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Although the impacts of surface water acidification on Atlantic salmon (<italic>Salmo salar</italic> L.) and brown trout (<italic>Salmo trutta</italic> L.) are well described, factors affecting recovery following pollution abatement are poorly understood. Paradoxically, despite increasing average pH over the last two decades, stocking efforts to rehabilitate damaged populations have not been successful. One possible explanation is that average pH measurements mask the effects of episodic fluctuations during high flow when pH is transiently reduced, metal concentrations are elevated and some organisms are affected adversely. However, because salmonid fish (i) avoid acid water and (ii) shelter within stream bed interstices, assessing the effects of acid episodes on their populations requires some understanding of how refuge use, refuge availability and refuge conditions affect recolonisation opportunities. This project therefore examined the effects of acid episodes on the behaviour of Atlantic salmon at different life stages as a possible explanation for the limited recovery of re-stocked populations. Sampling in acid sensitive-streams at low and high (episodic) flow revealed that the stream hyporheos was less acid than surface water in the same streams, with temperature and conductivity also more favourable in interstices. Laboratory experiments were then used to examine (i) the behaviour of Atlantic salmon alevins during a simulated episode in a vertical substrate-filled tank (Chapter 3) (ii) the behaviour of Atlantic salmon parr during a simulated episode in a shelter choice tank (Chapter 4) and (iii) if differences resulting from rearing environment affected the behaviour of Atlantic salmon parr during a simulated acid episode (Chapter 5). Hatchery-reared alevins avoided episodically acid conditions by moving into an area of more neutral pH opercular rate and mortality were both greater in acid water. Hatchery-reared pan- preferentially used a neutral shelter acid exposure also resulted in increased activity and opercular rate. Fish reared in a simulated wild environment were better able to avoid acid pulses (i.e. they showed greater use of neutral refuges) than hatchery-reared fish, but other behavioural responses (activity and opercular rate) were similar. These results illustrate the potential importance of the streambed during acid episodes as chemical refuges to salmonids, which both alevins and parr are able to exploit. However, at least for hatchery-reared fish, the success of re-stocking programmes could be improved by subjecting fish to acid stress- conditioning regimes prior to release.

Nutrients are essential in order that living matter can grow and reproduce successfully, and of particular importance are carbon (C), nitrogen (N) and phosphorus (P) (Stockner and Ashley 2003). C and N have a gas phase and are often readily available in freshwater ecosystems. P, however, does not have a gas phase, cannot be renewed and as such is often regarded as the element in shortest supply in most freshwater environments (Stockner and Ashley 2003). It should be noted, though, that other nutrients, for example silica, are also often of importance in freshwater ecosystems and that nutrients can be co-limiting in terms of primary production (Toetz 1999).

Freshwaters represent some of the most degraded ecosystems in the world, with approximately 56% of the European rivers being sufficiently altered by human activities to modify the composition of their biological communities. River fish communities are often used to indicate this altered status due to their ecological, recreational and economic value. In lowland rivers, habitat alterations include impoundments and activities such as channel straightening, impacting aspects of fish behaviour and lifecycle completion. Species such as European barbel B. barbus are particularly affected due to their propensity for long-distance migrations and requirements of high quality gravels for spawning. Consequently, B. barbus populations throughout Europe are increasingly threatened. Barbus barbus is indigenous to eastern flowing rivers in England, including the River Great Ouse that has been historically subjected to multiple alterations in channel morphology for flood defence and impoundments for land drainage. The river’s B. barbus population is now restricted to the upper reaches where they represent a key resource for angling, yet temporal and spatial data on their populations suggest relatively low abundances in recent years. Over the last 30 years, the regulatory authority responsible for their management (Environment Agency) have managed the population through a combination of enhancement stocking using hatchery-reared fish and habitat improvement schemes, especially gravel jetting of spawning substrates. There is, however, little knowledge on the effectiveness of these. Consequently, this research investigates B. barbus in rivers in England generally and the Great Ouse specifically by assessing the efficacy of stocking and habitat works to enhance populations. The initial research has focused on using scales from historical surveys on the fish communities of three rivers (including the Great Ouse) to determine the trophic relationships of the fishes using stable isotope analysis. Outputs indicated that scales can be used for this analysis and revealed that rather than sharing food resources with functionally similar species such as chub Squalius cephalus, B. barbus occupied distinct isotopic (trophic) space. Their diet was then assessed using stable isotope analysis on B. barbus scales from four English rivers to determine their major food resources. Results indicated that angling heavily modified B. barbus diet, with introduced bait (as pelletized fishmeal) being the most important dietary component. The next phase of the research built of these outputs of both these studies and assessed the impact and efficacy of enhancement stocking of hatchery-reared B. barbus. In both semi-controlled and wild conditions, analyses suggested that enhancement stocking with B. barbus has minimal detrimental consequences for other fishes such as S. cephalus, with strong patterns of trophic niche partitioning. Nevertheless, the efficacy of enhancement stocking might be limited, with low numbers of recaptured stocked B. barbus recorded in the study, with a concomitant genetic study revealing negligible introgression of stocked B. barbus genes into the population, despite the stocking activities. Given that enhancement stocking has been of limited success to improve B. barbus population abundance in the Great Ouse catchment, their spawning habitats were assessed in the river, including whether the physicochemical properties of the sediments and hyporhic water were limiting. Whilst results indicated good quality of hyporehic water, the subsurface sediment was high in fine content, particularly sand. Gravel jetting, a method to clear spawning gravels of fine content, was shown to only provide short term benefits (e.g. 3 months) in reducing this content of fines, with this benefit only apparent in surface sediments and not in the subsurface. An ex-situ experiment to assess the tolerance of B. barbus eggs and larvae to sand content in spawning substrata indicated no effect of high sand content on egg to emergence survival rates, but it did significantly decrease the timing of larval emergence from gravels. This early emergence of B. barbus larvae from substrates with high sand content could potentially impact their subsequent survival in the wild. Thus, the current management strategies employed in the River Great Ouse to enhance the B. barbus populations appear to have limited success, largely failing to meet their objectives. Thus, more holistic management approaches are outlined and suggested for implementation.

The European eel, Anguilla anguilla, is designated a threatened species and parasites are considered to be one of the contributory factors associated with the species decline. To address the lack of knowledge concerning parasite infections in the UK European eel population, a total of 140 specimens were obtained from the Environment Agency at 14 river sites across England and Wales. Each specimen was dissected and infection status determined for the different classes of helminth using a combination of morphological and molecular approaches, including a PCR-based restriction digestion approach to discriminate between the gill monogeneans Pseudodactylogyrus anguillae and P. bini. Overall, 101 eels (72.1 %) were infected with a total of 1504 helminths and these included gill monogeneans (prevalence = 35.7%), gastrointestinal nematodes (prevalence = 33.6%), the swim bladder nematode Anguillicoloides crassus (prevalence = 25.0%), acanthocephalans (prevalence = 30.0%) and cestodes (prevalence = 9.3%). Seven identified helminth species; the pathogenic pseudodactylids P. anguillae and P. bini, the pathogenic swim bladder nematode A. crassus, the gastrointestinal nematodes Spinitectus inermis and Paraquimperia tenerrima, and the tapeworms Proteocephalus macrocephalus and Bothriocephalus claviceps, are known eel specialists. A further 4 non-specialist eel helminths; the acanthocephalans Acanthocephalus clavula, A. lucii and the category 2 parasite Pomphorhynchus laevis, plus the gastrointestinal nematode Raphidascaris acus, were also identified. Helminth infection appeared to have a significant association with the larger eels and this was particularly evident for infections involving acanthocephalans. This presumably reflects the age and hence prolonged exposure to infection risk, as well as a more diverse diet of the larger, compared to the smaller, eels. Interestingly, the condition factor of the eels infected with helminths was also significantly greater than that of the uninfected eels. Helminth co-infections were commonly observed (54.5% of the infected eels) and the majority of these co-infections (75%) involved one, or both, of the pathogenic A. crassus and pseudodactylids. With regard to catchment sites, interesting differences were noted in the primary helminth infection data. Eel specimens analysed from the rivers in South East England contained the most numerous and diverse range of helminths. Indeed, helminth prevalence was 100% and co-infections, including up to 5 taxa, were common; pseudodactylids and acanthocephalans were present in all the observed co-infections. Eels sampled from rivers in North West England also contained a rich diversity of helminths and although pseudodactytlids were common, the gastrointestinal nematodes were the dominant taxa observed in co-infections. A. crassus and the pseudodactylids were the dominant helminths in co-infected eels sampled from South Wales and interestingly, even though this region had the second highest helminth prevalence, tapeworm infections were not observed. Only 50% of eels sampled from North Wales were infected with helminths; specifically, acanthocephalans and A. crassus were not observed in eels from this region and gastrointestinal nematodes were present in all the co-infections. Taken together, the data in this thesis confirms that European eels in the UK are commonly infected with a plethora of helminths. Some of the eel specimens exhibited known pathologies associated with their infections. However, the precise impacts that these helminths have upon eel health, and importantly the migratory capacity of the host, remain unknown and are worthy of further investigation.

Bitterling fishes lay their eggs on the gills of living freshwater mussels and are valuable models in behavioural and evolutionary ecology. To develop a fuller understanding of the coevolutionary relationship between European bitterling and mussels an aim of this study was to conduct a phylogenetic reconstruction of the colonisation of Europe by bitterling, and to resolve the taxonomic question of whether eastern and western populations of bitterling represent the same species using genetic and traditional morphological/meristic methods. A second aim was to obtain a better understanding of the life-history parameters of R. amarus in Europe, including larval growth parameters. Previous studies have suggested the European bitterling is either a single species with a wide but discontinuous geographic distribution, or a complex of species. Morphometric and meristic data identified differences between three putative species; with a clear distinction between the eastern Asian Rhodeus sericeus sensu stricto, western European bitterling R. amarus and colchian bitterling, R. colchicus. Polymorphism in the mitochondrial DNA control region was predominantly due to insertion/deletion events, making phylogenetic inference difficult. Cytochrome b data produced a phylogeny with strongly-supported differentiation between a clade of two R. sericeus haplotypes and a clade of six R. amarus/colchicus haplotypes. The starlike topology of the R. amarus/colchicus haplotypes in a minimum spanning network suggested a rapid radiation in this clade. The results are consistent with an hypothesis of relatively ancient divergence of R. sericeus from R. amarus/colchicus and more recent and rapid differentiation between R. amarus and R. colchicus. Analysis of otolith microstructure demonstrated a relationship between mussel availability for spawning and length of spawning season. In addition, these data strongly suggest the onset of exogenous feeding by larval R. amarus while still in their mussel host.

The focal species of the research was the freshwater cyprinid fish Garra ghorensis. Endemic to the southern Dead Sea basin of the Middle East, it is ‘Red listed’ by the IUCN as ‘endangered’. It inhabits the small rivers of the basin (‘wadis’), existing within fish communities of very low species diversity. The aim of the research was to inform conservation strategies for the species through investigations into their phylogeny, current distribution, life history traits and feeding relationships. Analysis of the mitochondrial DNA of G. ghorensis with other fishes of the Garra genus tested two contrasting hypotheses on their biogeographic origin: whether they were descended from Garra tibancia in the Arabian Peninsula or from a common ancestor shared with Garra rufa, which would have indicated dispersal from the Mediterranean basin and Mesopotamia. The phylogenetic tree clearly indicated that G. ghorensis shared a common ancestor with G. rufa and thus was of Mediterranean origin. These phylogenetic analyses were then important for interpreting G. ghorensis biogeography in relation to their natural range and current distribution. Surveys completed in 2010 provided data on their spatial distribution; this distribution was at least partially explained by historical geological and water salinity changes of the proto-lakes of Lake Samra and Lisan. These surveys also revealed that during the 2000s, there had been little change in G. ghorensis distribution, with populations still present in wadis that were recorded in 2002. However, at the surveyed sites, some alterations to the physical habitats and hydrology of the wadis were apparent, such as construction of impoundments. To assess the life history traits and feeding relationships of G. ghorensis, three locally abundant populations were studied. These were an allopatric population, a population sympatric with the native cyprinid Capoeta damascina and a population sympatric with the invasive cichlid Oreochromis aureus. The allopatric and sympatric native populations were present in wadis with minimal habitat disturbance, whereas the sympatric invasive population was present in a wadi with substantial alteration, including some impoundments that deepened the main channel and reduced the flow. Analyses of ages, growth rates and reproductive traits revealed that life spans, growth rates and reproductive investment were greatest at this disturbed site, despite being relatively altered from the apparently preferred habitat of the species. These results suggested that providing the hydrological disturbance at sites where G. ghorensis is present still enables the completion of their life cycle then their populations can withstand some aspects of habitat disturbances from anthropogenic activities. The feeding relationships of G. ghorensis were then assessed in relation to the presence of C. damascina and O. aureus in two of the sites, and used a combination of stomach contents analyses and stable isotope analysis. Results from both methods revealed whilst there were some overlaps in the trophic niches of the fishes, diets were based mainly on detritus and algae. These items are rarely limiting in freshwaters and thus whilst resources were shared, it was unlikely to result in high levels of inter-specific competition. Thus, an important ecological feature of G. ghorensis populations is their plasticity in life history traits and their resource use that enables some adaptation to disturbed environments. This suggests that their conservation management does not necessarily have to return their habitats to pristine conditions, as their adaptive capacity should enable some adaptation to the new conditions and thus continued population sustainability. Consequently, providing that development schemes prevent the destruction of the key habitats required for the completion of the G. ghorensis lifecycle, then their populations could remain sustainable in the face of continued development in the region.

The diversity of fields covered by this thesis is most apparent in Chapter 1, which gives an overview of the underlying philosophy and present level of understanding of the research. The role of modelling in science and the capabilities of different types of model are discussed. The academic sub-disciplines within which this thesis may be categorised are defined. The ecology of tunas is described as are satellite sensors that have been or could be used for fisheries applications. Case studies of such applications are reviewed. For Chapter 2, I analysed a large data set from the New Zealand surface longline fisheries for tuna, in order to identify whether and at what spatial scales tunas are aggregated. I applied methods that have not previously been used in the analysis of longline data and determine that these adult tunas are often caught in loose schools within a larger, sub-mesoscale area in which they are aggregated. In Chapter 3, I review present knowledge in tuna physiology and sensory biology, and develop and apply analytical models to determine reaction distances. This was an essential pre-cursor to the development of theoretical models in Chapters 4 and 5. The optimal foraging model had been previously anticipated in the literature but had not previously been realised. It provides a framework for addressing a long-standing and still unresolved debate as to what is 'controlling' tuna behaviour at ocean fronts. In Chapter 5, I describe and apply an important methodological synthesis for fisheries oceanography. While still requiring further development, this work nonetheless proves that it is possible to combine behavioural models for fish with whole-ocean circulation and production models that incorporate data from satellite sensors. Chapter 6 discusses further work that might follow from this thesis. Successful proposals have been made to the European Space Agency and the New Zealand Foundation for Research Science and Technology, which may now build on the work carried out here. I strongly advocate that further work to develop models linking fish distributions with environmental properties should include sea-going studies of pelagic trophic dynamics in specific areas of interest.

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