around an area that is a nursery habitat for swordfish. These results are promising for the use of static MPAs for the conservation of pelagic apex predators, but three of the MPAs in my study did not show any indication of increased fishing effort, increased catch, or changes in pelagic apex predator size near their boundaries over time. Therefore, the characteristics of the DeSoto Canyon and East Florida Coast MPAs may provide a template for how to best design new MPAs for pelagic apex predators. Both of these MPAs were established with the specific intent of reducing pelagic apex predator bycatch, in areas where there were historically high catch rates. Both areas are relatively large (> 85,000 km2) and are also closed year-round. In combination, these characteristics may provide protection for pelagic apex predators.

The ocean environment poses several adversities to usual mammalian function. Perhaps most consequential to life is the lack of air underwater. For marine mammals, like whales and dolphins, that are required to perform breath-hold dives to forage for prey, this necessitates a unique set of adaptations to efficiently manage oxygen resources while diving. In an era of global environmental change, this hostile habitat is expected to become increasingly challenging for air-breathing mammals; warming waters will necessitate deeper foraging trips and noisier oceans may compel unplanned dives to evade perceived threats. An understanding of marine mammals’ solutions to the physiological challenges of a dually-constrained lifestyle is therefore important not only to reveal how marine mammals are built to thrive where other mammals, particularly humans, falter but also the extent to which these adaptations may scale in a changing ocean environment. In this dissertation, I explore the physiological adaptations, particularly those of the cardiovascular and respiratory systems, that this taxon has evolved to mediate the challenges associated with breath-hold diving. I take a multi-scale approach to investigating these physiological traits, exploring hypotheses at the molecular, tissue-specific, and organismal scales. Accordingly, I leverage both familiar and emerging methodologies in the field of marine mammal physiology to examine adaptations that support the extended dive capacities of whales and dolphins. Cellular and molecular responses to environmental stimuli influence tissue-specific and organismal physiological responses. Despite the inextricable link between molecular and organismal physiology, studies of the molecular adaptations of marine mammals for diving are limited, in part due to the logistical complexity of obtaining molecular samples from this difficult-to-study group. To fill this gap, my collaborators and I deployed RNA-seq and enzymatic assays to examine the molecular-level changes that occur in bottlenose dolphins (Tursiops truncatus) performing extended breath-holds (Chapter 1). We demonstrated that dolphins exhibit transcriptomic and proteomic changes that occur in a time-dependent fashion during breath-holding that could support their ability to maintain selective perfusion during diving. The upregulation of ALOX5, a gene targeted for the treatment of eosinophilic asthma in humans, and lipoxygenase suggest a mechanism by which differential gene regulation could contribute to sustained vasoconstriction during the dive response. These findings illustrate the importance of responses at the molecular level for supporting the unique physiology of marine mammals. Coordinated, tissue-specific physiological changes are central to the mammalian dive response. During dives marine mammals drastically reduce their heart rate (fH) while narrowing the blood vessels that supply their peripheral tissues, thereby slowing oxygen consumption of the heart itself as well as reducing the supply of oxygen-rich blood to non-essential tissues. The factors that modulate fH and contribute to diving bradycardia are complex, largely because they are numerous and often linked, but are crucial to understanding oxygen consumption patterns and, ultimately, whole-organism physiology and behavior. Using simultaneous electrocardiographic (ECG) recordings and respirometry, I show that whales and dolphins exhibit a strong cardiorespiratory coupling that may support the conservation of blood oxygen for hypoxia-intolerant tissues during a breath-hold. This variation in fH with breathing, or respiratory sinus arrhythmia (RSA), is modulated by breathing rate (fR) in bottlenose dolphins such that slow breathing results in larger fluctuations in fH (Chapter 2). Following a breath, fH increases rapidly to a maximum and then decreases through the end of the inter-breath interval (IBI). Notably, some of the minimum fH’s of the RSA were comparable to reported diving fH’s for this species suggesting the importance of apnea alone in modulating the fH of a diving marine mammal. I also demonstrate that this cardiorespiratory coupling scales with body size and fR across five cetacean species suggesting both physical scaling laws and dynamic physiological needs play a role in determining the magnitude of the RSA (Chapter 3). These studies highlight the complexity of tissue-specific responses and the need to contextualize physiological rates. Ultimately, it is the interactions of tissues that determine organismal physiology – the fundamental constraint on an organism’s behavior. To investigate the connection between organismal physiology and behavior, I developed a novel method for extracting fR from free-ranging whale biologging tag data (Chapter 4). I found that the high-flow rate and large tidal volume breaths of cetaceans generate movement signals which are captured by the accelerometers of biologging tags, enabling respiration event detection from historical biologging tag datasets. I applied this tool to movement data collected from short-finned pilot whales in Cape Hatteras, North Carolina using digital acoustic recording tags (DTAGs) and examined variation in respiratory patterns associated with diving (Chapter 5). I found that whales vary their pre- and post-dive surface duration and post-dive fR in proportion to the duration and activity of upcoming dives illustrating the physiological challenge of preparing for and recovering from breath-hold diving and highlighting optimization of surface behavior required to support breath-holds. Physiological responses are coordinated across multiple levels of biological organization necessitating the use of various tools and techniques to fully elucidate the adaptations that support marine mammals’ capacity to dive for minutes to hours without a breath. The findings of this dissertation underscore that the physiological function of breath-holding whales and dolphins is coordinated across scales, the physiological responses of cardiovascular and respiratory systems are linked, and sensing vital rates can provide insights into the physiological demands of a dive. Future studies should continue to focus on integrating methods across scales to better understand the physiological function of these animals and its plasticity in a changing ocean.

There have been few efforts to evaluate the actual and perceived effectiveness of environmental management programs created by consensus-based, multi-stakeholder negotiation or negotiated rulemaking. Previous evaluations have used perceived success among participants as a proxy for actual effectiveness, but seldom have investigated the ecological outcomes of these negotiations. Fewer still, if any, have compared the actual and perceived outcomes. Here I evaluate and compare the social and ecological outcomes of the negotiated rulemaking process of marine mammal take reduction planning. Take reduction planning is mandated by the U.S. Marine Mammal Protection Act (MMPA) to reduce the fisheries-related serious injuries and mortalities of marine mammals (bycatch) in U.S. waters to below statutory thresholds. Teams of fishermen, environmentalists, researchers, state and federal managers, and members of Regional Fisheries Management Councils and Commissions create consensus-based rules to mitigate bycatch, called Take Reduction Plans. There are six active Take Reduction Plans, one Take Reduction Strategy consisting of voluntary measures, and one plan that was never implemented. It has been 20 years since marine mammal take reduction planning was incorporated into the MMPA. Early evaluations were promising, but identified several challenges. In the past decade or more, the National Marine Fisheries Service (NMFS) has implemented measures to set up the teams for success.

I used data from formal Stock Assessment Reports to assess and rank the actual ecological success of five Take Reduction Plans (Harbor Porpoise, Bottlenose Dolphin, Atlantic Large Whale, Pelagic Longline, and Pacific Offshore Cetacean) in mitigating the bycatch of 17 marine mammal stocks. In addition, I employed social science data collection and analytical methods to evaluate Take Reduction Team participants' opinions of the take reduction negotiation process, outputs, and outcomes with respect to the ingredients required for successful multi-stakeholder, consensus-based negotiation (team membership, shared learning, repeated interactions, facilitated meetings, and consensus-based outputs). These methods included surveying and interviewing current and former Take Reduction Team participants; using Structural Equation Models (SEMs) and qualitative methods to characterize participant perceptions across teams and stakeholder groups; and identifying and exploring the reasons for similarities and differences among respondents, teams, and stakeholder groups. I also employed SEMs to quantitatively examine the relationship between actual and perceived ecological success, and contrasted actual and perceived outcomes by comparing their qualitative rankings.

Structural Equation Models provided a valid framework in which to quantitatively examine social and ecological data, in which the actual ecological outcomes were used as independent predictors of the perceived outcomes. Actual improvements in marine mammal bycatch enhanced stakeholder opinions about the effectiveness of marine mammal Take Reduction Plans. The marine mammal take reduction planning process has all of the ingredients necessary for effective consensus-based, multi-stakeholder negotiations (Chapter 2). It is likely that the emphasis that the National Marine Fisheries Service places on empirical information and keeping stakeholders informed about bycatch, marine mammal stocks, and fisheries facilitated this relationship. Informed stakeholders also had relatively accurate perceptions of the actual ecological effectiveness of the Take Reduction Plans (Chapter 3). The long timeframes over which the teams have been meeting generally have increased cooperation. The professionally trained, neutral facilitators have produced fair negotiations, in which most individuals felt they had an opportunity to contribute. Participant views of fairness significantly influenced their satisfaction with Take Reduction Plans, which significantly affected their perceptions about the effectiveness of those plans (Chapter 2). The mandate to create a consensus-based output has, for the most part, minimized defections from the negotiations and facilitated stakeholder buy-in.

In general, marine mammal take reduction planning is a good negotiated rulemaking process, but has produced mixed results (Chapters 1 and 2). Successful plans were characterized by straightforward regulations and high rates of compliance. Unsuccessful plans had low compliance with complex regulations and sometimes focused on very small stocks. Large teams and those in the northeastern U.S. (Maine to North Carolina) were least successful at reducing bycatch, which was reflected in stakeholder views of the effectiveness of these teams. Take Reduction Team negotiations have not always produced practical or enforceable regulations. Implementation of take reduction regulations is critical in determining plan success and identifying effective mitigation measures, but because of a lack of monitoring, has not been characterized consistently across most teams. Additionally, elements like the "Other Special Measures Provision" in the Harbor Porpoise Take Reduction Plan have undermined the negotiation process by allowing the National Marine Fisheries Service to alter consensus-based elements without consensus from the team, which has led to hostility, mistrust, and frustration among stakeholders.

The final chapter of this dissertation provides recommendations to improve the outcomes and make them more consistent across teams. I based these recommendations on the information gathered and analyzed in the first three chapters. They are grouped into four broad categories - team membership, social capital, fairness, and plan implementation. If the National Marine Fisheries Service implements these suggestions, both perceived and actual ecological effectiveness of marine mammal Take Reduction Teams should improve, allowing these teams to fulfill their maximum potential.

Despite decades of study, the question of how to achieve sustainable small-scale fisheries is unresolved. Because small-scale fishing is diverse and hard to control, one management approach places fishers at the center of decision-making. Common-pool resource theory has assembled a large body of evidence that resource users, without top-down state control, are able to devise and enforce rules that lead to long-term sustainable resource harvest. The social and ecological characteristics (“design principles”) are well known for systems where this collective action is predicted to spontaneously emerge. However, it is poorly known what precipitates collective action when these design principles are absent. This dissertation draws insights about this question from a seemingly successful case from Baja California Sur, Mexico, where fishers have voluntarily created no-fishing areas (“Fish Refuges” or “Zonas de Refugio Pesquero”) in collaboration with the government fisheries agency and a non-governmental organization, Niparajá, in the absence of the design principles. This work is based on an in-depth study of these Fish Refuges including 180 days in the field from 2016-2018, participant observation, informal interviews, journaling, and semi-structured interviews (n=66). First, I found that collective action was possible because stakeholders had three competing visions about what the Fish Refuges were, each associated with criteria and evidence of whether the Fish Refuges were effective. This implies that policy flexibility to accommodate competing goals and evaluation criteria could facilitate collaboration for fisheries management. Second, I found that fishers’ knowledge was integrated in a process that did not recognize its legitimacy though what I call “ping-pong hybridization”, where the locus of decision making moved between stakeholders who could draw on their own knowledge systems. This implies that policies may be able to integrate multiple knowledge systems if the locus of decision-making moves back and forth. Third, I found that the property rights regime change away from de facto open access was possible because fishers were able to trade formal fishing rights for informal management rights, closing a fishing area to gain government trust and partnership. This work implies that insecure, unofficial, and tenuous property rights may be a first step of property rights regime change to achieve sustainable fisheries. In conclusion, bottom-up approaches to fisheries management may benefit from processes where different stakeholders can define the goals and methods used, and draw on their own knowledge systems to assess success. Shifts away from open access may be precipitated when fishers demand decision-making rights, even if these rights are tenuous.

An understanding of sensory ecology, how animals receive and respond to their environment, can be a powerful tool for the conservation of endangered species because it can allow us to assess the potential success of actions designed to mitigate particular threats. We have a general understanding of how sea turtles perceive and respond to certain visual, magnetic, and chemical cues, but we understand very little about how they perceive and respond to acoustic cues. This dissertation explores the acoustic ecology of sea turtles, focusing on their auditory capabilities, responses to acoustic stimuli and the implications of this knowledge for their conservation. I measured the underwater and aerial hearing sensitivities of juvenile green (Chelonia mydas), hatchling leatherback (Dermochelys coriacea), and hatchling hawksbill (Eretmochelys imbricata) sea turtles by recording auditory evoked potential responses to tonal stimuli. Green turtles detected tonal stimuli between 50 and 1,600 Hz underwater (maximum sensitivity: 200-400 Hz) and 50 and 800 Hz in air (maximum sensitivity: 300-400 Hz), leatherbacks detected tonal stimuli between 50 and 1,200 Hz underwater (maximum sensitivity: 100-400 Hz) and 50 and 1,600 Hz in air (maximum sensitivity: 50-400Hz), and hawksbills detected tonal stimuli between 50 and 1,600 Hz in both media (maximum sensitivity: 200-400 Hz). Sea turtles were more sensitive to aerial than underwater stimuli when audiograms were compared in terms of sound pressure, but they were more sensitive to underwater stimuli when audiograms were compared in terms of sound intensity. I also examined the behavioral responses of loggerhead sea turtle (Caretta caretta) to simulated low frequency acoustic deterrent devices (ADDs) and found that these turtles exhibited a mild, aversive response to these sounds. This finding indicates that low frequency tonal ADDs have the potential to warn sea turtles of the presence of fishing gear and suggest that field tests of ADDs are warranted. Finally, I conducted a comprehensive review of our knowledge of the acoustic ecology of sea turtles, examined the sources of marine anthropogenic sound sea turtles are able to detect, evaluated the potential physiological and behavioral effects of anthropogenic sound, identified data gaps, and made recommendations for future research.

Pinniped species undergo a life history, unique among marine mammals, that includes discrete periods of occupancy on land or ice within a predominantly marine existence. This makes many pinniped species valuable sentinels of marine ecosystem health and models of marine mammal physiology and behavior. Pinniped research has often progressed hand-in-hand with advances at the technological frontiers of wildlife biology, and drones represent a leap forward in the long-established field of aerial photography, heralding opportunities for data collection and integration at new scales of biological importance. The following chapters employ and evaluate recent and emerging methods of wildlife surveillance that are uniquely enabled and facilitated by drone methods, in applied research and management campaigns with near-polar pinniped species. These methods represent advancements in abundance estimation and distribution modeling of pinniped populations that are dynamically shifting amid climate change, fishing pressure, and recovery from historical depletion.Conventional methods of counting animals from aerial imagery—typically visual interpretation by human analysts—can be time-consuming and limits the practical use of this data type. Deep learning methods of computer vision can ease this burden when applied to drone imagery, but are not yet characterized for practical and generalized use. To this end, I used a common implementation of deep learning for object detection in imagery to train and test models on a variety of datasets describing breeding populations of gray seals (Halichoerus grypus) in the northwest Atlantic Ocean (Chapter 2). I compare standardized performance metrics of models trained and tested on different combinations of datasets, demonstrating that model performance varies depending on both training and testing data choices. We find that models require careful validation to estimate error rates, and that they can be effectively deployed to aid, but not replace, conventional human visual interpretation of novel datasets for gray seal detection, location, age-classification and abundance estimation. Spatial analysis and species distribution modeling can use fine-scale drone-derived data to describe local species–habitat relationships at the scale of individual animals. I applied structure-from-motion methods to a survey of three pinniped species, pacific harbor seals (Phoca vitulina richardii), northern fur seals (Callorhinus ursinus), and Steller sea lions (Eumetopias jubatus), in adjacent non-breeding haul-outs to compare occupancy and habitat selection (Chapter 3). I describe and compare fitted occupancy models of pacific harbor seals and northern fur seals, finding that conspecific attraction is a key driver of habitat selection for each species, and that each species exhibits distinct topographic preferences. These findings illustrate both opportunities and limitations of spatial analysis at the scale of individual pinnipeds. Ease of deployment and rapid data collection make drones a powerful tool for monitoring populations of interest over time, while animal locations, revealed in high-resolution imagery, and contextual habitat products can reveal spatial relationships that persist beyond local contexts. I designed and carried out a campaign of drone surveillance over coastal habitats near Palmer Station, Antarctica, in the austral summer of 2020 to assess the seasonal abundance and habitat use of Antarctic fur seals (Arctocephalus gazella) in the Palmer Archipelago and adjacent regions (Chapter 4). I modeled abundance as a function of date, with and without additional terms to capture variance by site, and used these models to estimate peak abundance near Palmer Station in the 2020 summer season. These findings leverage the spatial and temporal advantages of drone methods to estimate species phenology, distribution and abundance. Together, these chapters describe emerging applications of drone technology that can advance pinniped research and management into new scales of analytical efficiency and ecological interpretation. These studies describe methods that have been proven in concept, but not yet standardized for practical deployment, and their findings reveal new ecological insights, opportunities for methodological advancement, and current limitations of drone methods for the study of pinnipeds in high-latitude environments.

Primary production regulates fisheries yield, but testing the degree to which it is so is complicated by our limited ability to measure and model net primary production in the ocean. Herein, I analyze primary production and fisheries yields in the tropical Pacific Ocean, and how uncertainties in physiology parameterizations and in field primary production measurements used in the models’ formulations limit model skill. I find that primary production model choice has an effect on designating sustainable fisheries levels, that model parameterizations are not tuned to the tropical Pacific systems, and that model skill assessment is highly dependent on our understanding of local biomass-productivity dynamics. Moving forward, improving the primary production estimates in the tropical Pacific can be done incorporating understanding of local ocean dynamics into model skill assessments.

Animals experience hydrodynamic forces (lift, drag, and side) and moments (pitching, yawing, and rolling) as a result of motion in an aqueous medium. Under selective pressure, most cetaceans, including porpoises, dolphins, and whales, developed a streamlined body shape and modified limbs, which delay the separation of flow, create lower drag when they swim, and therefore decrease their locomotor cost. In order to calculate the locomotor cost and propulsive efficiency of cetaceans, accurate estimates of drag on marine animals are required. However, extra momentum imparted into the fluid from lift and side forces as well as pitching, rolling, and yawing moments (here, the parasitic loads) results in extra drag force on the animal. Therefore, in addition to streaming and delaying flow separation, animals must also minimize excess fluid momentum resulting from parasitic loads. Given the endangered status of the North Atlantic right whale (Eubalaena glacialis; hereafter NARW), analyzing the hydrodynamic characteristics of the NARWs was the focus of this work. Additionally, previous studies showed that body shape of NARWs changes with life stages, reproduction status, nutritive conditions or prey abundance, and the effects of entanglement in fishing gear. Therefore, in this study, computational fluid dynamics (CFD) analysis was performed on multiple 10 m three-dimensional NARW models with different body shapes (e.g., normal condition, emaciated, and pregnant) to measure baseline measurements of flow regimes and hydrodynamic loads on the animal. Swimming speeds covering known right whale speed range (0.125 m/s to 8 m/s) were simulated in most scenarios. In addition to the hydrodynamic effects of different body shapes, drag was also considered a function of parasitic loads. The NARW models were embedded with bone segments that allowed one to manipulate the body pose of the model via adjusting the flippers or the spine of the animal before measuring hydrodynamic drag. By doing so, momentum from parasitic loads was expected to be eliminated. CFD simulations revealed that drag on NARWs is dictated by its irregular outline and that the drag coefficient (0.0071-0.0059; or dimensionless drag) of on NARWs is approximately twice that of many previous estimates for large cetaceans. It was also found that pregnant NARW model encounters the lowest drag coefficient due to delayed flow separation resulting from enlarged abdomen, whereas the emaciated NARW model experiences the highest drag coefficient possibly due to the concavity at the post-nuchal region. These results suggested that drag on NARWs and their thrust power requirements were indeed affected by its body shape but the differences between the three NARW models tested were small. Lastly, minimum drag, which corresponds to the elimination of the parasitic loads, can be obtained by adjusting the pose of the animal. Thus, minimum drag occurs at the neutral trim pose. For the static, normo-nourished NARW model, simulations revealed that by changing the angle of attack of the flippers by 4.03° (relative to the free-stream flow) and pitching the spine downward by 5° while maintaining fluke angle, the drag was lowered by approximately 11% across the flow speeds tested. This drag reduction was relative to the drag study conducted on the same animal model but without body pose adjustments. Together the studies included in the present work explored and highlighted the capability of numerical methods in investigating the hydrodynamics and energetics of cetaceans. Future studies should address how computer solutions can be used to solve problems from a wider aspect. For instance, extra parasitic loads caused by attached gear as well as possible injuries due to the encounter with fishing gear should also be considered while evaluating the energy budget of the North Atlantic right whales.

Social structure is a key determinant of population biology and is central to the way animals exploit their environment. The risk of predation is often invoked as an important factor influencing the evolution of social structure in cetaceans and other mammals, but little direct information is available about how cetaceans actually respond to predators or other perceived threats. The playback of sounds to an animal is a powerful tool for assessing behavioral responses to predators, but quantifying behavioral responses to playback experiments requires baseline knowledge of normal behavioral patterns and variation. The central goal of my dissertation is to describe baseline foraging behavior for the western Atlantic short-finnned pilot whales (Globicephala macrohynchus) and examine the role of social organization in their response to predators. To accomplish this I used multi-sensor digital acoustic tags (DTAGs), satellite-linked time-depth recorders (SLTDR), and playback experiments to study foraging behavior and behavioral response to predators in pilot whales. Fine scale foraging strategies and population level patterns were identified by estimating the body size and examining the location and movement around feeding events using data collected with DTAGs deployed on 40 pilot whales in summers of 2008-2014 off the coast of Cape Hatteras, North Carolina. Pilot whales were found to forage throughout the water column and performed feeding buzzes at depths ranging from 29-1176 meters. The results indicated potential habitat segregation in foraging depth in short-finned pilot whales with larger individuals foraging on average at deeper depths. Calculated aerobic dive limit for large adult males was approximately 6 minutes longer than that of females and likely facilitated the difference in foraging depth. Furthermore, the buzz frequency and speed around feeding attempts indicate this population pilot whales are likely targeting multiple small prey items. Using these results, I built decision trees to inform foraging dive classification in coarse, long-term dive data collected with SLTDRs deployed on 6 pilot whales in the summers of 2014 and 2015 in the same area off the coast of North Carolina. I used these long term foraging records to compare diurnal foraging rates and depths, as well as classify bouts with a maximum likelihood method, and evaluate behavioral aerobic dive limits (ADLB) through examination of dive durations and inter-dive intervals. Dive duration was the best predictor of foraging, with dives >400.6 seconds classified as foraging, and a 96% classification accuracy. There were no diurnal patterns in foraging depth or rates and average duration of bouts was 2.94 hours with maximum bout durations lasting up to 14 hours. The results indicated that pilot whales forage in relatively long bouts and the ADLB indicate that pilot whales rarely, if ever exceed their aerobic limits. To evaluate the response to predators I used controlled playback experiments to examine the behavioral responses of 10 of the tagged short-finned pilot whales off Cape Hatteras, North Carolina and 4 Risso’s dolphins (Grampus griseus) off Southern California to the calls of mammal-eating killer whales (MEK). Both species responded to a subset of MEK calls with increased movement, swim speed and increased cohesion of the focal groups, but the two species exhibited different directional movement and vocal responses. Pilot whales increased their call rate and approached the sound source, but Risso’s dolphins exhibited no change in their vocal behavior and moved in a rapid, directed manner away from the source. Thus, at least to a sub-set of mammal-eating killer whale calls, these two study species reacted in a manner that is consistent with their patterns of social organization. Pilot whales, which live in relatively permanent groups bound by strong social bonds, responded in a manner that built on their high levels of social cohesion. In contrast, Risso’s dolphins exhibited an exaggerated flight response and moved rapidly away from the sound source. The fact that both species responded strongly to a select number of MEK calls, suggests that structural features of signals play critical contextual roles in the probability of response to potential threats in odontocete cetaceans.

The evolution of reproductive strategies involves a complex calculus of costs and benefits to both parents and offspring. Many marine animals produce embryos packaged in tough egg capsules or gelatinous egg masses attached to benthic surfaces. While these egg structures can protect against environmental stresses, the packaging is energetically costly for parents to produce. In this series of studies, I examined a variety of ecological factors affecting the evolution of benthic development as a life history strategy. I used marine gastropods as my model system because they are incredibly diverse and abundant worldwide, and they exhibit a variety of reproductive and developmental strategies.

The first study examines predation on benthic egg masses. I investigated: 1) behavioral mechanisms of predation when embryos are targeted (rather than the whole egg mass); 2) the specific role of gelatinous matrix in predation. I hypothesized that gelatinous matrix does not facilitate predation. One study system was the sea slug Olea hansineensis, an obligate egg mass predator, feeding on the sea slug Haminoea vesicula. Olea fed intensely and efficiently on individual Haminoea embryos inside egg masses but showed no response to live embryos removed from gel, suggesting that gelatinous matrix enables predation. This may be due to mechanical support of the feeding predator by the matrix. However, Haminoea egg masses outnumber Olea by two orders of magnitude in the field, and each egg mass can contain many tens of thousands of embryos, so predation pressure on individuals is likely not strong. The second system involved the snail Nassarius vibex, a non-obligate egg mass predator, feeding on the polychaete worm Clymenella mucosa. Gel neither inhibits nor promotes embryo predation for Nassarius, but because it cannot target individual embryos inside an egg mass, its feeding is slow and inefficient, and feeding rates in the field are quite low. However, snails that compete with Nassarius for scavenged food have not been seen to eat egg masses in the field, leaving Nassarius free to exploit the resource. Overall, egg mass predation in these two systems likely benefits the predators much more than it negatively affects the prey. Thus, selection for environmentally protective aspects of egg mass production may be much stronger than selection for defense against predation.

In the second study, I examined desiccation resistance in intertidal egg masses made by Haminoea vesicula, which preferentially attaches its flat, ribbon-shaped egg masses to submerged substrata. Egg masses occasionally detach and become stranded on exposed sand at low tide. Unlike adults, the encased embryos cannot avoid desiccation by selectively moving about the habitat, and the egg mass shape has high surface-area-to-volume ratio that should make it prone to drying out. Thus, I hypothesized that the embryos would not survive stranding. I tested this by deploying individual egg masses of two age classes on exposed sand bars for the duration of low tide. After rehydration, embryos midway through development showed higher rates of survival than newly-laid embryos, though for both stages survival rates over 25% were frequently observed. Laboratory desiccation trials showed that >75% survival is possible in an egg mass that has lost 65% of its water weight, and some survival (<25%) was observed even after 83% water weight lost. Although many surviving embryos in both experiments showed damage, these data demonstrate that egg mass stranding is not necessarily fatal to embryos. They may be able to survive a far greater range of conditions than they normally encounter, compensating for their lack of ability to move. Also, desiccation tolerance of embryos may reduce pressure on parents to find optimal laying substrata.

The third study takes a big-picture approach to investigating the evolution of different developmental strategies in cone snails, the largest genus of marine invertebrates. Cone snail species hatch out of their capsules as either swimming larvae or non-dispersing forms, and their developmental mode has direct consequences for biogeographic patterns. Variability in life history strategies among taxa may be influenced by biological, environmental, or phylogenetic factors, or a combination of these. While most prior research has examined these factors singularly, my aim was to investigate the effects of a host of intrinsic, extrinsic, and historical factors on two fundamental aspects of life history: egg size and egg number. I used phylogenetic generalized least-squares regression models to examine relationships between these two egg traits and a variety of hypothesized intrinsic and extrinsic variables. Adult shell morphology and spatial variability in productivity and salinity across a species geographic range had the strongest effects on egg diameter and number of eggs per capsule. Phylogeny had no significant influence. Developmental mode in Conus appears to be influenced mostly by species-level adaptations and niche specificity rather than phylogenetic conservatism. Patterns of egg size and egg number appear to reflect energetic tradeoffs with body size and specific morphologies as well as adaptations to variable environments. Overall, this series of studies highlights the importance of organism-scale biotic and abiotic interactions in evolutionary patterns.

Coastal ecosystems are made up of habitats that provide critical ecosystem services, including saltmarshes, seagrasses, mangroves, and oyster reefs. However, they are also some of the most threatened and are vulnerable to anthropogenic and environmental stressors. Oyster reefs have been harvested within a fraction of their historical abundance, resulting in the loss of the goods and services that they provide to the people and surrounding ecosystems. In this dissertation, I explore how shellfish aquaculture can serve to supplement those services. In Chapter 1, I address the limited availability of specialized stock for environmental conditions. North Carolina’s aquaculture industry has been growing. However, there is no commercial oyster hatchery operating out of North Carolina, and most hatchery-stocked oysters in the state come from non-local lines. The UNC Wilmington Shellfish Research Hatchery, however, has been working on developing North Carolina oyster lines, derived from populations of oysters collected from across the state coastline and kept in isolated populations. In Chapter 1, I grow three of these lines in a common environment and determine that there is no influence of genetic line on final size, but there may be a connection to recovery from stress. I then use a genome-wide scan to assess the population structure within and between the lines. From this, I found that the three lines were genetically distinct from each other and had limited inbreeding. Our study contributes to the broader literature on the impact of population history on performance and emphasizes the difficulty of maintaining genetic diversity in highly fecund marine species in hatchery environments. Understanding the genetic fitness of these stocks and the conditions they thrive in will improve the pipeline of hatchery production as well as downstream use, as oysters are often spread widely from commercial hatcheries to seed aquaculture and restoration alike. A consequence of the increase in aquaculture has been the addition of complex hard substrate into unstructured areas. Overharvesting and loss of oysters has resulted in bare or otherwise unstructured substrate and thus loss of habitat for many organisms that used oyster reefs for habitat, nurseries, and foraging grounds. The addition of complex structure, then, may also be supplementing those needs and returning habitat to the area. Because oyster reefs host a diverse range of taxa, many of which are transient users, to measure a broad swathe of the community with a traditional sampling scheme would involve multiple survey strategies and taxonomists and have minimal temporal resolution. Environmental DNA (eDNA), on the other hand, is a non-invasive, relatively low-manpower, taxonomically broad methodology that does not require taxonomic experts. Through collecting and sequencing DNA from cells naturally shed by living organisms into their environment, this survey strategy can be used in a range of environments and is particularly useful to record cryptic and transitory taxa. However, high sequencing and library preparation costs associated with this method are barriers to widespread implementation. In Chapter 2, I develop methods to sequence and analyse environmental DNA using the Oxford Nanopore GridION sequencing platform. While eDNA has great potential as a biomonitoring tool, one barrier to adoption is the high cost and lead time for sequencing and library preparation. Oxford Nanopore Technology (ONT) systems have been increasingly of interest as a lower upfront cost alternative to second generation sequencing, but there has been little work benchmarking expectations of the platform when using mixed and low-quality DNA samples, such as eDNA. In Chapter 2, I use a stepwise process to establish bioinformatic and technological limitations of the ONT platform that would influence eDNA analysis. During this process, I show that by clustering sequences based on similarity, error correction against other sequences in the cluster, and strict taxonomic assignment cutoff thresholds, Oxford Nanopore sequencing can be used to accurately perform eDNA sequencing with samples amplified with broad-spectrum PCR primers. However, the tradeoff to these steps is lower taxonomic resolution and lower sequencing depth. In Chapter 3, I assess the habitat value of small-scale aquaculture facilities and how it compares to that of intertidal oyster reefs by comparing the biological communities associated with oyster aquaculture and oyster reefs using environmental DNA and the methodology developed in Chapter 2. I find that a wide variety of taxa made use of oyster aquaculture, many of which were also found at oyster reefs. This included generalists like mud snails and polychetes as well as specialist fauna like blennies and mobile, higher trophic level taxa like drum and mullet. Although the taxa were widely shared, the community composition between the two habitats differed. Vertebrate taxa were recorded more often at oyster reefs, while most of the aquaculture community at a given time was composed of benthic and planktonic fauna. These findings illustrate that an expansive host of organisms can be found around oyster aquaculture, many of which are shared with oyster reefs, indicating that the structure provided by aquaculture gear has the potential to provide habitat provisioning services like that of oyster reefs. There is great potential for shellfish aquaculture to contribute positive services to the environment, but it is important to understand the benefits that are possible and the risks and negative impacts that may occur. This will allow for incorporating environmental impact into farm design and siting, and improve the long-term sustainability of aquaculture. The findings in this dissertation contribute towards understanding and improving the services provided by oyster aquaculture, including through contributing towards understanding the effect of hatchery selection and genotype-by-environment interactions on oyster stocks, improving accessibility of biomonitoring tools by developing an eDNA analysis pipeline using the Oxford Nanopore Technology sequencing platform, and examining habitat provisioning services of aquaculture gear.

Coral reef habitats are well-known for biodiversity, yet are declining worldwide due to multiple stressors from local to global scales. Scleractinian corals, as foundation species, contribute to building the three-dimensional reef structure, yet this structure can be degraded through natural or anthropogenic disturbances. Conservation actions such as restoration depend on an understanding of the spatial distributions of potential habitat. In this dissertation, I address how abiotic environmental limitations shape coral species habitat niches and relate to recovery from disturbances. To accomplish this, I first describe local limitations on reef recovery after physical disturbances and then scale up to regional models of environmental niche constraints on coral species and communities.

First, I compare divergent recovery trajectories at two proximal reefs disturbed by ship groundings that created abrupt and clearly delineated areas of altered substrate. Despite similar initial physical disturbances, there were marked differences between the grounding sites with higher coral recruitment and survival on disturbed pavement than rubble bottom, reference reef, or restoration structures. I hypothesized that subsequent episodic disturbances from rubble mobilization could be a mechanism driving divergent recovery patterns. To estimate whether local hydrodynamic conditions were sufficient to mobilize rubble, I used a combination of long-term monitoring, hydrodynamic modeling, and rubble transport mechanics to hindcast the potential for substrate mobility. Long-term model simulations of hydrodynamic forcing at the study sites show multiple events where bottom-orbital velocities exceeded thresholds required to mobilize rubble via sliding or overturning. The data and analyses indicate that the wave energy mobilizes rubble substrate multiple times annually and suggests a physical limitation on survival of coral recruits relative to those on pavement substrate. The combination of multiple hydrodynamic disturbances and unstable substrate limits coral recovery and contributes to prolonged habitat loss.

I next scaled up to a seascape approach to model how environmental limitations on individual species impact the coral community response. I used a joint species distribution modeling approach with new and spatially extensive coral monitoring data from Puerto Rico and the U.S. Virgin Islands. Using a multivariate spatial modeling approach, I explained relationships between species and environments and predicted species abundances (and associated uncertainties) into new, unsurveyed geographic areas in the U.S. Caribbean region. Joint model results showed how coral populations and communities are structured by geomorphological and climate factors. Species abundances and sizes showed correlations between species niches relative to depth, slope, wave energy near the seafloor, and thermal stress. Using inverse prediction, I showed how a scenario of increased wave energy or increased temperature ranges may shift habitats for individual species and impact overall species richness.

I then focused specifically on four of the major reef-building coral species that are currently listed as Threatened under the Endangered Species Act: Acropora cervicornis, Orbicella annularis, O. faveolata, and O. franksi. I modeled environmental limitations on species distributions in terms of occurrence, abundance, and size in Puerto Rico and the U.S. Virgin Islands. I used Bayesian Generalized Linear Models to predict species occurrence and abundance. I then compared results to the generalized joint attribute models that included abundance and size. Specific model applications were dependent on data availability. All species responded in different ways to environmental predictors, yet all showed environmental limitations from depth, wave energy near the seafloor, and thermal regimes.

In summary, in this dissertation I modeled limitations on coral habitat by abiotic variables and, in particular, wave energy. I applied multiple spatial quantitative approaches from local scales to seascape scales. Information about disturbance frequency and wave energy constraints on habitat recovery are applicable to support habitat restoration efforts. Predicted spatial distributions from community and species modeling approaches will support species-based and site-based restoration, conservation, and management efforts.

Disease is an important driver of coral loss regionally and is projected to become more severe as temperatures increase around the world. Although there has been substantial research into the abiotic factors (e.g. temperature, nutrients) controlling coral diseases, we know significantly less about the biotic factors (i.e. species interactions) influencing disease dynamics. We examined how the species living on and within corals affect coral tissue loss from a white syndrome-like condition on Heron Island in the southern section of the Great Barrier Reef. We exposed Acropora aspera fragments in flow-through tanks to a fully crossed factorial experiment with three factors: the presence of a common symbiotic crab (Cyclodius ungulatus), contact with a common macroalgal complex, and simulated wounding mimicking fish predation. We found that crab presence increased coral survival from a white syndrome-type disease by over 25%, likely by removing macroalgae if present and by cleaning infected tissue. Conversely, contact with macroalgae dramatically increased coral mortality, with the chance of survival dropping to nearly 0 by the end of 25 days for corals that were in contact with algae. Wounding had no direct effect on coral health, but wounded corals with crabs did significantly better than corals with no wounding and crabs, which may be the result of coral-crab signaling. We suggest that A. aspera may produce nutrient-rich mucus when wounded, which attracts crab symbionts that help slow disease progression. These results suggest that incorporating biotic interactions into restoration designs may dramatically improve restoration outcomes and that adding beneficial symbionts may improve disease resilience at a local level.

This dissertation focuses on the relationship of industrial shrimp aquaculture and shrimp diseases, with an emphasis on the agency of disease in shaping the history of shrimp production. Shrimp aquaculture is concentrated in developing tropical economies, with the significant majority of shrimp exported to consumers in the Global North. The rise of shrimp aquaculture has been accompanied by the development of new technologies and practices, designed to facilitate and govern the growth of the industry. While successful in making aquaculture the single largest production method for shrimp, these innovations also created ideal environments for the emergence and spread of shrimp diseases, which have caused significant and persistent production losses. Disease has brought volatility and risk to producer livelihoods, while also necessitating further technological modernization and development interventions to curb disease outbreaks.

This research draws on qualitative interviews and contextual economic analyses to explore the role of disease at multiple scales. Chapter 2 examines how disease has shaped industry discourses and he practice of shrimp aquaculture across contexts. The role of the concept of biosecurity is examined to highlight the territorial nature of disease prevention. Chapter 3 explores the context of shrimp aquaculture development in Aceh, Indonesia. This chapter applies the general ideas explored in Chapter 2, to a real-world case, highlighting how the pairing of shrimp and disease is managed as a single commodity. Chapter 4 explores the reach of disease globally, and across methods of production. The economic effects of disease on U.S. wild shrimping are explored, along with the role of disease as a narrative element in resisting global aquaculture.

It is argued that shrimp disease shapes commodity relationships, influencing production decisions, and development priorities at multiple scales. The unsympathetic quality of disease makes disease prevention an ideal project for enrolling broad coalitions of human and non-human actors, and negating the politics embedded in the relationship of disease prevention with commodification more broadly.

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Antillean manatees (Trichechus manatus manatus) were heavily hunted in the past throughout the Wider Caribbean Region (WCR), and are currently listed as endangered on the IUCN Red List of Threatened Species. In most WCR countries, including Haiti and the Dominican Republic, remaining manatee populations are believed to be small and declining, but current information is needed on their status, distribution, and local threats to the species.

To assess the past and current distribution and conservation status of the Antillean manatee in Hispaniola, I conducted a systematic review of documentary archives dating from the pre-Columbian era to 2013. I then surveyed more than 670 artisanal fishers from Haiti and the Dominican Republic in 2013-2014 using a standardized questionnaire. Finally, to identify important areas for manatees in the Dominican Republic, I developed a country-wide ensemble model of manatee distribution, and compared modeled hotspots with those identified by fishers.

Manatees were historically abundant in Hispaniola, but were hunted for their meat and became relatively rare by the end of the 19th century. The use of manatee body parts diversified with time to include their oil, skin, and bones. Traditional uses for folk medicine and handcrafts persist today in coastal communities in the Dominican Republic. Most threats to Antillean manatees in Hispaniola are anthropogenic in nature, and most mortality is caused by fisheries. I estimated a minimum island-wide annual mortality of approximately 20 animals. To understand the impact of this level of mortality, and to provide a baseline for measuring the success of future conservation actions, the Dominican Republic and Haiti should work together to obtain a reliable estimate of the current population size of manatees in Hispaniola.

In Haiti, the survey of fishers showed a wider distribution range of the species than suggested by the documentary archive review: fishers reported recent manatee sightings in seven of nine coastal departments, and three manatee hotspot areas were identified in the north, central, and south coasts. Thus, the contracted manatee distribution range suggested by the documentary archive review likely reflects a lack of research in Haiti. Both the review and the interviews agreed that manatees no longer occupy freshwater habitats in the country. In general, more dedicated manatee studies are needed in Haiti, employing aerial, land, or boat surveys.

In the Dominican Republic, the documentary archive review and the survey of fishers showed that manatees still occur throughout the country, and occasionally occupy freshwater habitats. Monte Cristi province in the north coast, and Barahona province in the south coast, were identified as focal areas. Sighting reports of manatees decreased from Monte Cristi eastwards to the adjacent province in the Dominican Republic, and westwards into Haiti. Along the north coast of Haiti, the number of manatee sighting and capture reports decreased with increasing distance to Monte Cristi province. There was good agreement among the modeled manatee hotspots, hotspots identified by fishers, and hotspots identified during previous dedicated manatee studies. The concordance of these results suggests that the distribution and patterns of habitat use of manatees in the Dominican Republic have not changed dramatically in over 30 years, and that the remaining manatees exhibit some degree of site fidelity. The ensemble modeling approach used in the present study produced accurate and detailed maps of manatee distribution with minimum data requirements. This modeling strategy is replicable and readily transferable to other countries in the Caribbean or elsewhere with limited data on a species of interest.

The intrinsic value of manatees was stronger for artisanal fishers in the Dominican Republic than in Haiti, and most Dominican fishers showed a positive attitude towards manatee conservation. The Dominican Republic is an upper middle income country with a high Human Development Index. It possesses a legal framework that specifically protects manatees, and has a greater number of marine protected areas, more dedicated manatee studies, and more manatee education and awareness campaigns than Haiti. The constant presence of manatees in specific coastal segments of the Dominican Republic, the perceived decline in the number of manatee captures, and a more conservation-minded public, offer hope for manatee conservation, as non-consumptive uses of manatees become more popular. I recommend a series of conservation actions in the Dominican Republic, including: reducing risks to manatees from harmful fishing gear and watercraft at confirmed manatee hotspots; providing alternative economic alternatives for displaced fishers, and developing responsible ecotourism ventures for manatee watching; improving law enforcement to reduce fisheries-related manatee deaths, stop the illegal trade in manatee body parts, and better protect manatee habitat; and continuing education and awareness campaigns for coastal communities near manatee hotspots.

In contrast, most fishers in Haiti continue to value manatees as a source of food and income, and showed a generally negative attitude towards manatee conservation. Haiti is a low income country with a low Human Development Index. Only a single dedicated manatee study has been conducted in Haiti, and manatees are not officially protected. Positive initiatives for manatees in Haiti include: protected areas declared in 2013 and 2014 that enclose two of the manatee hotspots identified in the present study; and local organizations that are currently working on coastal and marine environmental issues, including research and education on marine mammals. Future conservation efforts for manatees in Haiti should focus on addressing poverty and providing viable economic alternatives for coastal communities. I recommend a community partnership approach for manatee conservation, paired with education and awareness campaigns to inform coastal communities about the conservation situation of manatees in Haiti, and to help change their perceived value. Haiti should also provide legal protection for manatees and their habitat.

Diverse ways of knowing have been recognized by scholars in many disciplines to contribute creative perspectives and novel problem-solving approaches. In the environmental sciences, those dependent on natural resources and working daily with those resources are in one of the best positions to observe and learn from subtle changes in the environment. In the coastal marine and estuarine environment, these experiential knowledge holders are the fishers and their families. In North Carolina, these fishers live in historic villages and, with scientists and policymakers, serve as the downstream stakeholders in watershed management. These three stakeholder groups all have perspectives to contribute to research and management of water quality in the watershed. This dissertation starts by documenting definitions and perspectives of water quality from these three stakeholder groups, establishing the base of information from which future research and management takes place. It then specifically addresses the details of negotiating co-production of knowledge through an ethnographic account of a collaborative research project investigating water pollution. The process of information sharing was highlighted during this process by a facilitated workshop asking participants to reflect upon their collective understanding of water quality more broadly and to plan a research project resulting from a new shared, understanding. The third component of my investigation of different ways of knowing uses North Carolina's Fishery Resource Grant program, which funds collaborative research between fishers and scientists, as a case study of an institution supporting co-produced knowledge about water quality and how the structure of collaboration in funded projects affects the success of the program both scientifically and socially. Together, the three chapters tell a story about the diverse forms of knowledge regarding water quality and how they might work together to better understand the causes and effects of water quality as well as tailor solutions to fit this better understanding. Though the story is of one case, specific to water quality and the coastal communities that depend on it, the story is also one of few optimistic cases in environmental science.

Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ.

Increasingly the challenges of environmental governance are understood as global in nature and scope. Within fisheries, industrial fisheries have long been the global priority in fisheries science, policy instruments, and management techniques. Meanwhile, small-scale fisheries (SSF) have historically been relegated to the margins, framed as local, place-based, static practices from the past rather than global priorities. This dissertation examines the conditions and consequences of transformation in SSF governance, as SSF are becoming a global concern. The passage of a recent internationally negotiated policy for the small-scale sector signifies this monumental shift underway in global fisheries governance priorities: The Voluntary Guidelines for Securing Sustainable Small-Scale Fisheries in the Context of Food Security and Poverty Eradication (SSF Guidelines).By ‘following the policy,’ this research examines the dynamics of policy mobility (e.g., who and what came together to make and implement this policy) across multiple sites and scales of policymaking and implementation as the SSF guidelines are mobilized at global, regional, and national levels. The movement to transform fisheries governance is examined against past patterns in fisheries science and policy, including through analysis of a large-N dataset. The mixed methods used provide needed insights into how different actors (e.g., scientists, policymakers, civil society organizations) have grappled with the questions “governance of what, by whom, to what ends” in SSF through time. While the passage of the SSF Guidelines in 2014 was considered a landmark moment for the SSF sector, attention has now shifted to what they will become; whether and how this policy will ‘scale down’ and to what effects. Studying policy implementation is critical to understanding how transformative change happens in fisheries governance and environmental governance more broadly. Developed with ongoing input from civil society organizations, the SSF Guidelines are the first global policy designed explicitly for SSF. Endorsing gender equality, decent work, and human rights as necessary tenets of sustainability, this policy’s core principles stand in stark contrast to the status quo in fisheries governance. But what these principles will become is uncertain because policy implementation was left intentionally open-ended in the text of the SSF Guidelines which were written without pre-determined implementation targets or definitions of success. This dissertation addresses the central question: How is such an unconventional and unlikely policy mobilized in practice, and how are the ideas within translated in place? To this end, this research engages with the literature on global environmental governance, theories of scale from human geography and common-pool resource scholarship, and the emergent field of critical policy studies, extending these insights to the dynamics SSF governance, an understudied common-pool resource system undergoing transformation here and now. Amidst the wider movement to transform fisheries governance to be more equitable, this research focuses on the principle of gender equality within the SSF Guidelines. Emphasis is placed on how the principle of gender equality came to be part of a global policy instrument in the first place, and later, articulated as the focus of national policy implementation. While this is a multi-sited and multi-scaled story, the dynamics of national-level implementation are followed in the context of Tanzania, one country working to implement this policy in their vast inland and marine fisheries with a chosen focus on gender. Tracing the multi-stakeholder process of developing a national ‘roadmap’ to implement the SSF Guidelines there, this dissertation reveals how the goal of gender equality was translated into specific strategies determined in place, including through a collaborative effort to ‘map’ existing women’s fishing organizations and networks among them. Conclusions demonstrate that flexibility intentionally built into the design of global policies can create room for new understandings of what small-scale fisheries are, how they should be governed, and what a sustainable and desirable future for fisheries looks like—making space to imagine and enact alternatives that are more just and inclusive. Following the indeterminate arc of policy mobility then is critical to determining who steps into the space created by policy change. In the story of creating and implementing the SSF Guidelines, civil society organizations played an outsized role in affecting multi-scalar policy transformation.

Estimates of the energetic costs of locomotion (COL) are necessary to understand one of the potential impacts of anthropogenic disturbance on marine mammals. A new generation of biologging devices has enabled the measurement of fine-scale behavioral responses to disturbance, but calibration experiments are required to convert these measured changes in activity level into energy expenditure. Such calibrations have been conducted in many terrestrial and avian taxa but, due to logistical constraints, have been performed with only a few marine mammals. Very few studies have tested these calibrations against independent estimates of energy expenditure, such as measurements of caloric intake and the doubly labeled water (DLW) method. Calibration studies will help us to better understand how best to estimate energy expenditure from activity measurements. In my dissertation, I ask whether short-term increases in activity caused by disturbance may impact marine mammal energy budgets. I address this question with the long-term resident community of common bottlenose dolphins (Tursiops truncatus) living in Sarasota Bay, Florida, which experiences very high levels of traffic from small vessels. I first correlated overall dynamic body acceleration (ODBA) and energy expenditure with bottlenose dolphins in human care. I combined measurements of ODBA derived from accelerometry tags with respirometry during submerged swim trials. I then subtracted measured resting metabolic rate (RMR) from the energy expenditure of each trial to estimate COL. I found a linear relationship between ODBA and COL. Next, I deployed tags on the same dolphins for longer periods (24 hours) and combined COL, RMR, and specific dynamic action (SDA; energy expenditure associated with digestion) to estimate total daily energy expenditure. I compared this estimate of total daily expenditure with estimates derived from measurements of caloric intake records and DLW. The COL+RMR+SDA values largely agreed with the calories ingested, but the smaller DLW sample was considerably more variable. I then used the correlation between ODBA and COL to estimate the cumulative energetic costs associated with responses to vessels by wild dolphins in Sarasota. I analyzed 12 digital acoustic tag (DTAG) records for the presence or absence of vessels. I used periods without vessels as controls to calculate baseline estimates of COL for each animal. I then subtracted this baseline from total COL to derive the cumulative COL attributable to vessels. The overall increase in COL attributable to the response to vessels was less than 0.3% of estimated daily energy expenditure, suggesting that avoidance, while necessary to prevent injury or death, does not contribute significantly to the daily energy budgets of these dolphins. The methods I developed can be applied to a variety of other marine mammals to study the fitness consequences of anthropogenic disturbance. Future studies should focus on sensitive species that are likely to exhibit significant avoidance responses to acoustic stimuli.