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Funding: The authors thank the Coordination of Superior Level Staff Improvement (CAPES) from Brazil for providing a doctoral scholarship and grant CAPES-PRINT (grant no. 88887.370641/2019-00) to M.A. The National Council for Technological and Scientific Development (CNPq) from Brazil provided research grants to F.G.D.-J. (grant no. 308867/2019-0), and P.C.S.-L. (grant no. 305573/2013-6). Kelp gulls (Larus dominicanus) commonly feed on the skin and blubber of surfacing southern right whales (SRW, Eubalaena australis) in the near shore waters of Península Valdés (PV), Argentina. Mothers and especially calves respond to gull attacks by changing their swimming speeds, resting postures and overall behaviour. Gull-inflicted wounds per calf have increased markedly since the mid-1990s. Unusually high mortality of young calves occurred locally after 2003, and increasing evidence points to gull harassment as a factor contributing to the excess deaths. After leaving PV, calves undertake a long migration with their mothers to summer feeding areas; their health during this strenuous exertion is likely to affect their probabilities of first-year survival. To explore the effects of gull-inflicted wounds on calf survival, we analysed 44 capture–recapture observations between 1974 and 2017, for 597 whales photo-identified in their years of birth between 1974 and 2011. We found a marked decrease in first-year survival associated with an increase in wound severity over time. Our analysis supports recent studies indicating that gull harassment at PV may impact SRW population dynamics. Postprint

For nearly 200 years, the only natural source of the alcohol ambrein has been coproliths produced in about 1% of sperm whales and in related jetsam. However, the finding of ambrein in adipocere/faeces of human corpses, led us to hypothesise that ambrein might occur in the faeces of other mammals. Herein, we used a recently developed gas chromatography-mass spectrometry method, with suitable derivatisation of the hindered hydroxy group of ambrein, to screen a number of extracts of mammalian faeces. Minor proportions of ambrein were detected in digested human sewage sludge and in the dung of elephant, domestic cattle, giraffe and buffalo. Whether ambrein formation in the terrestrial species is associated with coprolith formation, is unknown, but solid deposits known as enteroliths and fecaliths occur in humans and some domestic animals.

For nearly 200 years, the only natural source of the alcohol ambrein has been coproliths produced in about 1% of sperm whales and in related jetsam. However, the finding of ambrein in adipocere/faeces of human corpses, led us to hypothesise that ambrein might occur in the faeces of other mammals. Herein, we used a recently developed gas chromatography-mass spectrometry method, with suitable derivatisation of the hindered hydroxy group of ambrein, to screen a number of extracts of mammalian faeces. Minor proportions of ambrein were detected in digested human sewage sludge and in the dung of elephant, domestic cattle, giraffe and buffalo. Whether ambrein formation in the terrestrial species is associated with coprolith formation, is unknown, but solid deposits known as enteroliths and fecaliths occur in humans and some domestic animals.

For nearly 200 years, the only natural source of the alcohol ambrein has been coproliths produced in about 1% of sperm whales and in related jetsam. However, the finding of ambrein in adipocere/faeces of human corpses, led us to hypothesise that ambrein might occur in the faeces of other mammals. Herein, we used a recently developed gas chromatography-mass spectrometry method, with suitable derivatisation of the hindered hydroxy group of ambrein, to screen a number of extracts of mammalian faeces. Minor proportions of ambrein were detected in digested human sewage sludge and in the dung of elephant, domestic cattle, giraffe and buffalo. Whether ambrein formation in the terrestrial species is associated with coprolith formation, is unknown, but solid deposits known as enteroliths and fecaliths occur in humans and some domestic animals.

Quantifying marine mammal abundance, site occupancy, and habitat use patterns is fundamental for the correct design and implementation of conservation and management schemes. Bottlenose dolphins in Irish waters form at least three distinct populations, two coastal and one pelagic, each ranging in different areas over unequal scales. While the abundance of all three has been estimated and core areas of use have been previously identified for the coastal populations, their habitat preferences have not yet been investigated sufficiently. In this thesis, generalised additive models were used to describe the habitat use of each population in relation to a suite of static and dynamic environmental parameters, over a range of temporal scales. Mixed models and generalised estimating equations were implemented to account for spatial and temporal autocorrelation when necessary. The habitat use of the pelagic population was modelled using two seasons (Summer and Winter) of aerial survey data of the greater part of the Irish EEZ and the models’ predictive capacity was tested on observations from two separate seasons. The interaction of environmental covariates with a habitat classifier was also tested to elucidate dolphin habitat use changes depending on whether they are in shelf, slope, or abyssal waters. The site occupancy of the coastal mobile population was modelled using five years of passive acoustic monitoring (C-POD) data from two locations on the west coast at an hourly, daily, and monthly scale. The second coastal population is resident in the outer Shannon estuary Special Area of Conservation and its abundance has been sporadically monitored for nearly two decades using boat-based photo-identification surveys. Encounter data from these surveys were used to model habitat use by incorporating a two-dimensional geographic coordinate term and an interaction with tidal phases. Given the irregular frequency of standardised surveys, I also assessed the potential of using a dolphin-watching boat operating in the same area as an alternative platform from which to derive a robust abundance estimate, using mark-recapture techniques. Different environmental covariates proved significant at each spatial scale, with dolphins showing season-, habitat-, and site-specific responses to each parameter. A higher probability of dolphin presence was predicted over the continental shelf and slope in the winter and in two primary areas in the summer, the southwest coast and the Porcupine Basin. Sea surface temperature and primary productivity were significant predictors of dolphin presence for both the pelagic and mobile coastal population, but not for the resident coastal population. Tidal level had a significant effect on dolphin detection in the coastal mobile population, with the likelihood of detections increasing at higher water levels. Tidal phase was also a significant predictor of dolphin presence for the resident population, with higher probabilities being predicted closer to a bottleneck feature during ebb tides. The abundance estimate generated from the dolphin-watching boat observations compared favourably to an estimate generated from a standardised survey the previous year. This indicates that, in years when standardised surveys do not take place, the dolphin-watching boat may provide a suitable interim platform for more frequent and efficient monitoring of this population. The results presented here highlight the importance of investigating habitat use at different spatial and temporal scales, provide valuable insights regarding areas used at different times by bottlenose dolphins, and form a baseline upon which to build further, more targeted investigations of the habitat preferences, demographic parameters, and abundance of each population, ultimately advancing our efforts at conservation and facilitating marine spatial planning.

Mid-latitude shelf-seas are highly productive regions that host a rich diversity of animals including large numbers of marine mammals and seabirds. These large vertebrate predators play a crucial role in the functioning of shelf-sea ecosystems. However, the combined effects of multiple anthropogenic stressors are driving unprecedented declines in many of their populations. Mitigating this depends upon effective conservation and integrated ecosystem based approaches to management, which require a comprehensive understanding of the habitat needs of marine predators. The foraging efficiencies of marine predators are closely tied to the availability of a number of oceanographic features. As such, these physical habitats represent critical locations within a species’ range whose preservation and protection should be of high priority. The collection of studies presented in this thesis aims to improve our understanding of the physical oceanographic processes that underlie the at-sea behaviours and distributions of marine mammals and seabirds in coastal and shelf-sea environments. A combination of at-sea boat surveying, animal-borne biologging, satellite remote-sensing, passive acoustics and numerical modelling was used to collect information on the distributions and foraging behaviours of a range of marine predators alongside the bio-physical characteristics of the oceanographic habitats they occupied. These data were then used to (1) examine the use of oceanographic habitats generated around tidal-mixing fronts and coastal topographic structures by a range of piscivorous species including bottlenose dolphins Tursiops truncatus, common dolphins Delphinus delphis, harbour porpoises Phocoena phocoena and northern gannets Morus bassanus, and (2) identify the physical processes underlying their creation. Original aspects of this work include the examination of the fine-scale bio-physical mechanisms that link marine predators to tidal-mixing fronts and coastal tidal-topographic structures. Main findings indicate that offshore habitats around tidal-mixing fronts are used by both common dolphins and northern gannets for foraging. Individuals associated with patches of increased sub-surface primary productivity, which were generated via a bi-weekly cycle of episodic turbulent mixing and stratification following an adjustment in the spatial position of a front with the spring-neap cycle. Moreover, around fronts, the dives of gannets were likely to be short and of a V-shaped strategy (with little active swim phase), which likely reflects an increase in the accessibility and catchability of their prey. In a coastal estuarine system, bottlenose dolphins were shown to associate with predictable downwelling features generated during flood tidal flows that were thought to act as a foraging aid. Together, these findings highlight the fundamental role physical oceanographic processes play in the structuring of marine ecosystems by providing vulnerable marine predators with prosperous and reliable foraging resources that they can exploit. This work has implications for both future studies of marine predator foraging ecology and the management of anthropogenic activities in coastal and shelf-seas. Natural Environment Research Council (NERC)

Communication is important for social and other behavioural interactions in most marine mammal species. The bottlenose dolphin (Tursiops truncatus, Montagu, 1821) is a highly social species that use whistles as communication calls to express identity and to initiate and maintain contact between socially interactive individuals. In this thesis, the degree of variability in whistle behaviour and whistle characteristics was examined between different habitats on a range of spatial scales. The whistle characteristics that best discriminated between different communities were investigated, along with exploration of whistle variation in relation to habitat type, levels of social interaction and relatedness. Finally, the use and variability of individually distinctive calls (signature whistles) within and between Irish and US waters were also examined. Relatively high levels of whistle variation were found within a genetically and socially isolated population of dolphins in the Shannon Estuary, reflecting the need for individual identification and distinctive whistles in a population with long term site fidelity and high levels of social cohesion. Variation between reproductively separate communities in Irish waters was relatively small except between animals in inshore compared with continental shelf waters. The greatest differences in whistle structure overall were evident between dolphins using inshore and offshore US waters, likely reflecting social isolation of the two distinct ecotypes that occur in these waters but also variation in behaviour or habitat conditions. Variation found among inshore communities in US waters reflected similarities in habitat use and levels of social interaction. These findings suggest that vocal variation is socially mediated, behaviourally maintained and dependent on levels of social contact between individuals. The findings contribute to our understanding of the interaction of factors influencing vocalisation behaviour in this behaviourally complex and ecologically plastic species.