At the commencement of this study all data on Manta rays were combined under the single species Manta birostris, and there was little information available on their ecology. Manta rays were frequently reported throughout the Maldives, and tourist manta-watching is an economically important activity in this region although no previous study of manta numbers or movements had been made. An individual identification method was developed based on the unique ventral marking pattern of each animal in order to record the identity and frequency of visit by mantas to the numerous cleaning and feeding areas. Information on sex, estimated size, and the markings pattern were collated in an Access database along with date/time and location of each animal sighting. Mantas were also observed and recorded photographically and on video being cleaned by cleaner fish and during feeding activity so that typical behaviours could be investigated. Analysis of the ID records and sightings data of over 1900 individually identified mantas has shown that the smaller reef-associated Manta alfredi is the predominant species in the Maldives. The majority of mantas (~74%) have been sighted only once, but this is probably due to a relatively low survey rate, with the remainder re-sighted between one and 34 times. Individual mantas which were re-sighted appeared confined to an atoll, visiting a number of cleaning stations around the atoll and migrating between east and west sides so as to be predominantly on the leeside to the prevailing monsoon. Only ~1% of mantas were reported in more than one different atoll with 270 km being the greatest distance between sites where an individual manta was reported, a range not previously recorded. A population study estimated populations of around 537 mantas in small atolls and 811 in large atolls. The population was ~65% female, and females were significantly larger than males. Reproductive periodicity appears low with only 26% of likely mature females ever being sighted pregnant over a 5 year period. Females which were reported pregnant produced offspring less frequently than every two years, on average. This low reproductive rate might put this small population at risk if local fishing practices changed. i The behaviour of mantas at cleaning stations was investigated as well as the identity and abundance of cleaner fish species. Feeding strategies are described and appear to show that feeding is a co-operative behaviour in mantas. These preliminary behavioural studies provide early insights into the ecology of this species.

No description available.

Understanding how the environment drives the pattern of adaptive radiation may be key to understanding tl1e role of ecology in evolution. The Lake Malawi Haplochomine cichlid fish radiation was seeded by riverine ancestors, yet extant riverine diversity is extremely low. Only Astatotilapia calliptera the putative ancestor of flock currently persists in both the lake and the rivers of the catchment. This presents us with a useful model for assessing tl1e role of environment in driving diversification within a single species. We predict that the contrast in disturbance regime may drive the difference in speciation rate between the two habitats. In tlus thesis, population genetic analysis, functional morphometries, and common garden experiments are used to investigate the level of variation between disturbed river populations and comparatively stable lake populations. The genetic analysis indicates minimal population structuring between Lake Malawi populations compared to within or between river systems. Morphometric data suggests that lake populations are locally diversifying despite this limited isolation. River morphologies are similar despite reduced mixing. Dietary analysis shows that differences in morphology are functional, with the key axis of variation ranging from hard-bodied animals to smaller non-animal resources. Common garden experiments show a clear trade-off between egg-size and number. The majority of sites including all river sites adopt a more conservative strategy focussing on high offspring number. One lake population adopts a high investment strategy. A comparison between lab reared morphology and wild caught morphologies shows that the majority of variation maintained in the wild is through plastic mechanisms. These results suggest that the unpredictability of the riverine environment constrains populations to bet-hedging strategies whilst the highly competitive nature of the lake promotes specialisation. This selection for specialisation could in turn lead to speciation, and may partly explain why speciation within Lake Malawi has been so spectacular

Systems that classify images by the individual animals they contain have widespread applicability in field-based ecology and conservation research, allowing individuals to be recognised repeatedly in a non-invasive way. The aim of this thesis is the design of such systems for animal species where individuals exhibit visually unique body morphologies, with the specific objective that individuals are recognised fully automatically. A two-stage approach is adopted to achieve this objective, as illustrated for the task of recognising individual great white sharks. First, a model is trained for automatic object part detection that combines a partitioning of ultrametric contour maps with shape descriptions and dense local features. This provides robust part detection but fine-grained segmentation accuracy is sacrificed in favour of computational efficiency. As such the approach is complemented by affinity matting for local edge refinement. The combination of part detection and affinity matting achieves robust, efficient and pixel accurate biometric contour detection. Second, a generative model combines evidence provided by densely sampled, multiscale local shape descriptions for biometric contour classification. The approach provides a discriminative representation of individuality while demonstrating robustness to sources of intra-individual variability introduced by partial occlusions and automatic shape detection errors. As an additional contribution, the distribution of individuality in dimensions of smoothing-filter scale, spatial location and descriptor complexity is quantified. Insights are provided to guide processes of image acquisition, shape representation, and efficient shape extraction. Finally, the generality of the contour representation is presented alongside a novel framework for discriminative cue combination in an application to individual humpback whale recognition. A detailed evaluation of the major system components is provided with results demonstrating fully automatic individual classification performance at accuracy and efficiency levels ready to assist human identification efforts.

The blue shark, Prionace glauca, a large oceanic/pelagic predator with a continuous circumglobal distribution in temperate and tropical waters, is the most abundant and widespread of all extant shark species. They are heavily exploited in targeted and incidental fisheries worldwide. Concerns have been raised over the sustainability of such exploitation as severe declines in numbers have been recently observed. Sound management of any exploited fishery requires a proper understanding of the population sub structuring and basic breeding biology of the species involved. This is lacking for this ecological and economically important inhabitant of the open seas. In this study, we have developed nuclear microsatellite and mitochondrial (mtDNA) molecular markers for blue sharks. These were used in an assessment of the global population genetic structure of the species involving over 900 specimens sampled over its distribution range. Based on micro satellite data and 21 blue shark litters (N = 578 embryos), we have characterised the mating system ofthe species. Results from the analyses of microsatellite (16 loci) and mtDNA sequence (3,1 07bp) data indicate the presence of multiple stocks on a global scale (i.e. genetic substructuring). These genetic stocks were defined by major oceanic regions, thus confirming earlier physical tagging studies, which suggest that the equator acts as a barrier to dispersal between northern and southern oceans. Analysis of data comprising 32 complete mtDNA genomes, representing the distribution range species, provides new insights into the evolutionary history of blue sharks. Microsatellite DNA profiling of blue shark litters revealed a high incidence of polyandry (80.0%) in the species. Females of multiply sired litters were larger than those of single paternity litters. Furthermore, females demonstrated a tendency to have litters sired by more males as they became older and larger. Results are discussed in light of the high energetic cost associated with the aggressive nature of copulations.

This multi-decade study on an isolated and unfished population of manta rays (Manta alfredi and M. birostris) in the Maldives used individual-based photo-ID records and behavioural observations to investigate the world’s largest known population of M. alfredi and a previously unstudied population of M. birostris. This research advances knowledge of key life history traits, reproductive strategies, population demographics and habitat use of M. alfredi, and elucidates the feeding and mating behaviour of both manta species. M. alfredi reproductive activity was found to vary considerably among years and appeared related to variability in abundance of the manta’s planktonic food, which in turn may be linked to large-scale weather patterns such as the Indian Ocean Dipole and El Niño-Southern Oscillation. Key to helping improve conservation efforts of M. alfredi was my finding that age at maturity for both females and males, estimated at 15 and 11 years respectively, appears up to 7 – 8 years higher respectively than previously reported. As the fecundity of this species, estimated at one pup every 7.3 years, also appeared two to more than three times lower than estimates from studies with more limited data, my work now marks M. alfredi as one of the world’s least fecund vertebrates. With such low fecundity and long maturation, M. alfredi are extremely vulnerable to overfishing and therefore needs complete protection from exploitation across its entire global range. With similar life history traits assumed for the lesser known M. birostris, adopting the precautionary principle, the same highly protective approach is justified. Through characterising habitat use of M. alfredi, it appears that their use of shallow coral reefs may be a function of behavioural thermoregulation and predator avoidance, with cleaning stations acting as focal gathering points where social behaviour is undertaken, such as courtship and mating. The frequent use of shallow protected lagoons by juvenile M. alfredi suggests these sites may act as nursery areas. The study underscores the importance of long-term research on long-lived species with conservative life history strategies if important ecological and management questions are to be answered.

Ecological interactions in the marine pelagic environment are difficult to study, mostly because the open-ocean is vast and largely inaccessible. Migration is a common ecological trait in pelagic settings, with large impacts on community structure and dynamics, and ecosystem functioning. However, migratory predators are rapidly declining worldwide, with unclear ecological consequences. Pelagic sharks have declined regionally by > 90% in the past 15 years, largely as a result of overfishing and by-catch. Shark vulnerability to fishery capture depends on individual movements, and on the presence of movement traits across individuals, populations or species, which may imply shared vulnerability. Yet, the movements of pelagic sharks and other migratory oceanic animals are difficult to monitor or reconstruct. Natural-abundance stable isotopes allow retrospective movement reconstruction, by relating the isotopic composition of animal tissues to geographically indexed measurements or predictions of isotopic ratios at the base of the food web (isoscapes). Where incrementally grown, metabolically inert tissues are available, movements can be reconstructed throughout life. However, the application of stable isotopes in bulk tissues to study migration is complicated by mixed baseline and trophic effects and, in pelagic settings, by large uncertainties in the spatio-temporal distributions of isotopic baselines. In this study, I explored how the ontogenetic movements of two pelagic shark model species, the blue (Prionace glauca) and porbeagle (Lamna nasus) sharks, could be reconstructed using modelled global ocean carbon isoscapes, and carbon and nitrogen isotopes in bulk cartilage collagen and single amino acids from vertebrae. To provide a possible solution for poor sampling of isotopic baselines, I developed a process-based, mechanistic carbon isotope model, predicting the likely spatio-temporal distributions of the carbon isotopic composition of phytoplankton across the global ocean. To provide information on pelagic shark life-history traits, I recovered individual-level life history carbon and nitrogen isotope records for bulk cartilage collagen from vertebrae of sharks caught across the North Atlantic. I also recovered comparable carbon isotope records for single amino acids, producing the first compound-specific isotopic dataset of within-individual ontogenetic variance in sharks. Consistent ontogenetic isotope patterns across individuals of each species revealed species level life-history traits. Whilst the interpretation of traits for bulk collagen using modelled isoscapes was ultimately limited from confounding influences from trophic level change, that of traits for essential amino acids conclusively demonstrated ontogenetic and transgenerational movement traits. During juvenile growth, blue sharks increasingly utilised foraging grounds with more positive carbon isotopic baselines, whereas porbeagles made increasing use of isotopically more negative grounds. Blue shark pupping and maternal foraging occurred in isotopically distinct grounds, with the possibility of natal homing by adult individuals. Pregnant female porbeagles, by contrast, migrated to isotopically distinct foraging grounds prior to giving birth. Isotope-derived information on ontogenetic movements complements tag-derived information over a snap-shot of the entire life of individuals, but explicit isoscape-based geo-location is limited by large uncertainties in isoscape models, and trophic influences on bulk tissue isotopic compositions.

Historically, whale sharks, Rhincodon typus, have been infrequently documented from the Arabian Gulf and the northern Gulf of Oman. This thesis documents the population and movement ecology of whale sharks within this region between 2011 and 2014. The Al Shaheen Area of Qatar and the Musandam region of Oman were the main hotspots for whale shark occurrence. The Al Shaheen oil field is located 90 km off the coast of Qatar in the Arabian Gulf. Platform workers reported 4351 individual whale sharks between 2011 and 2014 based on daily cumulative sightings. Peak numbers of whale sharks were observed between May and September from the west of Al Shaheen. Density estimates of up to 150 sharks within an area of 1 km2 were recorded. Most animals observed were actively feeding on surface zooplankton, consisting primarily of mackerel tuna Euthynnus affinis eggs. A total of 420 individual sharks were identified from their spot patterns from the entire region, with the majority (81%, n=341) encountered at Al Shaheen. Population size for the Arabian Gulf and Gulf of Oman combined was estimated using the program SOCPROG at 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295) with 120 sharks present on any given day. A mean residency period of 17 days within this area and 31 days outside the study area was estimated. A model representing a fully mixed population showed the best goodness of fit to investigate Lagged Identification Rate (LIR) of occurrence between two areas, inside and outside of the Arabian Gulf, suggesting a degree of interchange between the Arabian Gulf and Northern Gulf of Oman populations. Inter-annual re-sighting rates of sharks at Al Shaheen varied between 22 and 88%. The estimated total length (TL) for all sharks assessed in Al Shaheen was 6.9 m (± S.D. 1.24, N=296), with males (7.25 m ± 1.34, N=171) being larger than females (6.44 m ±1.09, N=78; t = 4.68, df = 247, P = 0.0001). This aggregation had a significant male bias (69% N=248), with the majority of males assessed as mature (63%, N=81). This is the first whale shark aggregation site dominated by mature animals. Length at which 50% of the animals were mature (TL50) was 7.29 m with all animals at 9 m being mature based on clasper morphology. Movements of individual sharks between the Qatari, Omani and UAE waters were confirmed by individual spot pattern recognition. Satellite tracking of whale sharks within the region showed that whale sharks prefer depths in excess of 40 m and rarely made dives deeper than 100 m. Temperature preferences were between 27 °C and 33 °C. Sharks were seen to aggregate in the summer and disperse widely throughout the region in the winter months outside of the tuna-spawning season. Genetic analysis of whale sharks from Al Shaheen determined that the whale sharks found in this area were genetically similar to the wider Western Indian Ocean populations. Stable isotope analysis showed distinct differentiation in feeding for sharks from Qatar, Tanzania and Mozambique. Anthropogenic threats from the region were found to include boat impacts, accidental and direct capture in nets and a target fishery using tail ropes. Species-specific protection should be considered within countries hosting regional whale shark hotspots and, in addition, whale sharks should be afforded protection within Al Shaheen.

No description available.

Large marine vertebrate species can exhibit vast movements, both horizontally and vertically, which challenges our ability to observe their behaviours at extended time-scales. There is a growing need to understand the intra- and inter-annual movements of mobile marine species of conservation concern in order to develop effective management strategies. The basking shark (Cetorhinus maximus) is the world's second largest fish species, however, a comprehensive understanding of this species’ ecology, biology and spatial behaviour in the north-east Atlantic is currently lacking. This thesis seeks to investigate the movement ecology of basking sharks using a suite of technologies to integrate biologging, biotelemetry, remotely sensed data, and ecological modelling techniques. I use satellite telemetry data from basking sharks tracked in 2012, 2013 and 2014 to quantify movements in coastal waters off the west coast of Scotland within the Sea of the Hebrides proposed MPA. Sharks exhibited seasonal residency to the proposed MPA, with three long-term tracked basking sharks demonstrating inter-annual site fidelity, returning to the same coastal waters in the year following tag deployment (Chapter 2). I reveal that sharks tracked into winter months exhibit one of three migration strategies spanning nine geo-political zones and the High Seas, demonstrating the need for multi-national cooperation in the management of this species across its range (Chapter 3). I examine the vertical space-use of basking sharks to improve an understanding of the processes that influence movements in all dimensions. Basking sharks exhibit seasonality in depth-use, conduct deep dives to over 1000 m, and alter their depth-use behaviour in order to remain within thermal niche of between 8 and 16 oC (Chapter 4). Finally, I combine contemporaneous data recorded by deployed satellite tags with remotely sensed environmental data to employ novel ecological modelling techniques to predict suitable habitat for basking sharks throughout the Atlantic Ocean (Chapter 5).