<p>Locomotion in any environment requires the use of energy to overcome the physical</p><p>forces inherent in the environment. Most large marine vertebrates have evolved</p><p>streamlined fusiform body shapes to minimize the resistive force of drag when in</p><p>a neutral position, but nearly all behaviors result in some increase in that force.</p><p>Too much energy devoted to locomotion may reduce the available surplus necessary</p><p>for population-level factors such as reproduction. The population of North Atlantic</p><p>right whales has not recovered following legal protection due to decreased fecundity,</p><p>including an increase in the intercalf interval, an increase in the years to first calf and</p><p>an increase in the number of nulliparous females in the population. This reproductive</p><p>impairment appears to be related to deficiencies in storing enough energy to meet the</p><p>costs of reproduction. The goal of this study was to determine whether increases in</p><p>moving between prey patches at the cost of decreased foraging opportunities could</p><p>shift these whales into a situation of negative energy gain. The first step is to</p><p>understand the locomotor costs for this species for the key behaviors of traveling and</p><p>foraging.</p><p>This study investigated the cost of locomotion in right whales by recording the</p><p>submerged diving behaviors of free-ranging individuals in both their foraging habitat</p><p>in the Bay of Fundy and their calving grounds in the South Atlantic Bight with a</p><p>suction-cupped archival tag. The data from the tags were used to quantify the oc-</p><p>currence of different behaviors and their associated swimming behaviors and explore</p><p>three behavioral strategies that reduce locomotor costs. First, the influence that</p><p>changes in blubber thickness has on the buoyancy of these whales was investigated</p><p>by comparing the descent and ascent glide durations of individual whales with differ-</p><p>ent blubber thicknesses. Next, the depth of surface dives made by animals of different</p><p>sizes was related to the depth where additional wave drag is generated. Finally, the</p><p>use of intermittent locomotion during foraging was investigated to understand how</p><p>much energy is saved by using this gait. The final piece in this study was to deter-</p><p>mine the drag related to traveling and foraging behaviors from glides recorded by</p><p>the tags and from two different numerical simulations of flow around whales. One, a</p><p>custom developed algorithm for multiphase flow, was used to determine the relative</p><p>drag, while a second commercial package was used to determine the absolute mag-</p><p>nitude of the drag force on the simplest model, the traveling animal. The resulting</p><p>drag estimates were then used in a series of theoretical models that estimated the</p><p>energetic profit remaining after shifts in the occurrence of traveling and searching</p><p>behaviors.</p><p>The diving behavior of right whales can be classified into three stereotyped be-</p><p>haviors that are characterized by differences in the time spent in different parts of the</p><p>water column. The time budgets and swimming movements during these behaviors</p><p>matched those in other species, enabling the dive shapes to be classified as foraging,</p><p>searching and traveling behaviors. Right whales with thicker blubber layers were</p><p>found to perform longer ascent glides and shorter descent glides than those with</p><p>thinner blubber layers, consistent with the hypothesis that positive buoyancy does</p><p>influence their vertical diving behavior. During horizontal traveling, whales made</p><p>shallow dives to depths that were slightly deeper than those that would cause ad-</p><p>ditional costs due to wave drag. These dives appear to allow whales to both avoid</p><p>the costs of diving as well as the costs of swimming near the surface. Next, whales</p><p>were found to glide for 12% of the bottom phases of their foraging dives, and the</p><p>use of `stroke-glide' swimming did not prolong foraging duration from that used by</p><p>continuous swimmers. Drag coefficients estimated from these glides had an average</p><p>of 0.014 during foraging dives and 0.0052 during traveling, values which fall in the</p><p>range of those reported for other marine mammals. One numerical simulation deter-</p><p>mined drag forces to be comparable, while the other drastically underestimated the</p><p>drag of all behaviors. Finally, alterations to the behavioral budgets of these animals</p><p>demonstrated their cost of locomotion constitutes a small portion (8-12%) of the</p><p>total energy consumed and only extreme increases in traveling time could result in a</p><p>negative energy balance. In summary, these results show that locomotor costs are no</p><p>more expensive in this species than those of other cetaceans and that when removed</p><p>from all the other stressors on this population, these whales are not on an energetic</p><p>`knife edge'.</p> / Dissertation

Marine mammal mass strandings have been documented for centuries, even going as far back as Aristotle. For just as long, the causes of these mass strandings have been questioned. With every species of cetacean known to have stranded, it is important to find trends to understand and prevent these strandings from occurring. With a heightened awareness of this issue, leading to the creation of marine mammal stranding networks throughout the United States in the 1990s, a more comprehensive approach to data collection has helped with the study. Issues such as seasonality, weather, topography, and disease have all been observed as a potential cause of these events. This study attempted to look at the Atlantic Coast of the United States, and its documented mass strandings from 1997-2011. Stranding data taken from the Northeast and Southeast US Marine Mammal stranding network database provided a basis for the study of these mass strandings. Many of the possible causes of these strandings, including seasonality, location, and species were studied. There was some correlation found between seasons and stranding, meaning there are certain times of the year when a cetacean pod may be more likely to strand.

Polycyclic aromatic hydrocarbons (PAH) have been linked to cancer in humans. Subsequently, 16 of them were listed as priority pollutants by the Environmental Protection Agency in the Clean Water Act. The Florida manatee (Trichechus manatus latirostris) is an herbivorous endangered species that could have the potential to accumulate these compounds. The waters they inhabit have been shown to have PAH concentrations in the sediment from 0.035 μg/g w.w. (wet weight) to 0.686 μg/g w.w. PAH bioaccumulate due to their lipophilic nature and the manatee has a thick blubber layer that may allow for the accumulation of these compounds. Forty-eight archived subcutaneous manatee blubber samples were collected from Florida Fish and Wildlife Conservation Commission Marine Mammal Pathobiology lab and analyzed for 16 known priority pollutant PAH. Samples were then compared to a standard using HPLC analysis. Concentrations were found to range from 0.001 μg/g w.w. to 84.84 μg/g w.w. All 16 priority pollutant PAH were found, however not all 16 were found in any one animal. Forty-six of forty-eight manatee samples analyzed were found to have at least one form of PAH. The number of occurrences of each PAH out of 48 samples ranged from 1-19. The highest average PAH concentration was acenaphthylene with 12.60 μg/g w.w. There was no significant difference (p-value >0.10) between total, carcinogenic and noncarcinogenic PAH, with levels of 2.01 μg/g w.w., 2.18 μg/g w.w. and 1.84 μg/g w.w. respectively. No significant difference (p-value >0.10) was found between year or location of carcass recovery as well as sex of manatee. Averages ranged between 0.02 μg/g w.w. and 18.92 μg/g w.w. for year and 0.15 μg/g w.w. and 5.68 μg/g w.w. for location. Male average levels were 5.21 μg/g w.w., while female averages and perinatal averages were 1.51 μg/g w.w. and 1.147 μg/g w.w. respectively.

Resolute Bay, a remote Arctic bay opening into Parry Channel, in the Canadian Arctic Archipelago, hosts diverse populations of marine mammals and fish at various times each year. These animals migrate through the bay following patterns linked to food availability and oceanographic conditions; however, these patterns are not well understood. The focus of this study was to measure the oceanographic properties of the waters in and around Resolute Bay and to record underwater sounds to obtain marine mammal temporal patterns and ambient sound levels. Results showed the water properties in Resolute Bay differed from the waters outside of the bay. Dissolved oxygen saturation levels in Resolute Bay decreased during ice-covered times, with lowest levels between May and July. Dissolved oxygen was replenished after the ice left the bay. Sudden changes in salinity, temperature, and dissolved oxygen were observed in Resolute Bay when outside waters entered. Mean third-octave band sound pressure levels were 85.3 dB re 1 μPa during high ice concentration, and 95.6 dB re 1 μPa during ice-free and freeze-up periods, and reached a maximum of 145.3 dB re 1 μPa when vessels were present. Belugas (Delphinapterus leucas) and narwhals (Monodon monocero) were only present in periods of low ice concentration, while bearded seals (Erignathus barbatus) and ringed seals (Pusa hispida) remained throughout the entire year. / Graduate / 2018-07-01

Background: Northern elephant seals transition from terrestrial nursing pups to pelagic foraging juveniles in a short period of just 8-12 weeks. During the post-weaning period, pups rely solely on the energy reserves gained during nursing for their caloric demands and water supply. The prolonged absence of food after weaning is the first of many fasts for which the seals have evolved adaptations such as decreased urine production and increased blubber reserves. The stressors experienced from learning to dive for the first time are also stressors that they will experience frequently as an adult and for which they have evolved adaptations. The purpose of this study was to understand the tissue-specific molecular fasting- and diving- induced adaptive responses of pups during this critical transition. Methods: To investigate these adaptive responses to fasting and diving, we collected skeletal muscle and (inner and outer) adipose tissue from early-fasting (< 1 week post-weaning) and late-fasting (8 weeks post-weaning) pups. We analyzed the samples with mass-spectrometry-based proteomics using two-dimensional gel electrophoresis. Proteomics is an invaluable tool for analyzing marine mammal physiology, as it provides a large, unbiased data set of proteins that offer a comprehensive set of mechanisms involved with the cellular processes being studied. Proteomics has only been used as analytical tool for marine mammal biology in two other studies, and it can be used as a tool leading to the discovery of novel, unanticipated results. Results and Discussion: Because muscles are utilized during locomotion, we expected the proteome of skeletal muscle to highlight important physiological changes as the pups learn to dive. Inner adipose is more metabolically active than outer adipose, so we anticipated it would show important changes in metabolism throughout their fast. Outer adipose was useful to detect changes in the proteome due to thermoregulation, as it experiences the most drastic change in temperature and pressure while the pups learn to dive. In all tissues, we found significant shifts in energy metabolism proteins that show a decrease in lipid metabolism and urine production, and an increase in alternative metabolic pathways, such as the pentose phosphate pathway, which produces precursors for nucleic acid synthesis. We also found increases in cytoskeletal proteins, skeletal muscle proteins, and oxygen-binding proteins that facilitate the development of diving ability in late-fasting pups. Lastly, changes in the abundance of oxidative stress related proteins showed increased use of antioxidant proteins to control the production of reactive oxygen species in late-fasting pups. This study provides insight into cellular and physiological responses in marine mammals during ontogeny and their adaptive capacity during a key transition from a terrestrial to aquatic lifestyle.

En partenariat avec l’entreprise Sercel, la thèse concerne la mise en œuvre d’algorithmes de reconnaissance des sons émis par les mysticètes (baleines à fanons). Cessons peuvent être étudiés grâce aux systèmes de surveillance par acoustique passive. L’entreprise Sercel, par ses activités sismiques liées à la prospection pétrolière, a son propre logiciel pour détecter et localiser les sources d’énergie sonores sous-marines. Le travail de la thèse consiste dès lors à ajouter un module de reconnaissance pour identifier si l'énergie détectée et localisée correspond bien à un éventuel mysticète. Les campagnes de tirs sismiques étant onéreuses, la méthode utilisée doit pouvoir réduire la probabilité de fausse alarme, la reconnaissance pouvant infirmer la détection. La méthode proposée est basée sur l’apprentissage de dictionnaire. Elle est dynamique, modulaire, ne dépend que de peu de paramètres et est robuste aux fausses alarmes. Une expérimentation sur cinq types de vocalises est présentée. Nous obtenons un rappel moyen de 92.1 % tout en rejetant 97.3 % des bruits (persistants et transitoires). De plus, un coefficient de confiance est associé à chaque reconnaissance et permet de réaliser de l’apprentissage incrémental semi-supervisé. Enfin, nous proposons une méthode capable de gérer la détection et la reconnaissance conjointement. Ce « détecteur multiclasses » respecte au mieux les contraintes de gestion des fausses alarmes et permet d’identifier plusieurs types de vocalises au même instant. Cette méthode est bien adaptée au contexte industriel pour lequel elle est dédiée. Elle ouvre également des perspectives très prometteuses dans le contexte bioacoustique. / In partnership with Sercel, the thesis concerns the implementation of algorithms for recognizing the sounds emitted by mysticetes (baleen whales). These sounds can be studiedusing passive acoustic monitoring systems. Sercel, through its seismic activities related to oïl exploration, has its own software to detect and locate underwater sound energy sources. The thesis work therefore consists in adding a recognition module to identify if the detected andlocalized energy corresponds to a possible mysticete. Since seismic shooting campaigns areexpensive, the method used must be able to reduce the probability of false alarms, as recognitioncan invalidate detection. The proposed method is based on dictionary learning. It is dynamic, modular, depends on few parameters and is robust to false alarms. An experiment on five types of vocalizations is presented. We obtain an average recall of 92.1% while rejecting 97.3% of the noises (persistent and transient). In addition, a confidence coefficient is associated with each recognition and allows semi-supervised incremental learning to be achieved. Finally, we propose a method capable of managing detection and recognition together. This "multiclassdetector" best respects the constraints of false alarm management and allows several types of vocalizations to be identified at the same time. This method is well adapted to the industrial context for which it is dedicated. It also opens up very promising prospects in the bioacoustic context.

As apex predators in coastal systems, bottlenose dolphins (Tursiops truncatus) are susceptible to persistent organic pollutant (POP) accumulation and retention over time, which has prompted continued interest in understanding the extent to which contaminant body burdens or other stressors are sufficient to cause adverse sublethal effects on energetic fitness, immune function, or reproduction. Increasing our knowledge of reproductive endocrinology in bottlenose dolphins may provide insight into changes in reproductive rates, thereby expanding the capacity to assess conservation status. This study used the Enzyme-Linked ImmunoSorbent Assay (ELISA) technique to examine peptide fertility hormones [inhibin A, inhibin B and anti-Müllerian hormone (AMH)] measured in serum of free-ranging dolphins (n = 129) of varying age, gender, and maturity status from three locations (Sarasota Bay, FL, Indian River Lagoon, FL, and southern Georgia). The primary research objectives were to establish hormone baselines, investigate AMH and inhibin use as reproductive biomarkers, and examine the potential use of these hormones as biomarkers of toxicant or other stressor effects on reproduction. AMH secretion differed significantly with gender (p < 0.001), where levels were approximately 1,000-fold higher in males than females (1,122 ± 427 ng mL-1 and 1.15 ± 1.25 ng mL-1, mean ± SD). Male AMH levels were related to maturity status, and linear regression analysis revealed a significant, negative relationship between male AMH and age, body length, body weight, and maximum girth in all populations. Of the parameters assessed, age was the best indicator of AMH levels in males. AMH concentrations in females did not vary significantly over time or with maturity status, but exhibited a decrease in some older individuals, potentially indicating an AMH decline in long-lived female dolphins. Inhibins did not differ significantly between age classes in males, but appeared to be an estrous cycle indicator in females, where inhibin peaks were likely related to follicular and luteal phases. These data provide new information on circulating serum AMH and inhibin levels in bottlenose dolphins, which appear to reflect a degree of gonadal function and show promise as reproductive biomarkers. Our findings suggest the possibility of toxicant effects on AMH and inhibin production, but not conclusively. Further investigation of mechanism(s) of action for contaminant-related reproductive toxicity will elucidate the diagnostic value of these hormones to assess the effects of POPs on fertility potential in bottlenose dolphins.

La reconnaissance joue un rôle important dans les systèmes de communication animale et plusieurs modalités sensorielles sont impliquées à cette fin. Bien que la reconnaissance mère-jeune ait été largement étudiée, il y a un manque d'information sur la reconnaissance multimodale et l'importance relative des différentes modalités dans ce processus. Dans cette thèse, j'ai exploré la communication multimodale chez un mammifère colonial - le lion de mer Australien (Neophoca cinerea). La reconnaissance mère-jeune est connue pour être multimodale chez cette espèce, mais les processus sous-jacents de la reconnaissance olfactive et visuelle, ainsi que les interactions entre les indices acoustiques, visuels et olfactifs, et leurs contributions relatives restent inconnues. Des analyses chimiques ont permis de déterminer si les profils chimiques diffèrent selon le sexe et l'âge, les colonies et les régions corporelles des animaux. La présence de similarités chimiques entre la mère et son petit suggèrent que l'appariement des phénotypes pourrait être utilisé pour la reconnaissance olfactive. J'ai examiné le rôle des indices visuels lors de la reconnaissance mère-jeune et j'ai constaté que les indices visuels spécifiques à l'âge sont utilisés par les femelles pour affiner la recherche de leur petit dans la colonie. Les jeunes ont également la capacité de distinguer divers indices visuels, qui peuvent être utilisés pour identifier les différentes classes de congénères. Enfin, j’ai pu aussi déterminer comment les indices acoustiques, olfactifs et visuels sont utilisés de manière synergique dans le processus d’identification individuel, et les résultats sont interprété dans une perspective coûts-avantages pour démêler les pressions évolutives sur chaque composante de ce système de communication. Si les différents indices sensoriels ont la capacité de transmettre des informations en isolation, leur rôle peut être différent lorsque d'autres indices sensoriels sont présents. Les résultats de cette recherche fournissent des résultats sans précédent, contribuant à une meilleure compréhension de la reconnaissance mère-jeune chez les mammifères, ainsi que des règles générales de communication chez les vertébrés. / Recognition plays an important role in animal communication systems and individuals often employ different sensory modalities to enact this activity. Although recognition has been widely investigated, especially for mother-offspring interactions, there is a dearth of information about multimodal recognition and the relative importance and interactions of various sensory cues. In this thesis, I explored multimodal communication in a colonial mammal – the Australian sea lion (Neophoca cinerea). Communication during mother-pup reunions is known to be multimodal in this species, yet the underlying processes of olfactory and visual recognition, as well as the interactions between acoustic, visual and olfactory cues remain unclear. Through chemical analyses, I determined whether chemical profiles differ among sex and age classes, colonies, and body regions of animals. Chemical similarities between mothers and pups indicate that phenotype matching may be used by Australian sea lions for olfactory recognition. I examined the role of visual cues in mother-pup recognition and found that age-specific visual cues assist mothers to refine their search for their offspring in the colony. Pups are capable of distinguishing various visual cues that can be used in the assessment of conspecifics. Having provided baseline information about the role of sensory cues in isolation, I determined how acoustic, olfactory, and visual cues are used in a synergistic way to ensure accurate mutual recognition and then interpreted the results using a cost-benefit perspective to disentangle the evolutionary pressures on each component of this communication system. I showed that although cues have the ability to convey given information in isolation, their role may be different when other sensory cues are present. Furthermore, there is a mutual dependency in the communication system, where the limitations imposed on one participant of the dyad affect cue use by the other. These findings contribute to a better understanding of mammal mother-offspring recognition and communication mechanisms in vertebrates.

Changes in marine production play a key role in determining the trophic structure of the northeastern Pacific Ocean. This is a region of great environmental fluctuations due to modern, historical, and paleo-environmental variability recorded throughout the Holocene. These fluctuations are recorded in the bone collagen of the marine mammals that reside in these waters. Marine mammal remains from four previously excavated archaeological deposits on Unalaska Island, Alaska are used as a proxy for marine production changes throughout the Holocene (4,500 BP to 350 BP). Historic and modern samples from museum collections, subsistence harvests, and previously published data provide a distinct contrast to prehistoric marine mammals. Stable carbon and nitrogen isotope ratios (δ13C and δ15N) derived from marine mammal bone collagen correlate to changes in marine production and food web length. The 13C and 15N of prehistoric marine mammal taxa covary through the Holocene, indicating no trophic level change with fluctuations in 13C. Changes in δ13C and δ15N of marine mammals are correlated to periods of environmental fluctuations within the Holocene. Cooler climatic periods (transitional interval, beginning of the Neoglacial Interval, and Little Ice Age) show enrichedδ13C, reflecting primary production increase, compared to warmer climate periods (end of the Neoglacial Interval into the Medieval Climatic Anomaly). Unidentified cetacean bones are isotopically distinguishable into orders Mysticeti (baleen) and Odontoceti (toothed) due to different feeding ecologies. The δ13C depletion in modern pinnipeds compared to prehistoric is likely caused by the effect of increased anthropogenic atmospheric CO2 and resulting decrease in primary production.

Chronic physiological stress impacts animal fitness by catabolizing metabolic stores and suppressing reproduction and immunity. This can be especially deleterious for capital breeding carnivores, such as marine mammals, which rely on lipid stores accrued during intensive foraging to sustain prolonged periods of fasting associated with reproduction. Therefore, chronic stress may cause a decrease in fitness in these animals, leading to population declines and potentially detrimental shifts in food web dynamics as a result. However, the impacts and indicators of chronic stress in animals are currently poorly understood. To identify downstream mediators of repeated stress responses in marine mammals, adrenocorticotropic hormone (ACTH) was administered once daily for four days to free-ranging juvenile northern elephant seals (Mirounga angustirostris) to stimulate endogenous corticosteroid release. I then compared blubber tissue transcriptome responses to the first and fourth ACTH administrations to determine the effects of acute and chronic endocrine stress, respectively. Gene expression profiles showed differences in responses to single and repeated ACTH administration, despite similarities in circulating cortisol profiles. We identified 61 and 12 differentially expressed genes (DEGs) in response to the first ACTH and fourth administrations, respectively, 24 DEGs between the first and fourth pre-ACTH samples, and 12 DEGs between ACTH response samples from the first and fourth days. Annotated DEGs were associated with functions in redox and lipid homeostasis, suggesting potential negative impacts of repeated stress on marine mammals. In addition, protein expression profiles were discrete between single and repeated ACTH administrations, and identified changes in expression of extracellular proteins that were not detected at the transcriptome level. We identified 8 and 7 differentially expressed proteins (DEPs) in response to the first and fourth ACTH administrations, respectively, including 5 DEPs in the overall ACTH response, 1 DEP between the first and fourth pre-ACTH samples, and 10 DEPs between ACTH response samples from the first and fourth days. Differentially expressed proteins in response to repeated ACTH administrations were associated with extracellular matrix (ECM) remodeling and suggest a link between glucocorticoid-induced adipogenesis and ECM remodeling in blubber. Other differentially expressed proteins were associated with increased lipid metabolism and decreased immunity, consistent with transcriptome data. Together, the use of transcriptomics and proteomics to detect responses to repeated stress provides more comprehensive insight into the marine mammal stress response and highlights the importance of using multiple discovery-driven approaches for understanding stress physiology. The gene and protein markers identified in this study may be used to identify stressed animals and discriminate between acutely and chronically stressed individuals with higher sensitivity than hormone measurements alone.