The sperm whale is the largest of the toothed whales (Odontoceti), and inhabits deep waters from equatorial to Polar Regions. Sperm whales are social and commonly l r . found in small groups. However, sociality varies according to sex and age. Immature males form bachelor groups that disperse as they mature, mature males are frequently encountered alone. Sperm whales are renowned for their diving capabilities. Therefore, surface observations are only possible for 10 to 15 minutes every hour. Consequently, the sperm whale is an ideal candidate for investigation using genetic markers. Genetic variation can reveal information on geographical structuring of populations and, on a finer scale, the social organisation within these groups. The focus of this thesis is an investigation into the structure of populations around the Azores. To date, this work represents the most comprehensive molecular investigation into North Atlantic sperm whales. Since 1988 sloughed skin samples have been collected from the Azores but, to facilitate the comparison between local and global structuring, samples were also obtained from a number of geographically distinct regions. Twelve microsatellite loci and a marker to indicate sex were selected for screening. Genetic variation was sufficient to allow identification of individuals with a high degree of accuracy. A system of scoring the amplification quality was found to be both a simple and accurate method of determining the reliability of a genotype. Errors were found to arise infrequently, hence their influence in the final dataset was considered negligible. Of the 467 sloughed skin samples collected from the Azores, 102 individuals were identified. The majority of these samples had been collected from groups. As groups are presumed to be matrilineal, the identification of mother calf pairs was anticipated. However the samples revealed few parent offspring combinations. Within a group the majority of whales were related at the level of half )siblings. This indicates that I I Azorean groups comprise of individuals related through either the maternal or paternal lineage. Full siblings were also identified, which suggests that a degree of mate choice can occur. The first insight into the relationships within bachelor groups arose when two such groups, stranded off the coast of Scotland, were examined. Individuals within the groups were predominantly unrelated to each other. However, potential half/sibling relationships within the groups were identified. A mother offspring pair was identified between an Azorean whale and one of the stranded whales. Microsatellite data from Atlantic (n=I32) and Pacific (n=I59) sperm whales revealed low, but significant, inter-ocean variation. However, examinations of populations structuring on a finer scale (geographic regions) failed to reveal any consistent pattern of differentiation. This lack of differentiation is surprising when compared with other cetaceans, all of which show increased genetic differentiation with distance.

Gray whales (Eschrichtius robustus), while engaged in underwater signalling, circumvent noise in the acoustical channel by the structure and timing of their calls. Data yielding this conclusion were collected during an acoustical study on gray whales and their habitats (1981-1984). Sonographic analyses of tape recordings were used to quantify the acoustical repertoire, the ambient noise characteristics of the area, and the relationship between the animals' calls and the environment. The acoustical responses of whales to artificially increased levels of noise were documented during playback experimentation in Mexico. Nine sound parameters were inspected and compared between control and experimental conditions: calling rates, call types, frequency range of signals (Hz), emphasized frequencies (Hz), received levels of sounds (dB re 1 μPa), call duration (sec), percentage of calls exhibiting frequency modulation, number of pulses per series, and repetition rates of signals. The observed surface behavior of gray whales in response to noise (i.e., dive durations, movements and abundance) was also investigated. Analyses yielded: a description of gray whale call types; a characterization of the acoustical habitats occupied by this species, including a list of sources contributing to the ambient noise and a profile of the propagation characteristics of the study area; a determination of the relationship between whale calls and their habitats; and the acoustical capabilities and strategies of whales in response to noise. The plasticity observed in the overall behavior of this whale is of adaptive significance when considering the dynamic nature of noise in the environment. Typically, the multiple strategies employed by the whales when faced with various noise situations enable them to minimize the detrimental effect that noise has on their underwater signalling. Gray whale responses varied with the sound source and may also differ relative to the geographical range and/or general behavior of the animal. It is concluded that ambient noise (both natural and man-made) has a profound effect on the behavior of this coastal species and that acoustical calling is modified to optimize signal transmission and reception. / Science, Faculty of / Zoology, Department of / Graduate

With catches of over 360,000 individuals, Antarctic blue whales Balaenoptera musculus intermedia were harvested to near extinction by commercial whaling in the past century. Antarctic blue whales are an important ecological component of marine ecosystems as they ensure the circulation of nutrients in the pelagic environment making such nutrients accessible for primary production. However, their recoveries; distributions; migrations; large-scale response to environmental variabilities are poorly known. This thesis explored the distribution, seasonal occurrence, behaviour and response of Antarctic blue whales to environmental conditions in the high and low latitudes. I used Antarctic circumpolar acoustic data collected from sonobuoys deployed in the austral summers of 1997 through 2009 during the International Whaling Commission’s Southern Ocean Whale and Ecosystem Research (IWC SOWER) line-transect surveys. I also used recent acoustic data from three autonomous acoustic recorders (AARs) deployed between 2014 and 2015; two of these AARs were deployed on oceanographic moorings in the low latitudes and one AAR was deployed on a dedicated mooring in the high latitudes. Characteristic Z-call and feeding associated D-call of Antarctic blue whales; and sometimes low frequency downsweeping ~28-15 Hz eastern Antarctic fin whale B. physalus calls, were detected using an automated detection template and visual verification methods. I used random forest model to determine pattern of environmental preferences, spatial occurrence and behaviour of Antarctic blue whales. Distance to southern boundary of the Antarctic Circumpolar Current, latitude, longitude and distance from the nearest Antarctic shores were the main geographic predictors of blue whale call occurrence and behaviour during IWC SOWER cruises. Satellite derived sea surface height (SSH), wind stress, wind direction, water depth, sea surface temperature (SST), chlorophyll-a and wind speed were important environmental predictors of blue whale occurrence and behaviour during IWC SOWER cruises. Antarctic blue whale call occurrence and call rates varied significantly in response to inter-annual variabilities of those environmental predictors during those cruises. Migratory Antarctic blue and fin whales were acoustically detected in South African waters between May and August with fin whales present till November. Diel call rate patterns of both whale species varied between seasons. Wind speed, SSH, SST, chlorophyll-a, time of the day and Ekman upwelling index were important predictors of Antarctic blue and fin whale call occurrence and behaviour off the South African west coast. Off the Maud Rise, Antarctica, call occurrences and rates of Antarctic blue whales peaked in March and were detected throughout the whole year suggesting asynchronous migrations to the low latitudes and part of the population remaining in the Maud Rise during winter. Fin whale calls were only detected in January and March. Wind speed, distance to the sea ice extent, sea surface height, sea surface temperature and time of the day were important predictors of Antarctic blue and fin whale call occurrence and behaviour. Information emerging from this thesis will improve the management and conservation of these highly depleted species. This thesis provides the first acoustic recordings of Antarctic blue and fin whales in the southern Benguela ecosystem; and provides preliminary information on which to concentrate further research effort to investigate abundance, distribution and seasonality of these large baleen whale populations in both high and low latitudes. / Thesis (PhD)--University of Pretoria, 2018. / National Research Foundation / Zoology and Entomology / PhD / Unrestricted

The long-term monitoring of the South African southern right whale population has revealed a decrease in sightings along the coast and an increase of calving intervals within the last few years, causing changes in the species´ demographics causing a decrease in annual population growth rate (6.5% y -1 ). Because reproductive success is linked to body condition, the purpose of this study was to conduct a visual health assessment based on overhead photographs from the annual aerial southern right whale surveys and detect potential links between visual health condition of parous females and the increased calving intervals. Additionally, it was aimed to find relationships between visual health of parous females and environmental indices of the Southern Ocean, representing food availability. To allow global comparison of the results, the method used for the visual health assessment was developed in collaboration with international southern right whale researchers from Australia and South Africa. The health indices were adapted from a visual health assessment method developed for northern right whales and include body condition, skin condition, the presence of cyamids around the blowholes and rake marks on the skin. The results showed that these health variables derived from overhead photographs were sufficient to detect visual health changes over time. Within the study period (2005 – 2017), there were two years in which whales had a significant decreased visual health (i.e. increased health score) than average; 2008 and 2014. No direct link between the observed health condition and calving intervals could be found, possibly due to the lack of data on calving intervals post-2014 as well asthe assessment of breeding females only (i.e. breeding females are in good enough conditions to reproduce). However, significant relationships were found between visual health and Southern Ocean productivity (p< 0.001) and climate indices (p < 0.05) with a 0-year lag. These results clearly indicate a link between southern right whale visual health condition and Southern Ocean food availability in one feeding ground, suggesting that this may be the primary feeding ground for parous females during pregnancy. Understanding the links between visual health, reproductive success and climate/food availability helps to understand changes in the population’s demographics and to predict the resilience of the species. Additionally, the standardization of the method allows for global comparison.

In search of evidence for or against the endothermic dinosaur hypothesis, a recent study by Ruben et al. (1996) revealed that endotherms tend to have larger nasal cross-sectional areas than ectotherms of the same mass. The reason offered for this observation was that larger nasal passages are needed to house the complex respiratory turbinates possessed by endotherms. Whales were excluded from the study on the grounds that they have no nasal turbinates. In the present study, the cross-sectional area of the nasal passages of nine species of Odontoceti were measured by the use of latex casts. The regression of log cross-sectional area vs. log mass yielded the same line for the whales of the current study as for the endotherms of the previous study. Alternative explanations for the large nasal cross-sectional area of endotherms are sought.

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Approved for public release, distribution unlimited / This study sought to experimentally quantify the sonar performance of omni-directional receivers as a means to passively detect vocalizing Odontocetes. To accomplish this objective, controlled experiments using a calibrated mid-frequency sound source were conducted on the San Clemente Island Underwater Range (SCIUR) in July 2002. Six Odontocete signals were selected for transmission: 2 orca and 2 pilot whale whistles, and sperm whale and Risso's dolphin clicks. Several hundred iterations of each signal were broadcast at stations 300 m to 12,000 m from the range's moored, three-element array. Statistical analyses were performed on the output of an energy and matched filter detector to quantify detection probability (P(D)) and range limits as a function of false alarm rate (P(FA)), signal type, and signal to noise ratio (SNR). The matched filter was generally the superior performer, detecting the orca2 and pilot1 whistles beyond 5000 m with a 90% P(D), 1% P(FA), and source level (SL) of 140 dB re 1 æPa. For the same conditions, the orca1 and sperm whale calls were detected at 1500 m, but the pilot2 and Risso's dolphin signals were not detected at the peak realized SNR of (-2) dB. The energy detector had no detections with a 90% P(D) and 1% P(FA) at this (-2) dB SNR, but all signals except one orca whistle were detectable beyond 1000 m with a 50% P(D) and 1% P(FA). The sperm whale was the exceptional energy detector performer, with detection ranges exceeding 7 km (140 dB re 1 æPa SL) at the 50% P(D) and 1% P(FA) / Lieutenant Commander, United States Navy

Le sujet de thèse porte sur l'étude des baleines à bosse, espèce migratrice. L'objectif est, à partir del'étude de leurs déplacements, de mieux comprendre leur distribution, leurs comportements, leurstratégie d'alimentation et de reproduction. Ce travail s'appuie sur plusieurs missions dédiées à lapose de balises satellitaires sur des individus évoluant dans les zones d'alimentation (Arctique) et leszones de reproduction (Caraïbes).La thèse est articulée autour de 4 articles. Le 1er intitulé "From whaling to tagging: the evolution ofknowledge regarding humpback whales in their North Atlantic breeding grounds" décrit l'historiquedes connaissances actuelles sur la population de baleine à bosse de l'Atlantique Nord, à partir desinformations consignées lors de la chasse industrielle à la baleine jusqu'aux observations les plusrécentes.Le 2e chapitre, intitulé "Local and migratory movements of humpback whales satellite tracked in theNorth Atlantic Ocean", détaille les routes migratoires sud-nord d'individus de RépubliqueDominicaine (Silver Bank) et de Guadeloupe (Antilles françaises). Dans un 1er temps, nous noussommes focalisées sur les déplacements dans la zone de reproduction. Les résultats ont montré unetrès grande mobilité, remettant en cause les hypothèses établies visant à décrire des individusrestant sur une zone donnée (pour les groupes actifs et/ou les chanteurs par exemple). Nous avonségalement montré des mouvements erratiques, sans pouvoir définir un modèle de prédiction detrajectoires à moyen terme (c'est-à-dire sur plusieurs jours). Dans un 2e temps, nous avons travaillésur les routes migratoires, qui restent encore actuellement un sujet de recherche majeur pour cetteespèce de mammifères qui détient le record avec plus de 6000km par trajet entre ses airesd'alimentation et de reproduction, avec 2 objectifs en particulier : d'une part, mieux appréhender lesmotivations des individus pour privilégier telle ou telle route migratoire, et d'autre part, savoir si lesroutes migratoires contribuent au mixage des différents stocks des baleines à bosse. Nos résultatsont montré clairement 2 routes privilégiées par les baleines à bosse de la Caraïbe : les individusprésents en République Dominicaine remontaient le continent américain, alors que ceux deGuadeloupe choisissaient une voie transatlantique, vers l'Islande et potentiellement la Norvège.Le 3e chapitre, basé sur l'article : "Individual variation in movements of humpback whales satellitetracked in the eastern Aleutian Island and Bering Sea", est dédié à l'étude des déplacements desbaleines à bosse pendant leur période d'alimentation près du Dutch Harbor en Alaska, de 2007 à2011. Nous avons montré les habitats des baleines à bosse dans cette région. Nous avons égalementprécisé les stratégies individualistes pour s'alimenter.Le dernier chapitre, basé sur le chapitre "Assessing implantable satellite tag extrusion using lightsensors", présente les difficultés actuelles de l'utilisation des balises Argos, pour l'étude des baleinesà bosse. Cela concerne principalement le système d'attache. L'objectif est d'avoir une idée sur lavitesse d'éjection et de voir s'il y a une corrélation entre la façon de poser la balise, son endroit sur labaleine et la durée totale de maintien sur l'individu.Pour conclure, ce travail a mis en évidence de nouvelles connaissances sur les stratégies individuellesdes baleines à bosse dans leurs aires d'alimentation, de reproduction mais aussi au cours des routesmigratoires. L'utilisation des balises satellitaires est une nouvelle alternative attractive pour l'étudede cette espèce hautement mobile. / This dissertation has been prepared in manuscript format and contains four individual papers. Each paper/chapter is formatted for the journal to which it has been, or will be, submitted. In the first manuscript, “From Whaling to Tagging: The evolution of knowledge regarding humpback whales in their North Atlantic breeding grounds”, I describe the evolution of humpback whale research from the days of Yankee whaling to the most recent satellite telemetry project in the West Indies breeding grounds. The humpback whales that over-winter in the West Indies are part of one of the most heavily studied whale populations in the world; projects conducted in this area have served as models for humpback whale research world-wide. This manuscript will be submitted for publication in Mammal Review in 2014. In my second manuscript, “Local and migratory movements of humpback whales satellite tracked in the North Atlantic Ocean”, I report the results of a satellite telemetry project that was conducted in the winters of 2008 through 2012 in the breeding areas of Silver Bank (Dominican Republic) and Guadeloupe (French West Indies). The results from this project add a level of detail to the current knowledge about North Atlantic humpback whale habitat use, migration, and population structure that could not be obtained without current satellite tagging technology. This paper has been reviewed and accepted for publication by the Canadian Journal of Zoology and will be published by November, 2013 ii In my third manuscript, “Individual variation in movements of humpback whales satellite tracked in the eastern Aleutian Islands and Bering Sea”, I report the results from a satellite telemetry project conducted off Dutch Harbor, (Alaska, USA) in the summers of 2007 through 2011. Satellite telemetry from this project showed the fine-scale use of foraging habitat in a North Pacific feeding ground. Additionally, a long-distance, within-season travel event was recorded in 2010, prompting speculation about the humpback population structure throughout the Bering Sea. This manuscript has been reviewed and accepted for publication by Endangered Species Research and will be published by November, 2013. In the fourth manuscript, “Assessing implantable satellite tag extrusion using light sensors”, I report the results of a novel approach for remotely quantifying tag rejection; the use of tag-mounted light sensors to indicate extrusion rate. The data for this paper were collected during a 2011 follow-up study aimed at assessing the behavioral and physiological responses of Gulf of Maine humpback whales to current tagging methods. Tag diagnostic technology like this, while still being developed, could significantly improve future telemetry work by updating tag design and placement methods to increase overall project efficiency. This paper has been accepted as a poster presentation at the 20th Biennial Conference on the Biology of Marine Mammals (December 2013, Dunedin New Zealand). It will be updated with the results from the 2013 Gulf of Maine tagging field season and submitted to a peer reviewed journal in 2014.

Every year hundreds of cetaceans strand on New Zealand beaches. Options for dealing with disposal of their carcasses are few, creating significant problems for the Department of Conservation (DOC). More often than not their carcasses are buried in beaches at or just above high water mark, near where the animals have stranded. The primary objective of this thesis is to determine the effects of cetacean burial on beach sediments, and evaluate potential health and safety risks associated with this practice. A secondary objective of this thesis is to appraise the appropriateness of one location DOC has repeatedly transported cetacean carcasses to and buried within beach sediments, Motutapu Island in Waitemata Harbour. The chemical effects of cetacean burial over a six-month period are reported for two sites at which animals were buried in 2008, Muriwai and Pakiri beaches; the biological effects of this burial are reported for one of these sites, Muriwai Beach, 12 months post burial. Intertidal faunal and floral inventories are provided for six sites around Motutapu Island, and these then compared and contrasted with inventories compiled from an additional 290 intertidal sites between Whangarei Heads and Tauranga Harbour, North Island East Coast, to appraise the relative uniqueness of intertidal species diversity around Motutapu Island. At both Muriwai and Pakiri beaches, nitrogen and phosphate concentrations in surface sands changed considerably following cetacean burial, although over six months the effect was localized and elevated concentrations of these two chemicals that could be attributed to a buried carcass did not extend more than 40 m from the site of whale burial. Deep-core profiles revealed nitrogen and phosphate concentrations at and in the immediate vicinity of cetacean burial approximately six months after burial to be markedly elevated to the level of the water table, but elevated concentrations attributable to the buried carcass were not observed greater than 25 m from the site of burial. Elevated concentrations of nitrogen and phosphates in beaches persist in surface sediments for at least six months post burial. Twelve months post cetacean burial no significant difference in species richness or abundance were apparent in intertidal communities extending along transects proximal to and some distance from the Muriwai Beach carcass; there is no evidence for any significant short-term (to 12 months) biological effects of cetacean burial in beaches. Of those shores on Motutapu Island accessible by earth-moving equipment and large vessels capable of dealing with and transporting large cetacean carcasses, Station Bay appeared to be the most appropriate site for whale burial. However its small size and relatively high biological value (fairly high species richness for comparable shores between Whangarei Heads and Tauranga) renders it an inappropriate long-term option for whale burial. Other shores on Motutapu Island host some of the highest species richness of all shores surveyed between Whangarei Heads and Tauranga Harbour, rendering them entirely inappropriate locations for burying cetaceans, over and above other variables that may influence disposal location identification (such as archaeological sites, dwellings and accessibility). Motutapu Island is not considered an appropriate location for cetacean burial within beaches. Alternative disposal strategies need to be explored for dealing with cetaceans that strand on Auckland east coast beaches. Although burial is the most convenient and most economical strategy to dispose of cetacean carcass, especially in mass stranding events or when cetaceans are of large size, and the biological effects of this practice are not considered significant (for the one whale that could be studied), persistent enrichment of beach sediments with organic matter could result in prolonged persistence of pathogens in beaches, causing unforeseen risks to human health and safety. Recommendations are made to minimize possible threats to public following burial of cetaceans in beaches, until the potential health risks of burial are more fully understood.