Knowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or spatially-limited studies carried out to date. Funded by the Italian Cooperation through a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect methodology. The main aims of the thesis were (a) to estimate cetacean abundance, (b) to determine distribution patterns and habitat use of the cetacean species, (c) to investigate movement patterns for species for which individual recognition techniques were suitable and (d) to identify areas of conservation concern for cetaceans with a particular focus on existing protected areas. Eight species were identified, of which five were commonly encountered (Stenella longirostris, S. attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare (Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance using design-based line transect sampling techniques were obtained for five species: S. attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69); T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed that the two Stenella species were widely distributed across the study area. In contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in particular Satayah offshore reef), and T. aduncus was mainly found along the coast with possibly separate sub-populations in the northern and southern study area. G. griseus was only encountered in the southern part. The information provided in this study will allow the development of a conservation strategy for the protected areas and will serve as baseline information to carry out future survey work in the Red Sea.

Beaked whales are comparatively unknown social mammals due to their deep-ocean distribution and elusive habits. The deep-ocean is the largest biome on Earth and the final frontier for human expansion. Since their first discovery, beaked whales have remained largely hidden from science. In this era of rapid technological advancement, genetic and genomic methods are key tools for population biologists and are particularly useful in describing rarely seen species. Using DNA-barcoding and nuclear markers, the publications in this thesis provide data on the distribution and external appearance of two species of beaked whale: the spade-toothed (Mesoplodon traversii) and Derinayagala’s whale (Mesoplodon hotaula). These whales were previously known from only a handful of tissue and bone specimens. Long-term efforts have facilitated the collection of samples of Gray’s beaked whale (Mesoplodon grayi) and we have used shot-gun sequencing to characterise the mitochondrial genome and isolate species-specific nuclear microsatellite loci. Using genetic species and sex identification, together with museum specimens and multivariate analyses, we provide clear evidence of sexual dimorphism in cranial dimensions and geographic variation in external morphology. No genetic differentiation was evident in Gray’s beaked whales across a large study area (~ 6,000 km). With a large female effective population size (Ne) and genetic homogeneity, we hypothesise that gene flow is facilitated by large-scale oceanographic features, such as the sub-tropical convergence. Genetic kinship analyses within Gray’s beaked whale groups suggest that the whales that strand together are not related. Both sexes disperse from their parents and these groups are not formed through the retention of kin. These results are consistent with a ‘fission-fusion’ social system that has been observed in some oceanic dolphin species. Taken together, these data provide the first insights into the population dynamics, dispersal and social organisation in Gray’s beaked whales. These publications highlight the value of using genetics alongside other techniques to describe inter- and intraspecific diversity. For beaked whales, the dead can tell us much about the living.

The northern Norwegian killer whale (Orcinus orca) is an important predator but little is known about its population dynamics, particular in response to changes in its main prey, the highly dynamic Norwegian spring spawning (NSS) herring (Clupea harengus). The main aims of this thesis were to estimate killer whale population parameters, to explore the future viability of the population, and to explore the response of this predator to changes in distribution and abundance of its main prey over the last 25 years. Population size was estimated as ~ 700 individuals, taking heterogeneity of capture probabilities into account and correcting for unmarked animals. Apparent survival rates of 0.974 (SE = 0.006) for adult males and 0.984 (SE = 0.006) for adult females were estimated accounting for temporary emigration, transience and trap-dependency. Temporary emigration was greater for males than females. Calving intervals ranged from 3 to 14 years (mean = 5.06); equivalent to 0.197 calves per mature female per year. Future viability of the killer whale population was evaluated under various plausible scenarios. The baseline scenario using the best available information predicted a viable population and indicated that the population may be increasing size. Analysis of data on naval sonar activity, killer whale sightings and herring abundance showed that naval sonar activity appeared to have a negative effect on killer whale presence during a period of low prey availability. A time lag of four years was found between the first sign of NSS herring changing its distribution and reduced killer whale presence inside the fjord system. Analysis of energy budgets showed that killer whales spent more time travelling/foraging in 2005/06 than the 1990s. The fjord system was inferred to be a preferred habitat for killer whales when there was a higher density of NSS herring in this area compared to offshore area.

Behavioural responses can reveal important fitness trade-offs and ecological traps in evolutionarily novel contexts created by anthropogenic stimuli, and are of increasing conservation concern due to possible links to population-level impacts. This thesis illustrates the use of proxies for energy acquisition and expenditure within multivariate and state-based modelling approaches to quantify the relative time and energetic costs of behavioural disturbance for a deep-diving marine mammal (Physeter macrocephalus) in foraging grounds in Kaikoura Canyon (New Zealand) and near Lofoten Islands (Norway). A conceptual framework is first developed to identify and explore links between individual motivation, condition and external constraints to behavioural disturbance [Chapter 1]. The following chapters then use data from behavioural response studies (BRS) to: 1) derive biologically relevant metrics of behaviour [all chapters], 2) investigate effects of boat-based focal follows and tagging procedures [Chapters 2-3], and 3) relate responses to specific disturbance stimuli (distance, approach, noise) from whale-watching [Chapter 2], naval sonar and playback of presumed natural predator (killer whale Orcinus orca) sounds [Chapter 4]. A novel hidden state model was developed to estimate behavioural budgets of tagged sperm whales from multiple streams of biologging (DTAG) data [Chapter 3]. Sperm whales traded off time spent at foraging depths in a non-foraging and non-resting state in response to both tag boat presence, 1-2 kHz naval sonar (SPL 131-165 rms re 1μPa) and mammal-eating killer whale sound playbacks, indicating that parallel non-lethal costs were incurred in both anthropogenic disturbance and presumed antipredatory contexts. While behavioural responses were highly variable by individual, biologically informed state-based models appeared effective to control for variability in energy proxies across different functional contexts. These results and Chapter 5 “linking buzzes to prey” demonstrate that behavioural context is a signal that can aid understanding of how individual non-lethal disturbance responses can impact fitness.

Effective management of the potential environmental impacts of naval sonar requires quantitative data on the behaviour and hearing physiology of cetaceans. Here, novel experimental and analytical methods were used to obtain such information and to test the effectiveness of an operational mitigation method for naval sonar. A Bayesian method was developed to estimate whale locations through time, integrating visual observations with measurements from on-animal inertial, acoustic, depth, and Fastloc-GPS sensors. The track reconstruction method was applied to 13 humpback whale (Megaptera novaeangliae) data sets collected during a multi-disciplinary behavioural response study in Norwegian waters. Thirty-one controlled exposure experiments with and without active transmissions of 1.3-2 kHz sounds were conducted using a moving vessel that towed a sonar source. Dose-response functions, representing the relationships between measured sonar dose and behavioural responses identified from the reconstructed tracks, predicted that 50% of the humpbacks would initiate avoidance at a relatively high received sound pressure level of 166 dB re 1 µPa. Very similar dose-response functions were obtained for cessation of feeding. In a laboratory study, behavioural reaction times of a harbour porpoise (Phocoena phocoena) to sonar-like sounds were measured using operant conditioning and a psychoacoustic method. Auditory weighting functions, which can be used to improve dose-response functions, were obtained for the porpoise based on the assumption that sounds of equal loudness elicit equal reaction time. Additional analyses of the humpback whale data set provided evidence that ramp-up of naval sonar mitigates harmful sound levels in responsive cetaceans located directly in the path of the source, and suggested that a subset of the humpback whale population, such as mother-calf pairs, and more responsive species would benefit from the use of sonar ramp-up. The findings in this thesis are intended to inform sound exposure criteria and mitigation guidelines for anthropogenic noise exposure to cetaceans.

Data collected during boat-based and aerial surveys were used to describe population structure, movements, temporal patterns of migration and skin condition of humpback whales in breeding sub-stock C1-S off southern Africa. Results confirmed that the migration route along the south coast of South Africa is linked to the winter ground off Mozambique. A lack of exchange between breeding sub-stocks C1-N and C1-S was found, suggesting that these are independent of each other. Molecular analysis revealed unexpected levels of population structure between the migration route and the winter ground of C1-S, as well as the possibility that this migration route is also utilised by some individuals from breeding sub-stock C3. A skin condition of unknown aetiology that primarily affects humpback whale mother-calf pairs was identified. The first assessment of its prevalence and severity was made, providing a baseline for future monitoring. Humpback whale abundance in an inshore region of Bazaruto Archipelago, Mozambique was estimated and attempts were also made to use the limited information off Plettenberg Bay/Knysna, South Africa. In addition to improving our understanding of humpback whales from Breeding Stock C, knowledge about another baleen whale species utilising the southwest Indian Ocean was extended. The first evidence of southern right whale presence off the coast of Mozambique since the cessation of whaling was documented. It remains unknown whether this is a remnant sub-stock or the recovering South African sub-stock reoccupying its historical range.

The main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables. The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night. Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection. Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast. The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.

Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina), have overlapping ranges but contrasting population dynamics around the UK; whilst grey seals have generally increased, harbour seals have shown significant regional declines. A robust analytical methodology was developed to produce maps of grey and harbour seal usage estimates with corresponding uncertainty, and scales of spatial partitioning between the species were found. Throughout their range, both grey and harbour seals spend the majority of their time within 50 km of the coast. The scalability of the analytical approach was enhanced and environmental information to enable spatial predictions was included. The resultant maps have been applied to inform consent and licensing of marine renewable developments of wind farms and tidal turbines. For harbour seals around Orkney, northern Scotland, distance from haul out, proportion of sand in seabed sediment, and annual mean power were important predictors of space-use. Utilising seal usage maps, a framework was produced to allow shipping noise, an important marine anthropogenic stressor, to be explicitly incorporated into spatial planning. Potentially sensitive areas were identified through quantifying risk of exposure of shipping traffic to marine species. Individual noise exposure was predicted with associated uncertainty in an area with varying rates of co-occurrence. Across the UK, spatial overlap was highest within 50 km of the coast, close to seal haul outs. Areas identified with high risk of exposure included 11 Special Areas of Conservation (from a possible 25). Risk to harbour seal populations was highest, affecting half of all SACs associated with the species. For 20 of 28 animals in the acoustic exposure study, 95% CI for M-weighted cumulative Sound Exposure Levels had upper bounds above levels known to induce Temporary Threshold Shift. Predictions of broadband received sound pressure levels were underestimated on average by 0.7 dB re 1μPa (± 3.3). An analytical methodology was derived to allow ecological maps to be quantitatively compared. The Structural Similarity (SSIM) index was enhanced to incorporate uncertainty from underlying spatial models, and a software algorithm was developed to correct for internal edge effects so that loss of spatial information from the map comparison was limited. The application of the approach was demonstrated using a case study of sperm whales (Physeter macrocephalus, Linneaus 1758) in the Mediterranean Sea to identify areas where local-scale differences in space-use between groups and singleton whales occurred. SSIM is applicable to a broad range of spatial ecological data, providing a novel tool for map comparison.