We consider a data set comprising encounters between gray seals off Sable Island in the autumn of 2009. We apply Spatial Point Pattern data analysis approaches to this data set and demonstrate the effectiveness of these techniques. Specifically we propose using point processes for clustered data; the Inhomogeneous Poisson process, and the subset of cluster processes called Cox processes. We utilize maximum likelihood methods to produce a model for the mean intensity of the seal encounters which includes spatial covariates. We then consider the impact of inhomogeneity and review minimum contrast methods for fitting the Cox process models, specifically the Thomas and Matern cluster processes. We demonstrate that these methods allow us to gain valuable insight into the nature and extent of grey seal encounters at sea. Finally we validate both our conclusions and the approach taken using the most recent data available, that of autumn 2010.

There is a problematic interaction going on between grey seals and the small scale coastal fisheries in the Baltic. A large number of seals are by-caught and drowned each year, and the viability of the fishery is threatened by catch losses caused by the seals. Traditional mitigation methods are not sufficient, or have in some cases not been properly evaluated. Available methods of quantifying and analysing the catch losses are also insufficient. This thesis consists of three parts, each studying a different angle of this conflict. In the first part, new models for estimating catch losses are presented. In addition to the commonly used method of counting the number of damaged fish in the nets, the new models also allow for an estimation of the hidden losses. Hidden losses may be fish that are completely removed from nets without leaving any traces, fish that escape through holes in the net torn by the seals, or even fish that are scared away from the fishing gear. Such losses were found to be significant, and hence it is now clear that the traditional models seriously underestimate the total losses. The new models also allow for a deeper analysis of the interaction process. The first presented model compares catches between adjacent days (day-pairs), the second uses nets that are pre-baited before deployment, and the third relies on a detailed inspection and repair of all seal-induced damage to the net meshes. In the second part, some traditional methods of mitigating the conflict are evaluated. A commercially available Acoustic Harassment Device was tested in a field trial. AHDs were deployed at several set-traps for salmonids for three consecutive years. The damage reducing effect was persistent throughout a season, as well as over the full three-year test period, and no “dinner bell” effect was observed. When seal attacks became frequent in the 1980´s, several of the traditional salmon traps were reinforced with newly developed extra strong net materials. These materials dramatically reduced the damage to the nets, and to some degree also the catch losses. However, the losses were still substantial, and the traditional gear was gradually phased out when better solutions emerged. In the third part, new methods of mitigating the conflict are evaluated. A salmon trap was built, using net meshes which were large enough to allow seal-chased fish to escape through, but which would still guide and confine non-stressed fish. The trap was fitted with a fish chamber with a double wall of very taut netting, separating the catch from the surroundings by a fixed distance. Interference by seals was significantly reduced with this construction. Field experiments revealed that seals used their above-water vision to locate and search out buoys of the type that are used in the fisheries. Larger buoys were more readily found than smaller. A set of trials was initiated where certain geographical areas were made unattractive for seals prior to their seasonal arrival to the region, by deploying stationary AHDs. Finally, aquarium experiments demonstrated that underwater vision and hearing were equally important in seals’ detection of fish in a test box. It was also found that there was a “near zone”, within which seals stayed focused on a fish and attempted to catch it by a quick thrust of the head. These studies strongly suggest that new seal-safe fishing gear and mitigation methods should be based on, and would benefit from, an in-depth understanding and analysis of natural seal behaviour.

This thesis examines fatty acid (FA) and polychlorinated biphenyl (PCB) dynamics in a marine top predator, the grey seal (Halichoerus grypus,) and their transfer during lactation from mother to offspring. It examines regional and annual variations in FA composition and PCB loads, and also how the physical and chemical characteristics of these molecules (e.g. their polarity and size) can affect the rates of accumulation, mobilization and transfer of specific FAs or PCBs. Two UK grey seal colonies (North Rona (NR) and Isle of May (IOM) were studied during three consecutive years (1996-1998 and 2004-2006). Lactating grey seals and their pups were repeatedly captured during the lactation period and sampled for blubber, serum and milk and analysed for FAs and PCBs. Overall, the two colonies were clearly distinguished from each other, suggesting that the main prey species had different FA composition, and possibly that the seals from these colonies had different diets . These differences are probably a direct consequence of differences in prey community structure in the two regions where seals from these two colonies are thought to feed. Within each colony, annual differences could be detected between some years but not between others. During 1996-98, IOM seals showed a clear change in their FA profiles while NR seals did not. In contrast, during 2004-2006 NR seals showed a clear change while IOM seals did not. The changes observed in IOM during 1996-1998 are consistent with the large-scale regime shift that occurred in the North Sea during the 1990‟s. The relative proportions of each FA that were mobilized from blubber and transferred to the milk during lactation were very similar between colonies, and could be explained to a large degree by their physico-chemical properties. For a given carbon chain length the mobilization increased with increasing number of double bonds; and for a given number of double bonds the mobilization decrease with increasing carbon chain length. However, the mobilization also appeared to be influenced by the specific nutritional requirements of the growing pups. For instance, FAs that are considered essential for pup development or efficient energy storage (e.g. saturated FAs) were more highly mobilised than expected. This selectivity was also reflected in the FA composition of the different body compartments (maternal blubber and milk, pup blubber) that persisted throughout lactation. These changes were also similar between the colonies. Colonies could also be clearly distinguished by their blubber PCB profiles. IOM seals had higher total concentrations on average than NR seals (1327.9 vs. 680.2 ng/g lipid in 2005 and 1199.7 vs. 819.0 ng/g lipid in 2006). IOM seals also had higher total amounts in both years (79.2 vs. 38.0 mg in 2005 and 61.7 vs. 53.4 mg in 2006). One of the main differences between colonies was that females from IOM had higher concentrations of highly chlorinated congeners than NR seals. PCB concentrations in blubber increased towards the end of lactation. Serum and milk PCB concentrations also increased rapidly, especially for the highly chlorinated congeners. These results were consistent with other studies showing the increase in concentrations as a result of lipid loss. Serum concentrations stayed constant during the first part of lactation and increased at late lactation. This was also observed in milk PCB concentrations. The changes in the PCB profiles in the three body compartments were very similar between colonies. However IOM seals always had higher total concentrations of PCBs in all of the body compartments. The concentrations of individual congeners relative to PCB-153 showed that blubber contained higher proportions of the highly chlorinated PCBs relative to other tissues. There were no clear changes in these proportions in blubber during lactation, but the relative proportions of highly chlorinated PCB In serum and milk increased throughout lactation while the less chlorinated PCBs stayed constant. The highly chlorinated PCBs were found in lower concentration in the milk compared to the less chlorinated compounds suggesting a selective release from blubber to blood and a selective transfer of PCBs to the milk.

Over the past decades technological developments have both changed and increased human in influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals (Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of such methods in the prediction of sandeel occurrence. Lastly this thesis provides a quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.

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.