Young sandeels (0- and 1-group fish) form a substantial part of the total stock biomass at Shetland. As well as forming the basis for a local fishery at Shetland, they are also an extremely important prey item for many seabird species which breed around Shetland coasts. Improving our understanding of recruitment dynamics is vital for managing the Shetland fishery whilst minimizing adverse affects on breeding seabirds. Therefore, this thesis has concentrated on analyzing recruitment patterns and developing models to simulate hypothetical recruitment scenarios. Various models were developed and/or parameterised to simulate recruitment. Firstly, as there appeared to be no clearly defined stock-recruit relationship, time series models were applied to expose and improve understanding of patterns in the data. However, the relationship between stock and recruitment cannot be ignored if spawning stock biomass changes through exploitation. Therefore, Shepherd (1982) and Ricker (1954, 1975) stock-recruit models are parameterised using bootstrap analysis. For the Shepherd model, which is the more complex of the two, bootstrap analysis identified models which could be considered as "constant recruitment" models - that is no influence of spawning stock biomass on recruitment. It was found that four very low recruit years, which occurred in the late 1980s when spawning stock biomass was generally high or moderate, were strongly influencing model fit. This prompted the question: are these low recruit years typical of the range of recruitment for the given spawning stock biomasses or can they be considered outliers? In the face of uncertainty (although there is no biological reasoning) these data points were removed and the stock-recruit models re-parameterised. This enabled curves with 95% confidence intervals to be parameterised for both stock-recruit models (Shepherd & Ricker). The autoregressive model parameterised earlier was combined with the stock-recruit models so recruitment in any year was expressed as a function of SSB and of recruitment in the previous year.

This research investigates the policy response to the 2007-2010 sanitary crisis in the Chilean salmon industry, the second largest producer and exporter of salmon in the world. This industry is an emblematic case of the possible consequences of employing an intensive natural resource model for development. The research draws upon the two literatures on policy learning and policy change, and crisis and disaster management, and upon the system failure to explain the causes and consequences of the sanitary crisis in the industry. The thesis employs the qualitative method of case study and utilises primary and secondary sources of data and information. The main argument of the research is that the process of policy learning during and following catastrophic events is very different from the process of the policy learning during normal times. The main findings are, firstly, in the case of the Chilean salmon industry, the sanitary crisis disrupted the industry governance processes, including the regulatory framework of the industry, opening a window for radical institutional change. Secondly, potentially radical measures were part of a set of policies that emerged as initial responses, after which a set of more incremental policy responses were developed and applied. Moreover, the sanitary crisis was not transient nor episodic but was enduring, persistent and dynamic. Thirdly, the policy responses to the sanitary crisis destabilised the consensus in the Chilean industry causing conflict and ambiguity over policy responses. The thesis contributes to the policy learning and policy change literature in the context of catastrophic events by extending the view this literature offers on dramatic events such as crises, by considering them as dynamic and persistent situations, analysing their potential as precipitators of radical policy change, and providing a means for considering the timing and processes by which this radical policy change may occur and be directed toward better social outcomes.

Molecular ecology is one of the most important branches of evolutionary biology, and it uses the advantages of molecular techniques such as PCR-RFLP, sequencing, microsatellite analysis, and most recently the introduction of next generation sequencing, to address outstanding issues in the fields of population genetics and phylogeny. The genomic approach has been influential in providing new information relevant to traditional questions in ecology, such as genetic differentiation, speciation, species adaptation and others. The rationale of the present thesis was to incorporate the advantages of both the PCR-RFLP and sequencing techniques to gain information on the genetic variability of two commercially-important crustacean species, namely the Norway lobster Nephrops norvegicus and the giant freshwater prawn Macrobrachium rosenbergii. Nephrops norvegicus exhibits large morphological variability even between adjacent populations. The first objective of this thesis was to investigate the genetic variability of N. norvegicus from three localities, the Clyde Sea area and North Minch (North Sea) as well as Icelandic waters. The phylogeographic study found no significant differentiation between populations from the studied areas (FST: 0.01819). This finding is consistent with outcomes from previous studies that N. norvegicus populations were not geographically structured. Outcomes from the present study strongly suggest that environmental factors, rather than genetic factors, are more likely to play a more significant role in the high morphological differentiation observed in this species. A study of the most important freshwater crustacean species, Macrobrachium rosenbergii was then undertaken as a contribution to understanding the most complex biogeography in the world, the Indo Australian Archipelago (IAA). The IAA has incredible species richness and endemism and is the location of 4 out of 25 world’s biodiversity hotspots, namely the Sundaland, the Philippines, Indonesia and Wallacea. Within the IAA is the location of Wallace’s line and Huxley’s line, the most abrupt faunal transition in the world that lies between the Sunda and Sahul shelves. The studied species used in the present thesis, M. rosenbergii is an ideal model species as it has a wide geographical distribution across the IAA. The present phylogeographic study screened the COI segment using the sequencing technique to study M. rosenbergii populations collected from eight locations in Malaysia in the peninsular and east of Malaysia. These populations exhibited high genetic differentiation (FST: 0.62503) mainly due to the sample from Sabah. However, the adjacent population (Sarawak) was similar to that in Peninsular Malaysia, even though Northern Sarawak showed sub-population differentiation from the main cluster (cluster I) indicating that the genetic diversity of Northern Sarawak was more restricted. Beside, cluster II observed in the study indicated and confirmed the recent aquaculture activities of restocking the Kedah, Perak and Sarawak populations. Knowledge of the levels of genetic differentiation in N. norvegicus and M. rosenbergii could assist in the management of the species. N. norvegicus could be managed as one stock and conservation and recovery programme could be carried out based on the knowledge that all studied populations exhibited lack genetic differentiation within and between populations. In contrast, M. rosenbergii that possessed high level of genetic differentiation have to be managed separately, especially for a unique population such as the one in Sabah. The outcomes of this study could also be useful for future research in the conservation of wild population, as well as aquaculture management and product improvement purposes. The finding of Sabah as a unique population could potentially be useful for aquaculture improvement programmes. One of the most important aspects is to see whether Sabah population possessed high resistant to the disease infection. A preliminary study was conducted to investigate the susceptibility of a Malaysian wild population of M. rosenbergii to infection by the human food-poisoning bacterium V. parahaemolyticus. Nonetheless, the virulence stage of the bacterial strain, the status of the immune system of the host, the size and age of the experimental animals as well as the dose of injected bacteria might all have contributed to the inconclusiveness of the results. However, the principle of screening wild populations for disease resistance is sound, and may lead to improvements in the quality of the broodstock used in the Malaysian aquaculture industry.

The breakdown of reproductive isolation leading to inter-specific hybridization is a widespread phenomenon amongst cyprinid fishes. There are seventeen cyprinid species occcurring in the British Isles, within five sub-families, giving rise to some ten different types of hybrid. Most of these belong to the sub-family Leuciscinae. The most commonly occurring hybrids are probably those between roach, Rutilus rutilus (L.), and common bream, Abramis brama (L.). In this study the phenomenon of hybridization amongst species of the Cyprinidae was investigated through: an experimental breeding programme to investigate the nature of inter-species and hybrid gamete compatibilities; the identification of species and hybrids from the experimental breeding programme through the analysis of morphometric, meristic and genetic characters (genetic characters were analysed using enzyme electrophoresis); the comparison of morphmetric, meristic and genetic information of natural fish with similar features of fish from the experimental breeding programme to identify the occurrence of post Fl hybridization in natural populations; the use of restriction enzyme analysis of mitochondrial DNA to elucidate the importance of maternal ancestry in a natural hybrid population. The breeding programme found, for the species in this study, that there was no success in cross-fertilization of taxa between different sub-families. Interspecific gamete compatibility was only found within the leuciscine sub-family. In cases where a hybrid cross produced progeny it was also noted that the reciprocal cross was successful. This suggests that there is not a genetic barrier to gamete compatibility resulting from the sexual directionality of a hybrid cross. Female roach/common bream hybrids also produced progeny when crossed with males of leuciscine species. Identification of the progeny of the experimental breeding programme showed that the genetic techniques of enzyme electrophoresis was more reliable than the statistical analysis of meristic and morphometric traits in the identification of species and their Fl hybrids. However, genetic information alone cannot establish precisely the nature of post Fl hybrids and in the identification of backcrossed roach/common bream hybrids it was noted that meristic information was needed to support genetic data. In the two natural hybrid populations of roach/common bream and rudd/common bream, from the Forty Foot Drain and Essex University Lake respectively, the analysis of morphometric, meristic and genetic characters found no evidence of post Fl hybridization in these waters. It is suggested that absence is due to either the limitations of the sampling methods or biological processes. Possible biological processes include factors such as the inappropriate mating behaviour of Fl hybrids or the inferior fitness of post Fl hybrids. The analysis of mitochondrial DNA did not yield sufficient results to elucidate the importance of maternal ancestry in hybridization. It is suggested that this aspect of hybridization is of such critical importance that it must become the subject of a future research programme. The importance of the causes and consequences of inter-specfic hybridization in fishes are discussed. It is suggested that, because they are rarely investigated in hybrid studies, these become incorporated into research programmes in the future. These areas of investigation will have implications for fisheries management, freshwater ecology, genetic conservation and species integrity.

Overexploitation of many fish stocks underlines the need for more effort directed towards stock management so that the sustainability of resources is assured. To avert the tragic consequences of overfishing in coastal waters, a growing body of theoretical and empirical research provides evidence in support of cooperation among resource users to manage their commons. This study aimed to investigate the factors that contribute to the emergence and evolution of collective action in fishermen's communities to manage their coastal fish resources in South Al-Batinah, Sultanate of Oman. The study emphasises the importance of a collective action approach to fish resource management with examples from three fishing towns.In order to understand why fishermen choose to participate (or not to participate) in local collective action to manage fish resources, the researcher focuses on six main sets of issues that influence fishermen's decisions: economic factors; awareness of resource exploitation problems; institutional rules in use; social identity, group size and heterogeneity among resource users. Social and demographic factors as well as vessel configuration were also considered.Data collection for the study was carried out using three methods: questionnaire, semi-structured interview and observations of fishermen's activities. Statistical reports and other research papers carried out in Oman were also reviewed. The study found that there is a management institution that governs the fishing activities of the fishermen in the study area. Fishermen in the area inherited an indigenous management institution, which was established hundreds of years ago. It was also found that fishermen were very aware of the resource exploitation problems. High awareness of the resource exploitation problems coupled with high interdependence among users might induce them to work collectively to mitigate harm to their long-term welfare.The results of testing a number of hypotheses indicated that among the reasons which may influence collective action, are high economic dependence on the fishery,individuals' social identity as fishermen, awareness of the resources exploitation problems, risk aversion and heterogeneity (differences in objectives and interests).The study findings indicated that individuals using common resources are faced by various "assurance" and "chicken" problems. In both the PD game and the Assurance game, the preferred outcome is mutual cooperation. Whereas the predicted outcome of the former is defection, the latter suggests the possibility that the preferred outcome (i.e., cooperation) will occur, because individuals' decisions in the commons are influenced by a complex set of factors, rather than strictly materialistic self-interest. The analysis presented in this study examined several of those factors for their influence on individual behaviour. The findings of this study strongly suggest that the presence of local management institutions to coordinate the fishermen's activities in the study area is the key factor in avoiding the worst outcome (universal defection). The game structure has been changed from a Prisoner's dilemma to a Privileged game or a game of Chicken where the benefits from cooperation are maximized. It is the role of the institutions to determine how the cost of providing the public goods might be shared among participants.

The dynamics of demersal fish species assemblages and stocks on the continental shelf of Ghana, West Africa were investigated using data from trawl surveys conducted between 1963 and 1990, and in relation to marine environmental and nearshore forcing factors. Time series analysis was used to examine the dynamics of the marine environment. Classification and ordination methods were used to identify fish assemblages and to identify factors that determine assemblage formation and dynamics. The response of the identified assemblages to changes in the Ghanaian shelf ecosystem were assessed. Between 1964 and 1992, three distinct environmental time blocks (ETBs) in the continental shelf ecosystem off Ghana were recognised. In the first ETB (i. e. before 1972) sea surface and bottom temperatures were relatively high and salinity was low. The second ETB (1972 - 1982) was characterised by low temperatures, high but stable salinity, reduced rainfall and freshwater input into the sea. In the third ETB (1982 - 1992), the system bore a resemblance to the first block with rising temperatures and decreasing salinity. Six fish species assemblages were identified, namely the supra-thermocline sciaenid and lutjanid assemblages, two sparid assemblages (shallow and deep elements), the deep shelf assemblage and the upper slope assemblage. During ETB I and ETB3, the assemblages were easier to identify using ordination techniques, than during ETB2. Species diversity also decreased during ETB2 especially in waters between 10 and 50 m deep. This behaviour of the assemblagesis attributed to the increase in abundance of Balistes capriscus, a species that dominated the ecosystem for nearly 20 years from about 1971, and the observed environmental changes. The estimated density of demersal fish was higher in the upwelling season than in the thermocline season and decreased from 50 kg ha-1 in 1963-64 to 32.4 kg ha-1 in 1990. The density reached its lowest value of 22.5 kg ha-1 in the period between 1973 and 1977. The potential yield of the total demersal biomass (excluding triggerfish) is estimated to be 36,000 - 55,000 mt per annum. With landed catches exceeding 60,000 mt in some years, it is apparent that the resource is over-exploited. A number of policy options are discussed and recommendations for the management of the fishery are made.

The main aim of this thesis was to study intra- and inter-specific competition among juvenile Atlantic salmon and brown trout. The study concentrated on two critical times for survival: first, the period from shortly after emergence until later in the summer when individuals first establish territories; and second, during the winter, when many salmonid populations experience a bottleneck. In addition, the stability of social hierarchies and the influence these have on growth and survival were studied on older individuals in the summer. Experiments were carried out in a variety of conditions ranging from small arenas and artificial stream channels where behavioural interactions among fish could be observed, to the wild where it was possible to test inferences derived from laboratory observations in an ecological context. Both salmon and trout are known to undergo a behavioural shift in winter, switching from being primarily diurnal during the summer to being predominantly nocturnal in winter. Atlantic salmon and brown trout forage in slow-flowing water at night and shelter in interstitial spaces in the substrate during the day. This thesis shows that salmon and trout compete for both foraging (chapter 2) and sheltering (chapter 3) habitat in winter, illustrating that competition between the two species is not restricted to the summer months. Trout were shown to dominate salmon in competition for foraging habitat, forcing them to move into shallower water or become more diurnal (chapter 2). Intra- and inter-specific competition for shelters was equal in intensity and more dependent on arrival time (prior residency) than species identity (chapter 3). This competition could have short- and long-term survival consequences for over-wintering fish, particularly Atlantic salmon, and have implications for the carrying capacity of streams.

The potential impacts of marine aquaculture operations on the environment are reviewed. The reported effects of suspended mussel farms on the benthic environment are examined and the potential impacts discussed. A framework to assess the impacts of suspended mussel farms is presented. The use of simulation models to predict the impact of fish farm wastes on the benthic environment is discussed and the mathematical theory supporting such models is presented. The applicability of these models to mussel farming is discussed and the data required to undertake such modelling identified. The effect of increased sedimentation on the macrobenthic community, physical structure and biogeochemistry of the surficial sediment around three suspended mussel farms are examined. At one site, the benthic community was subjected to bulk sedimentation, organic enrichment and reduced macrobenthic infaunal diversity. Elevated levels of organic carbon were recorded close to the farm. At the remaining two sites, benthic impacts were less clear and not demonstrably due to the mussel farms. The settling velocity of mussel faeces and pseudofaeces was required to enable modelling of particles ejected from the farm sites. An experiment was devised to measure this parameter.- The settling velocity of mussel faeces (~0.5 cms-I ) was less than pseudofaeces (~1 cms-I ). Differences in these settling velocities were attributed to the organic content and particle size of the excreted matter. The particle tracking model DEPOMOD (Cromey et at., 2000a) was used as a platform from which to develop a simulation model predicting the benthic impact of suspended mussel farms. Parameters within the model were modified to be represent a mussel farming scenario. Data from the three sites surveyed were applied to the model. Although the model results compared favourably with the field data, the model tended to overestimate the benthic impact as measured by the Infaunal Trophic Index. The results of the model are discussed and improvements and further experiments are identified.

Perceived conflicts between piscivorous birds and commercial freshwater fisheries are common, and such a perception exists at Loch Leven, a wetland of international importance for nature conservation and a famous commercial brown trout Salmo trutta fishery, where Great Cormorants Phalacrocorax carbo have been shot in large numbers. This thesis describes the foraging behaviour of cormorants wintering on Loch Leven. It summarises changes in wintering numbers over a 32 year period, and reviews data on fish populations, fish stocking rates, angling catches and angling effort in order to seek evidence of detrimental impacts of cormorants on the fishery, and beneficial effects of large-scale cormorant shooting. Finally, this thesis considers turnover within the wintering cormorant population, and its implications for cormorant control. Cormorants spent most of the time roosting, and a single peak of feeding activity occurred early in the morning. Compared to early or late winter, cormorants showed higher foraging activity during mid-winter. Both solitary feeding and flock feeding were recorded, with flock feeding predominating. Solitary feeding was distributed over a wide area. The intensity of flock feeding was less evenly distributed, with 36% of grid squares not used. Overall, 78% of flock feeding activity took place in 23% of grid squares and 59% took place in 13% of grid squares. The best predictor of both solitary feeding and flock feeding intensity of use was mean water depth. Mean water depth was also the best predictor of winter brown trout distribution, although winter brown trout distribution was not a predictor of either solitary feeding or flock feeding intensity of use.

Five species of sea turtle are known to nest on the north and east coast beaches of Trinidad, West Indies. In descending order of abundance: the leatherback (Dermochelys coriacea), the hawksbill (Eretmochelys imbricata), the green (Chelonia mydas), the olive ridley (Lepidochelys olivacea) and the loggerhead (Caretta caretta). This thesis investigates a number of aspects of the ecology and conservation of the sea turtles nesting and foraging on the north coast. Prior to this project, little research had been carried out on the north coast region, largely due to the difficulties of accessing the nesting beaches. The main aims of the project include making reliable estimates of the annual nesting population size of each species, to identify the main threats to the turtles at various life stages, and to make recommendations on how best to conserve the sea turtles in Trinidad. Overall, this thesis offers an up-to-date overview of the status of the sea turtle populations nesting on the north coast of Trinidad. The results presented here highlight Trinidad’s importance as a region for turtles, especially for nesting leatherbacks, foraging greens and nesting and foraging hawksbills. This study will be useful in assisting the Trinidadian Government to meet their obligations under the Biodiversity Convention, and in facilitating the assessment of the remaining leatherbacks in the Atlantic. Recommendations are made for future conservation and management.