Studies of the phenotypes of animals at different parts of their geographic range often reveal striking variability. It is of considerable fundamental and applied interest to discover the extent to which such variation depends on genetic as opposed to environmental differences. A first step towards disentangling these effects is to use an empirical approach known as the common environment method in which wild-caught juveniles from different regions are reared under common laboratory conditions. I used this approach to determine the population and thermal responses of Atlantic cod, a species with a wide distribution and geographic variation in life history traits. Life history traits were investigated in cod from three areas around the British Isles of differing thermal regimes, namely St Andrews Bay on the Scottish east coast, the Clyde Sea on the Scottish west coast, and from near Lowestoft in the southern North Sea. Concurrently haemoglobin genotype and behaviour were also studied. Spatially significant differences in life history traits and thermal responses were revealed in juvenile and adult growth rate, gonadal investment and behaviour, suggestive of population differentiation. Behavioural differences between cod of differing haemoglobin genotypes were also demonstrated. Results suggested that juvenile growth rates may be modified by competitive interactions. At a group level, growth rate of cod from the Clyde Sea was suppressed in the presence of cod from St Andrews Bay. Pairwise trials demonstrated that cod from the Clyde Sea consumed a higher prey share than those from St Andrews Bay but that those from St Andrews Bay were more aggressive and thus could potentially restrict feeding of cod from the Clyde Sea, resulting in a reduced growth rate. There were no population differences in the distribution of haemoglobin genotype, but haemoglobin genotype did have a strong influence on behaviour in pairwise contests. Cod of the HbI-2*2 genotype displayed a higher level of aggression than other genotypes and this effect was stronger than the population difference. Juvenile cod from the Clyde Sea exhibited a growth rate 24 % higher than those from St Andrews Bay. Cod from the Clyde Sea and from Lowestoft expressed higher growth rates as adults than those from St Andrews Bay. Body size and thus growth appeared to be the main driver of fecundity in the females and body size and liver were the main influences on gonadosomatic index (GSI) in the males. Females from the Clyde Sea invested more into fecundity than those from St Andrews Bay and males from St Andrews Bay had a higher testis investment than those from the Clyde Sea and Lowestoft. Temperature had a large influence on both the juvenile growth and egg development. Growth rate increased linearly and in parallel over the experimental temperatures, within their normal range. Egg development was strongly affected by temperature, resulting in a decrease in hatch time and an increase in embryonic cardiac rate, and a smaller larval size at hatch for a given temperature at higher temperatures. Temperature did not directly influence fecundity or GSI in males but warmer temperatures resulted in higher growth rates and thus a larger body size, which in turn resulted in a greater fecundity or GSI. These differences in life history traits, demonstrated under controlled environment conditions, raises the possibility that there may be a genetic basis to the variation and that cod may be locally adapted to their thermal environments in areas around the British Isles. However, effects of environmental differences prior to capture, including maternal effects, cannot be ruled out. This greater understanding of life history variation in cod will be important in the conservation of phenotypic diversity, vital for the long-term persistence of the species, while the findings of plasticity in response to temperature will enhance predictions of responses to sea temperature rise.

Marine Protected Areas (MPAs) have been suggested as one of the solutions to coral reef fisheries management. It is thought that their effects on biomass, species diversity and habitat could improve surrounding fisheries yields through fish migration and increased recruitment. However, MPAs' benefits on surrounding fisheries are difficult to establish due to the lack of historical data. Furthermore, the lack of involvement of stakeholders have led to a number of failures. MPAs in the form of No Take Zones (NTZ), which aim to promote the sustainable use of fisheries resources, might contribute to the successful management of coral reef fisheries. However, few studies have considered their benefits from the point of view of surrounding fishing communities. It is evident that if stakeholders are to be further involved in MPA management, they need to perceive the benefits. The hypothesis tested was that if NTZs are of benefit to surrounding communities, their food security situation would be improved. The fieldwork was carried out in Southern Kenya with five fishing communities located around a long established MPA. The study showed that a range of food security indicators gave good information on MPAs' benefits to the surrounding communities. It was found that these benefits were highly affected by distances. Thus, although fishing households were the least food secure, they were better off if they fished nearer the protected reefs. Households dependent on MPA-related tourism were the most food secure but this dependency decreased with the communities' distance from the main tour operators. The results showed that MPAs' benefits were not equally shared by the communities bearing most of the costs. In addition, it was also found that tourism seasonality does not always compensate for the seasonality of other activities. Furthermore, tourism could not be assumed to develop around MPAs and provide reliable alternative employment.

The thesis examines the possible causes of decline of Spartina anglica marshes along the south coast of Britain with emphasis on the Solent marshes. The study shows that although there may be some genotypic differences between S. anglica gathered from sites in Britain. The disparities are not large enough to explain the significant differences in morphological vigour of S. anglica observed in the field. It concludes that the discrepancies observed in the field are the result of phenotypic differences resulting from environmental factors. The work shows that in the S. anglica marshes of the south coast, anaerobic soil conditions prevail with impeded drainage being the most likely cause of the dwarf growth forms and lack of re-colonisation of pans and mudflats observed in the field. The thesis concludes that the ultimate demise of the S. anglica marshes of the south coast of England is the result of frontal and creek erosion of the mature marsh and the failure of S. anglica to establish itself on the newly exposed sediments of the foreshore. When S. anglica establishes itself in a flood /ebb neutral zone of an estuary, it changes the bathymetry to that of ebb dominant morphology. As a result eroded sediment is swept away with the outgoing tide. Furthermore, S. anglica is then unable to recolonise the exposed foreshore sediments because of its low redox potential resulting from poor permeability which is the consequence of the of historic overburden pressure of a once colonising marsh.

Poor salmonid spawning habitat due to excessive fine sediment inputs has been identified as a major factor limiting survival in chalk rivers. A lack of knowledge about the complex processes and factors affecting survival was the driver for this study and gaps in the research were identified concerning the sources of fine sediment and the impact organic material had on salmonid survival in chalk streams. Consequently the main objectives of this study were to characterise spawning habitat quality of a chalk catchment, assess the sources of sediments accumulating within artificial redds, describe the composition of organic sediments using emerging technology and to create a novel method to assess the sediment oxygen consumption of those sediments. Methods were based around a catchment wide field based monitoring programme, consisting of artificially constructed spawning gravels which allowed hyporheic measurements to be taken, and sediment analysis and sediment oxygen consumption methods were carried out using different laboratory methods. Spawning habitat characteristics of the chalk catchment were found to exhibit; low sediment accumulation rates although original levels of fine sediment were high, high organic matter content, variable intra-gravel flow and intra-gravel oxygen concentrations and groundwater influences. Primary sources of fine sediment accumulating in spawning gravels and suspended sediments were found to be attributed to catchment surface sources, namely pasture (50-68%) and arable (32-50%) using inorganic and organic parameters. Organic composition of redd gravels was found to be dominated by protein material rather than humic substances, the more commonly found fluorescent compound in freshwater systems and the sediment oxygen consumption of sediments varied throughout the catchment and was found to consume the greatest oxygen in <63μm size fraction. Application of sediment oxygen consumption rates to existing parameter based models that predict salmonid survival, highlighted the need to address the sensitivity of current models to rivers experiencing low sediment accumulation rates. Outcomes of this study further the knowledge of the sources, organic composition and sediment oxygen consumption capacity of fine sediments accumulating in spawning gravels which can lead to appropriate mitigation on chalk rivers to improve salmonid spawning habitat.

Anthropogenic use of waterways is reducing connectivity at a rate faster than any time in geological history, sometimes causing serious declines in fish populations. Free passage of fish throughout the watercourse is necessary for species utilising different habitats for e.g. residing, spawning and feeding. Fish passes are employed to mitigate for impoundments, but are historically biased in design towards upstream migrating salmonids. Driven partly by more holistic environmental legislation, there is now an increasing interest in other species and life-stages, requiring development of fish passage criteria for multiple species during up- and down-stream migrations. To address these knowledge gaps this research programme undertook laboratory experiments with upstream migrant river lamprey, Lampetra fluviatilis, and downstream migrating European eel, Anguilla anguilla, and brown trout, Salmo trutta. The use of a large open-channel flume allowed control of the motivational state of, and stimuli encountered by the fish. The fish responses to a variety of model weirs and screens placed in the flume were assessed, allowing attainment of species and life-stage specific swimming capability and behavioural information. This research demonstrated that using large flumes where volitional swimming allows natural compensatory behaviours to be undertaken, provides more realistic swimming capability information for fish pass criteria than some traditional methods (i.e. confined swim chambers). Dependent on species and direction of movement, all structures tested had some level of impediment to migration, with small gauging weirs almost completely impeding movement of upstream migrant river lamprey under the conditions presented. Downstream migrant anguilliforms were seen to demonstrate structure oriented, thigmotactic behaviour compared to salmonids which responded to flow fields. Under high velocities, this lack of reaction to hydraulic cues may result in a higher probability of damage and mortality at facilities traditionally designed to protect salmonids. The information provided by this research, e.g. accurate swimming speeds and fish response to associated hydraulic conditions, will aid the production of effective multi-species fish pass facilities

No description available.

The 1995 UNFSA creates a door for fishing entities’ participation in conservation and management regimes regarding straddling and highly migratory fish stocks through separate RFMOs. However, fishing entities are different from states, leading to some ambiguous circumstances in RFMOs, especially in high seas enforcements. This thesis reviews the concepts of fishing entities and considers fishing entities’ status in international law of the sea and the RFMOs. Then, it considers the role of fishing entity enforcement in high seas with being equivalent to a flag state and non-flag state. This thesis then considers the problems that fishing entities may encounter in high seas enforcement. Finally, it represents the practices of fishing entity enforcement in high seas with a special reference to the role of Taiwan in RFMOs.

This thesis examined novel and previously utilised parameters of egg quality to determine and define reproductive success in farmed and wild salmonids. The effect of holding environment and inter-female variation on salmonid egg quality was also examined. Furthermore, two nutritional feed trials were undertaken to investigate whether organic Se, supplemented into salmonids broodstock diets, was vertically transferred to their eggs and what affect this dietary supplementation had on egg quality. Finally, the possibility that morphological and biochemical adaptations are present on the chorion of eggs from European whitefish (Coregonus lavaretus) was investigated in a resident Scottish population. Chapter 2 examined methods to determine egg quality using eggs from a single population of brown trout (Salmo trutta). Egg survival, provided a biologically relevant definition for egg quality, which was used throughout this study to assess the importance of selected egg quality parameters. Based on a review of the literature and the relationship between parameters of egg quality and egg survival rates, three determinants of egg quality were chosen for further examination. These were chorion breaking strength, elemental concentrations within the egg and the protein profile of the chorion. Brown trout broodstock from a single population were separated prior to spawning and exposed to two different holding units, ‘Ae system’ or ‘S.C.E.N.E. system’ at two sites. Eggs were stripped from females and 13 determinants of egg quality collected, analysed individually, combined by principle components analysis into an integrated egg quality score which was validated against egg survival. The multivariate egg quality score differed significantly between fish held in the Ae and S.C.E.N.E. systems. Egg survival, chorion breaking strength and Se chorion concentrations were higher in eggs produced by broodstock held in the S.C.E.N.E. system compared to those in the Ae system. Alternatively, chorion concentrations of P and K were higher in eggs from fish held in the raceway system. This data highlights the complex interactions between the holding environment and pre-ovulating fish and resultant egg quality. The variation in egg survival in individual Atlantic salmon (Salmo salar) reared in the same environment was assessed and used to examine the suitability of chorion measurements as parameters of egg quality. There was a significant difference in the egg survival rates between individual salmon. Results also show that there was also variation in egg survival, chorion breaking strength, chorion elemental concentrations and chorion protein concentrations and profiles between individual Atlantic salmon. Subsequent analysis of the data showed that there was no difference in these egg quality parameters between high and low egg survival rates. Furthermore, there was no correlation between egg survival and the chorion quality parameters recorded during this study. The results show that individual variation between fish is an important factor affecting egg quality. Broodstock Atlantic salmon were fed a standard commercial diet, with or without the addition of a supplemented nutritional mix, which included 0.5mg/kg of Sel-plex (organic Se). The Se content of the eggs and livers of each fish were assessed as was egg survival rates and proteomic analysis of the egg chorion. Concentrations of Se in the eggs of the individuals fed the supplemented diet were significantly higher than those fed the non-supplemented diet. However, the egg survival rate was also significantly lower in the supplemented group of fish. The assessment of the chorion protein profile and its proteomic structure was inconclusive. These results support the hypothesis that dietary selenium is vertically transferred to immature eggs during oocyte development. The lack of a linear relationship between Se egg concentrations and egg survival suggests that the lower survival rates of eggs from broodstock fed the supplemented diet in this trial was due to another nutritional component of the diet rather than the Se. Selenium enriched eggs from Atlantic salmon fed a supplemented diet and eggs from conspecifics fed a non-supplemented diet were tested for their ability to resist infection by Saprolegnia under incubation conditions similar to those used by the aquaculture industry. There was no significant difference in the presence/absence of infection, infection rate or survival between eggs produced by Atlantic salmon fed the supplemented and non-supplemented diet. Therefore, it was concluded that supplementation of broodstock diet does not alter the resistance of eggs to Saprolegnia. The presence of adhesive mechanisms on the surface of European whitefish eggs was examined from a population found within Loch Eck, Scotland. European whitefish eggs remain non-adhesive in a solution chemically similar to ovarian fluid, but become adhesive seconds after contact with water. Examination of the ultrastructure of the chorion showed that the morphology altered significantly after contact with water with nodule-like protuberances attached to connective filaments on the surface, present in water hardened but not non-water hardened eggs. Biochemical analysis also showed the presence of Chain A, RNase ZF-3e in the chorion of water hardened but not non water hardened eggs. Histochemical staining of the chorion showed that the externa, but not the interna stained positively for the presence of glycoproteins. Egg adhesive mechanisms allow European whitefish eggs to remain in optimal spawning grounds where factors such as mechanical damage, predation, desiccation and hypoxia are minimised.

The primary purpose of the dissertation is to quantify the efficiency and operation of various types of fish passes for dams. This is achieved through a novel experiment of testing juvenile salmon in a scale model fish-passes with a range of small structures including vertical slots, orifices, weirs and combinations of all three. Direct comparisons of the efficiency of each type of fish pass in terms of upstream migration. Two identical physical models were constructed, one at the Fisheries Research Services Freshwater Laboratory at Almondbank, Perth, Scotland where observations were made of fish behaviour. The other model at the University of Glasgow, Glasgow tested only hydraulic conditions. The physical models were simplified representations of a reach of a river downstream of a dam, weir or any other obstruction to fish migration. A removable cross wall incorporating one of the types of pass tested divided the flume into two pools. A significantly higher proportion of fish moved through submerged orifices or vertical slots than through weirs for a given flow rate and velocity. The orifice and vertical slot passing efficiencies are directly correlated to the velocities existing in their vicinity. To reach the weir/slot/orifice devices, salmon parr tended also to stay near the bottom of the flume and followed a path along the sides of the arena, which provided them with low velocities and cover. In the vicinity of the weir/orifice/slot devices, the movements of salmon parr were consistent with energy-conserving strategies. Clearly, the extrapolations of results from the behaviour of small to large salmon remains cautious, the intention of this research being to characterise the behaviour of small salmon and to develop clear testable hypotheses about how large salmon may respond to water flow. Preliminary field tests were then conducted at Tongland Dam fish pass to test the main recommendation extrapolated from the parr behavioural study. The particular situation of this fish pass, which contains both weirs and orifices, allows a comparison between the two. Passive Integrated Transponder (PIT) tags together with antennae installed at a weir and an orifice were used to individually monitor the movement of wild spawning salmon passing through the fish pass. The results of the field test are as yet, inconclusive.

In 2005, Atlantic salmon (Salmo salar L.) migrating to the United Kingdom exhibited swollen, haemorrhagic vents, symptoms not previously recorded. The condition was latterly termed Red Vent Syndrome (RVS), and subsequently observed across the North Atlantic. RVS has been pathognomonically associated with one of the most abundant parasites within the marine environment, the ascaridoid nematode Anisakis simplex, which also causes Anisakiasis in humans. Although A. simplex is commonly found in Atlantic salmon, heavy infestation of the vent region is novel, and the expression of RVS has not been prevalent in other fish species. Red Vent Syndrome has been well studied, however, the causes of the condition, and the reasons driving the novel site of infestation exhibited by A. simplex, have not been clarified. The aim of this PhD therefore, is to provide new information regarding the underlying factors of the infestation of the vent region by A. simplex, and the emergence of RVS. This study therefore: i) assessed the relationship between nematode burdens within the viscera and musculature, in comparison to the vent in 117 adult Atlantic salmon; ii) compared the genetic structure of A. simplex present in the vent region and the viscera using the entire nuclear internal transcribed spacer (ITS) region; iii) investigated migratory route and feeding ground of Scottish salmon populations using stable isotope analysis of dorsal muscle tissue and parasite component communities and, iv) assessed the expression of the cytokine TNF-α1 within vent muscle tissue using (q)RT-PCR, in relation to RVS severity. Phylogenetic analyses have shown that it is A. simplex sensu stricto infesting the vent region. The results show that there is a significant positive relationship between the nematodue burden in the body (viscera and musculature) and in the vent region. Isotopic signatures of salmon populations showed no significant differences, however, A. simplex intensities between populations on the East and North coasts of Scotland suggest geographical differences in A. simplex transmission pathways. Finally, the expression of TNF-α1 is not significantly different between RVS severity, and nematode burden. Out of the four studied factors, increasing nematode intensities in Atlantic salmon populations, and the significant positive relationship of nematode intensities between the body (viscera and musculature) and the vent, are likely to explain the infestation of the vent by A. simplex. The underlying causes of RVS however remain uncertain and require further research. With incidences of RVS observed across a number of populations over a large spatial area, regional and global effectors such as warming sea surface temperatures, and the North Atlantic Oscillation are expected to play key roles in its aetiology.