Three experiments were conducted to investigate the effects of dietary supplementation of a ß-(1,3)(1,6)-D-glucan derived from the yeast Saccharomyces cerevisiae, on growth performance parameters and intestinal functionality in mirror carp (Cyprinus carpio L.) and on progression of a chronic, pre-existing mycobacteriosis in zebrafish (Danio rerio). The 1st experiment revealed that mirror carp fed diets containing 1% and 2% ß-glucan showed significant improvements in growth performance compared to fish fed both the control and the 0.1% ß-glucan containing diet. Equally, fish fed diets supplemented with 1% and 2% ß-glucan displayed significantly higher infiltration of leukocytes into the epithelial layer of in the anterior intestine. This effect was not observed in the posterior intestine. There were no significant differences in the intestinal absorptive surface area and number of goblet cells in either intestinal region. Compared to control fed fish, the haematocrit value was significantly elevated in fish fed the 2% ß-glucan diet. The blood monocyte fraction was significantly higher in fish fed the 1% and 2% ß-glucan diets. No significant changes were observed in the other blood parameters assessed. In the 2nd experiment, culture-dependent microbiology unveiled that aerobic heterotrophic bacterial levels in mirror carp intestinal microbiota were unaffected by dietary β-glucan after two and four weeks. No effects were observed on the allochthonous lactic acid bacteria (LAB) populations at either time point, however, reduced autochthonous LAB populations were observed at week four. PCR-DGGE confirmed these findings through a reduction of the abundance of autochthonous LAB operational taxonomical units (OTUs) in β-glucan fed fish compared to the control fed fish. DGGE analyses also revealed that dietary β-glucan reduced the number of OTUs and the species richness of the allochthonous microbiota after two weeks, but not after four weeks. In contrast, dietary β-glucan reduced the number of OTUs, the species richness and diversity of the autochthonous microbiota after two weeks, and those parameters remained reduced after four weeks. Intestinal microvilli length and density were significantly increased after four weeks in fish fed diets supplemented with 1% β-glucan. The 3rd experiment comprised of two individual trials where dead or moribund fish displayed the classical clinical signs of mycobacteriosis. In experiment I (200 days), zebrafish were fed diets supplemented with 0% (control, C) or 0.1% ß-glucan (B). In experiment II (63 days), zebrafish were fed diet C or diet B continuously or both diets intermittently (CB) in weekly intervals. Dietary ß-glucan failed to improve survival rates in both experiments. In experiment II, histopathological analysis revealed absent (normal appearance), moderate and severe manifestations of granulomas. Ecological microbial community analysis of intestinal samples collected at day 63 showed significantly higher number of OTUs, species richness and diversity in treatments B and CB compared to the control treatment. In conclusion, high dietary ß-glucan supplementation levels enhanced growth performance, leukocyte infiltration in the anterior intestine and the ultrastructure of the enterocytes in mirror carp without detrimental effects on intestinal morphology or the haemato-immunological parameters assessed. In addition, intestinal microbial communities were altered in healthy mirror carp and diseased zebrafish. It was also demonstrated that dietary ß-glucan failed to impact the progression of a pre-existing mycobacteriosis in zebrafish. Future research is required to investigate the underlying reasons for the observed effects by applying advanced molecular techniques, and whether these effects occur under commercial husbandry, or in different fish species.

Successful implementation of an Ecosystem Approach to Fisheries Management requires modifications to current management processes, some of which are already in motion. Recognition that poor understanding and inadequate management of stakeholders can impede efficient implementation of management policies means that stakeholders are no longer on the periphery of fisheries research. 'Ecosystem-approach' models and their outputs, indicators, have become prevalent and are important tools for understanding and communicating the condition of system properties. There are three components to the thesis; 1) an analysis of stakeholders, their interests, and categorisation methods, 2) a worked example of the ability of a suite of indicators to contribute practical information to the decision making process using an analogy of Signal Detection Theory and historical data for the Celtic Sea and 3) a Priority Inclusion Tool is proposed, capable of integrating multiple, divergent stakeholder interests with signals from numerous indicators, identifying preferred management responses for each stakeholder. Results from the stakeholder analysis indicate that counterproductive stake holder stereotyping may have occurred previously and adopting evidence-based approaches to stakeholder analysis may reduce subjective interpretation of stake holder interests. The indicator analysis demonstrates the challenge of combining indicator signals on different aspects of the system, i.e. economic and ecological, which may have conflicting implications for managers. A framework is developed to combine indicator signals, determined from their reference values, to evaluate the potential for satisfying a specific management priority. The degree of conflict and agreement among stakeholders can be assessed and visualised from the outputs of the Priority Inclusion Tool. The results from this thesis have significant implications for stake holder involvement and the use of indicators in fisheries management. If the stakeholder-indicator relationship is not given serious consideration in the management process, attempts to implement an EAFM could be ineffective due to a lack of stakeholder support, understanding and compliance.

Brown trout (Salmo trutta L. 1758) is one of the most polymorphic vertebrate species described. While originally endemic to Europe, West Asia, and North Africa, it is now found in all continents, bar Antarctica. Its presence outside its natural distribution range is attributed to anthropogenic mediated introductions, due to its popularity, both as fine cuisine and a formidable sport fish. In many countries such as Canada, New Zealand, and Argentina, S. trutta has become a successful invasive species, competing with and often displacing native species. Despite its success elsewhere, S. trutta populations within its native range are exposed to a number of pressures that potentially threaten their long-term sustainability. These include, habitat disturbance and fragmentation, pollution, over exploitation, competition with introduced species, as well as stocking activities. Of principal importance for ensuring the sustain ability of S. trutta populations is a sound understanding of the distribution and drivers of diversity, in particular genetic variation. This thesis primarily focuses on the study of population genetic structure of S. trutta in Lough Neagh, Northern Ireland. This Lough, the largest in the British Isles, is highly productive, relatively shallow, and supports a commercial fishery, in which adult migratory S. trutta are intermittently exploited. Angling of adult S. trutta that either migrate from the Lough into the surrounding rivers and tributaries to spawn, or are resident within these watersheds throughout their entire life cycle, is not only very popular pastime, but also an important component of the local economy. Using a comprehensive sample set comprising over 5,400 individuals, a high resolution spatial map of genetic structuring within and among the major tributary rivers and streams around the Lough Neagh catchment was established. The populations, inferred using multiple analytic methods, are shown to provide high accuracy for genetic stock identification of individuals of unknown origin. A preliminary assessment of a mixed stock sample from Lough Neagh indicated that one catchment, Six Mile Water, is the single largest contributor to the mixed fishery, suggesting is deserves special focus in any management plan aiming to ensure the sustainability of the commercial fishery. The description of genetic structuring around Lough Neagh is presented as an important progression towards the establishment of a long-term management plan for S. trutta in this region. In addition to this major study (chapter 5), three additional studies introducing; 1) a powerful marker panel consisting of 38 microsatellite for S. trutta population genetics investigations, 2) a general purpose software for population genetic analyses, and 3) a software application for the exploration of gene flow, are also presented (chapters 2-4). Two further studies, one examining genetic variation in two populations of S. trutta from the Scottish highlands previously reported to be monomorphic (chapter 6), and another investigating the genetic consequences of a catastrophic fish kill for a population of S. trutta (chapter 7) also provide further insights of direct relevance to the conservation or management this important fish species.

The series of papers round which this thesis is based highlight the inherent problems in assessing larval fish feeding success from sampling programmes and gut contents analysis, and show through novel observations, that counting the number of food items in the gut is not necessarily a good indication of feeding success. Food type, digestibility and size, gut passage rates and the particular lipid classes the food contains, must all be considered, illustrating the difficulties in interpreting larval fish energetics from field studies. The resistance to digestion demonstrated for copeped eggs, means that a potentially rich source of energy cannot be utilised. This may have severe nutritional consequences for the early larvae of many important commercial fish species which can feed heavily on these eggs, possibly influencing ultimate recruitment levels. While much can be learned from coarse grid, depth integrated plankton sampling, interpretation of relationships between food availability and larval condition was shown to require precise sampling of the larvae in their actual feeding environment. Intense integrated and vertically stratified plankton sampling allowed the most detailed observations on food selection by fish larvae ever carried out and demonstrated their considerable foraging adaptability, even in a changing food environment. Food availability is undoubtedly an important factor in larval fish survival because of its affect on condition and growth rates, but many other factors are now known to be involved and it is accepted that recruitment in a species may be decided at almost any stage of early development. The traditional approach to understanding the environmental impact on larval survival and fish recruitment has been by observational field ecology and correlation techniques. However, more recently, advances in mathematical modelling techniques in which we are involved, are allowing the representation and simulation of both physical and biological oceanographic processes. Progress in understanding how selective forces generally shape recruitment will depend increasingly on these exciting new techniques.

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The overall theme of this thesis has been the study of the effects of well known and potentially novel stressors on fish health and how some of these may be modulated by dietary supplements of micronutrients, using both in vitro and in vivo analysis. In vitro experiments with cultured fish cells (EPC-A1, GFSk-S1) evaluated the potential of niacin and selenium to reduce cytotoxicity and genomic instability (DNA damage) induced by ultraviolet radiation exposure, following assay validation with reference toxins. Whilst cytotoxicity was determined by the neutral red retention (NRR) assay, genomic stability was evaluated by either a standard or modified version of the single cell gel electrophoresis (SCGE) or 'Comet' assay. Niacin as nicotinamide (NAM) significantly reduced levels of UVB induced DNA damage (single strand breaks). Selenium supplements, as sodium selenite or seleno-L-methionine also showed a protective effect against H202, UVA and UVB induced cytotoxicity and oxidative DNA damage. An additional in vitro study was carried out to identify environmental nanoparticles as a potential novel source of stress for fish. Titanium dioxide (Ti02) nanoparticle exposure to GFSk-81 cells caused dose-dependent increases in cytotoxicity (NRR assay) and oxidative DNA damage (Comet assay). These effects were exacerbated by combined exposures of Ti02 with UVA. Electron spin resonance (ESR) and spin trapping suggested that Ti02 induced oxidative stress may be primarily due to the production of hydroxyl radicals (OH). Two in vivo experiments were carried out in order to evaluate the effects of husbandry stress (netting and confinement stress) on antioxidant capacity, immune function and genomic stability in trout (Oncorhynchus mykiss) and carp (Cyprinus carpio) , In both studies on trout and carp, certain health parameters were shown to be sensitive to husbandry stress, and may be useful biomarkers of stress in future studies. Total antioxidant capacity (TAC) was reduced in both carp and trout after stress. Respiratory burst capacity of blood leukocytes was also affected by stress but differently in carp than in trout. In carp, husbandry stress apparently stimulated the production of free radicals by leukocytes whereas in trout it was suppressed. In trout, stress was also shown to increase oxidative DNA damage, as measured by the Comet assay. Health parameters that appeared not to be significantly affected by husbandry stress in this study include SOD activity, ALP activity, red blood cell fragility and complement activity (for carp only). In the second experiment on carp, a 10 week feeding trial was also conducted prior to stress induction to evaluate the potential modulatory effects of selenium, zinc and vitamin E on any husbandry induced stress effects observed. Health parameters were also evaluated pre stress in order to elicit any effects of micronutrient supplementation on health parameters in unstressed fish. Selenium supplementation significantly increased glutathione peroxidase activity post stress, but not pre stress, indicating an increased requirement of selenium in stressed fish. No other differences were observed between dietary treatments for any parameter measured either pre stress or post stress, indicating that levels of selenium, zinc and vitamin E were probably sufficient in the control diet. Further work is needed to enhance our understanding on the interaction between, and the role of, stress and dietary micronutrients in fish health using a suite of assays to monitor all aspects of fish health, both in vitro and in vivo.

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This thesis compares two independent radiations of catfish in Lake Tanganyika, Claroteine and Synodontis catfishes, to investigate generalities in patterns and processes of diversification between radiations in an ancient “island-like” environment. The introductory chapter places this work in a theoretical context and explores previous research on taxa from Lake Tanganyika. Chapter two provides the first molecular phylogeny of species in the sub-family Claroteinae from Lake Tanganyika, including additional putative species of the genus Phyllonemus. This phylogeny is fossil calibrated to assess when diversification occurred and molecular species delimitation is also performed. Chapter three investigates geographic structure in one species from each radiation, Lophiobagrus cyclurus (from the Claroteine radiation) and Synodontis multipunctatus. Each species was sampled from multiple localities along the length of Lake Tanganyika and their DNA sequenced using restriction site associated (RAD) sequencing to produce large genomic datasets. These datasets allow the comparison of geographic patterns between taxa and, in the Lophiobagrus dataset (which also includes the closely related species L. aquilus), an investigation into the extent of introgression. Chapter four investigates niche partitioning and morphological diversification in both the claroteine and Synodontis radiations. These analyses are conducted using a single dated molecular phylogeny containing both of the radiations allowing explicit comparisons. Eco-morphological divergence is assessed using both morphological measurements thought to be ecologically relevant (e.g., size of the eye) and stable isotope ratios of both nitrogen and carbon as a proxy for niche space. While the first three chapters investigate generalities in the patterns and drivers of diversification by comparing two independent radiations in the same “island-like” environment, Chapter fives takes a different approach by placing one of the Lake Tanganyika radiations, Synodontis, in its broader phylogenetic context. In this chapter morphological diversification is investigated in the largely riverine continental radiation of Synodontis found throughout sub-Saharan Africa.