No description available.

A variety of nonspecific humoral and cellular immune-parameters were investigated in several families of farmed Atlantic salmon, Salmo salar, known to exhibit differential susceptibilities to Aeromonas salmonicida (furunculosis) in the field (fishfarm) situation. Nonspecific phagocyte functions, respiratory burst activity and leucocyte migration, were not found to be selected for in resistant families. However, nonspecific humoral factors, complement, a2-macroglobulin (aa2m) and non-a2m-antiprotease activity were found to be selected for, with resistant families possessing higher activities during challenge situations. Thus, both complement and antiprotease activity (particularly a2-macroglobulin) are regarded as potential resistance markers against furunculosis. The manner in which these factors affect the disease course of furunculosis are discussed. Antigen specific cytokine assays were developed in response to A. salmonicida antigens following vaccination against this pathogen. Antigen specific proliferation and macrophage- activating factor (MAF) production were demonstrated against A. salmonicida antigens. The potential ability to screen for differential antigen specific responsiveness as a way to assess one facet of the contributions of vaccine design and selective breeding to disease resistance were investigated. Both vaccine formulation and family origin of salmonids were found to influence in the induction and magnitude of antigen specific responses. Reasons for the observed results are discussed.

The salmon louse, Lepeophtheirus salmonis (Krøyer), is an obligate ectoparasitic copepod that lives on the external surface of salmonid fish. It is the most common parasite on cage reared Atlantic salmon (Salmo salar L.), costing the aquaculture industry in Scotland millions of pounds each year to control. Traditional methods used to control sea lice have centred on the use of chemical pesticide treatments, which are expensive, hazardous to handle, potentially deleterious to the marine environment, and are sometimes ineffective. Furthermore, the misuse use of two previously efficacious chemotherapeutants has led to a build up of resistance in sea lice populations. The aims of this study were to investigate a potential alternative control strategy, concentrating on the isolation of the naturally occurring enemies of sea lice, and evaluating their potential for use as biological control agents. A screening protocol was undertaken to examine sea lice removed from harvest size farmed fish and wild Atlantic salmon, to look for the presence of epibiotic and hyperparasitic organisms on the external surfaces of the sea lice. A screening protocol was also undertaken to look for invasive microorganisms, such as fungal pathogens, internal symbionts, and other internal hyperparasites. Sea lice were examined microscopically for the presence of external epibionts and obvious signs of internal invasion by microorganisms and parasites. Surface sterilised sea lice were incubated on growth media to screen for the presence of fungal pathogens. Fresh tissue squashes were performed on lice showing clinical signs of infection and screening / diagnostic PCRs were used to detect and identify endosymbionts and invasive pathogens and parasites. Wax histology, TEM and SEM were used to further investigate host parasite interactions in order to evaluate pathogenicity where appropriate. In vitro and in vivo challenge trials were performed with an isolated hyperparasite to effect transmission and to determine pathogenicity. The stalked suctorian ciliates Ephelota gemmipara and Ephelota gigantea, and the monogenean worm Udonella sp. were frequently found utilising L. salmonis as a substrate. High densities of Udonella were observed on the cephalothoracic shield and genital segment of adult lice, and very high densities of Ephelota spp. were found on the genital segment, abdomen, and egg strings. The prevalence and seasonal pattern of occurrence of these epibionts were assessed. Fourteen fungal isolates were obtained, but failed to sporulate in vitro culture and were hence not identifiable. No endosymbionts were detected in either the body cavity or the egg strings by using the screening and diagnostic PCRs. An hyperparasitic microsporidian was found heavily parasitising adult sea lice. The microsporidian infection arose in the epidermal cells lying beneath the cuticle, infection was not observed in other tissues. Horizontal transmission was assumed as developing eggs and egg strings were not seen to be infected. The ultrastructure and complete developmental cycle of this hyperparasite in the salmon louse were described. Specific PCR primers were designed for use as a diagnostic tool and a molecular phylogeny was constructed using rRNA gene sequences. Taking into account its taxonomic positioning, its morphology and its unique characteristics, it appears that this parasite represents both a new genus and a new species. The microsporidian was not found at all farm sites visited and was not detected in sea lice from wild caught Atlantic salmon. The microsporidian infected up to 10% of lice sampled when most prevalent, but was sometimes absent, and showed no clear seasonal pattern in its occurrence. Transmission of the microsporidian hyperparasite to uninfected sea lice was not achieved and evidence for an alternative / intermediate host for the microsporidian is presented. This is the first report of a microsporidian from sea lice, and indeed from marine copepods; it is also the first report of a hyperparasitic microsporidian in crustacea. The potential for the epibionts and endobionts found in association with sea lice to be used as biological control agents are presented.

Local and international demand for Lake Victoria’s fish has begun to outstrip supply. Production from the fishery has attained its sustainable limits, the diversity of catch has declined and subsequently employment and levels of earnings among fishers have become less secure. Under prevailing conditions, aquaculture offers the most immediate solution to augmenting fish production and sustaining earnings from the sector. It may also provide an avenue through which the diversity of aquatic resources can be increased through for example, the culture of indigenous species; in this case the African catfish (Clarias gariepinus), particularly as a polyculture species with conventional tilapia (Oreochromis) culture. To ensure that benefits be derived from the culture of C. gariepinus, an assessment of its potential as a candidate species and of appropriate production options was done within the context of fish farmers’ local socio-economic, environmental and biotechnical constraints. This was especially necessary because of the persistent poor performance of aquaculture as a farm enterprise among Ugandan farmers and the need to improve their livelihoods. Hence also, a systems approach was chosen as the basic research framework. The study was conducted in 3 of the 5 agro-ecological zones in the Lake Victoria basin, namely: the Banana Millet Cotton (BMC), Intensive Banana Coffee Lake Shore (IBC) and Western Banana Coffee Cattle (WBC) farming systems. Rapid Rural Appraisals (RRAs) were used to obtain data from a total of 104 fish farming units out of an estimated 212 in the study area. The tools used included semi-structured interviews, ranks and scores, discussions with key informants. Wealth rankings were conducted in 50 villages from which a total of 238 fish farmers were ranked. Quantitative data on farmers’ management and production was obtained from a subset of 54 fish farming units. 69 ponds were sampled. Data on the marketability of C. gariepinus for table fish was obtained from a total of 25 markets where 65 fish-sellers and 97 fish consumers were interviewed. Information on market potential of C. gariepinus as bait was obtained from 14 landing sites where 118 line fishermen and 38 dealers were interviewed. The information obtained from the RRAs provided an insight into the social, financial and human capital farmers had invested into aquaculture. It also provided information on the environmental constraints in terms of the ability to generate natural physical capital for aquaculture. The effect of the interaction of these factors on farmer’s production was analysed using Principal Component Analysis (PCA). Impact on yield was analysed with the PCA in relation to state (inputs), rate (management) and intrinsic (farmers and farm characteristics plus location) variables within the context of fish species currently farmed. The potential entry points for C. gariepinus were subsequently derived based on key constraints and marketability. Poor performance of enterprises was noted by the fact that over 50% of farmers had had no returns, either in cash or food from their ponds. In general, farmer’s management practices were adaptive rather than strategic. Key variables causing greatest variance and unstable production in current systems were found to be: (i) se d - notably stocking density, size at stocking, stocking ratios and cost (ii) frequency and regularity with which feed and fertiliser were applied (iii) pond size (iv) location within the agro-ecological zones. Though there was variance between zones, maize bran and cow dung were t e most widely used feed and fertiliser inputs in all zones respectively. It was also found that in a typical polyculture context, O. niloticus was the most marketable fish Two experiments were designed to test comparative economic returns for monoculture and polyculture based on the above findings (i) the effect of stocking density on pond yield and economic returns of O. niloticus fed maize bran in earthen ponds fertilised with cow dung (ii) the effect of varying cow dung and maize bran input levels on pond yield and economic returns in O. niloticus – C. gariepinus polyculture. The potential of farming C. gariepinus as bait was also assessed from secondary C. gariepinus hatchery information. The financial returns were assessed based on farmers’ actual local costs of production and prevailing local market prices. Results indicated that (i) farming C. gariepinus as either a table fish or bait resulted in higher yields, better returns, improved productivity and utilisation of inputs, better technical and economic efficiency compared to O. niloticus monoculture. (ii) C. gariepinus in the farming system has the potential to reduce the risk of aquaculture as a livelihood option. (iii) The farming potential and constraints were significantly agro-ecological zone-specific and also influenced by farmers’ profiles: therefore different options may be appropriate (iv) It is more important for farmers if yields were defined in shillings based on local costs rather than tonnes, as the units of exchange affecting investment and operating decisions were numbers and size.

As well as reducing the level of protein in feeds, the strategy of replacing fishmeal with alternative protein sources may be an effective approach towards reducing costs and offering more sustainable feeds for aquaculture. Within the framework of this study, four trials were conducted to evaluate the nutritional potential of selected animal by-products, namely: Poultry Meat Meal (PMM), steam Hydrolysed Feather Meal (HFM), Enzyme treated Feather Meal (EFM) and Spray Dried Haemoglobin (SDH), as pat1ial substitutes for fishmeal in the diet of gilthead sea bream. The research strategy employed followed a two phase scheme which consisted of determining ingredient restrictions in the first place and validating subsequent formulations on the biological performances of the fish in the second place. Ingredient restrictions were related to nutrient specification, digestibility and palatability, whereas biological performances of the fish were assessed in terms of growth response, feed utilization, nutrient assimilation, tissue integrity and composition as well as basic health status. Using a classical experimental design for the dete1mination of apparent digestibility coefficients (ADCs), 8 diets (made with the individual ingredients plus 3 blends) were tested in trial I. This trial demonstrated that protein and energy of PMM and SDH were highly digested by gilthead sea bream (80%) whilst protein ADC. for the feather meals were much lower (22-23%). It was moreover observed that processing feather meal with an enzymatic treatment did not yield any significant benefit over the standard steam hydrolysed method, and that combining feather meals with blood meal was clearly not advantageous. This preliminary investigation also yielded valuable numerical ADC for essential amino acids (EAA), revealing In some cases significant discrepancies with regard to the overall protein digestibility (e.g. isoleucine: 54%, and methionine: 60% in SDH). In the second trial, six iso-energetic/iso-nitrogenous diets were formulated on a protein digestibility basis to test various inclusion rates of PMM, SDH and EFM over a period of 9 weeks. In comparison to the fishmeal reference diet, results indicated that diet with a 25% replacement of fishmeal by PMM was effective in supporting the growth of gilthead sea bream (SGR: 1.78%) and conve1iing feed into body weight (FCR: 1.33) (P<0.05). Higher inclusion rates of PMM resulted in lower performance, but moderate inclusions of SDH and EFM were equally shown to be feasible without impairing fish productive values. These findings were further supported by histological and haematological assessments which provided evidence that such inclusions did not disrupt gut integrity, create anaemia conditions (P<0.05) or affect the physiological function of the liver. On the basis of trial 3 it was apparent that palatability of PMM could represent one of the main factors limiting the inclusion of this commodity in the diet for gilt head sea bream (daily feed intake/unit of time measured at 3.3g/min tor fishmeal and 2.6g/min for PMM). Finally, in accordance with the measurements of lipid inclusion in hepatocytes (trial 2) and the fatty acid analysis of the carcass (trial 4), it is believed that the high lipid content of PMM could represent further argument toward the limitation or dietary PMM incorporation as long as a high quality product is desired. From this study it is concluded that practical diets li)r gilthead sea bream would greatly benefit in terms of both nutrition and economics from adequate inclusions (considering specific ingredient restrictions) of animal by-products.

It is widely accepted that size selective mortality induced by commercial fishing can and does cause changes in life history traits that include shifts in maturation age, growth rate and body size. However, whether these changes are the result of fisheries induced evolution (genetic change) or phenotypic plasticity is still unclear. Moreover, where evolution is rapid, epigenetic or regulatory change has also been found to drive major shifts in life history change. To examine the genetic and phenotypic response to size selective harvesting, a previous study (van Wijk 2011a) subjected guppies to divergent size-specific selection. Following selection, a significant difference in both body size and age at maturation was identified as well as signatures of selection at five candidate loci. The project described here utilised these selection lines to examine the genome wide factors contributing to such life history shifts. To assess the genome wide response to size selective harvesting, RAD sequencing was employed to identify and type large numbers of SNPs in individuals from the selection lines, as well as individuals from the generation prior to selection. Significant and consistent signs of selection were identified at 37 SNPs, the majority of which were located on the sex chromosome. The results showed that, in addition to previously observed genetic change, additional regions of the guppy genome responded to, and were associated with, observed phenotypic shifts. Variation in the level of predation in wild populations creates variation in life history traits similar to those seen after size selective harvesting. We therefore examined the 37 SNPs identified by the RAD sequencing of the selected lines in 18 populations of wild guppy. No consistent signs of selection were identified in these wild populations, suggesting that the genetic architecture underpinning variation in life history traits in the guppy varies in different populations. To determine the role of epigenetic change the focus has been on DNA methylation. In order to assess the levels of DNA methylation a technique known as methylation sensitive AFLP has been used. Using this technique, comparisons of the level of DNA methylation between both the selection lines and the before and after selection fish were made as well as comparisons in the levels of DNA methylation between a range of tissue types from the guppy. Results showed that patterns of DNA methylation differ significantly between different tissues in the guppy. Genome wide patterns of genome wide methylation did not differ significantly between the selection lines, however locus-specific variation in DNA methylation was identified.

The Corydoradinae catfish are a diverse sub-family of neo-tropical catfishes (order Siluriformes) with more than 170 species described to date. One of the most compelling features of this sub-family is the enormous amount of variation in genome size. With species containing between 0.5 pg and 4.8pg of DNA, variation is comparable to that found across the Teleostei as a whole. Previous phylogenetic analysis identified nine distinct lineages within the Corydoradinae, with more basal lineages possessing smaller genomes and with largest genome sizes found in the most derived lineages. To date, nothing is known about the mechanism that drove this genome expansion in the Corydoradinae, though Whole Genome Duplication (WGD) events have been suggested. Here, the incidence of WGD events has been investigated using a Hox gene and a restriction site associated DNA (RAD) sequencing data set. Both data sets identified a major duplication event at the base of the group, with additional duplication events occurring across the family. These duplication events were shown to have led to relaxed purifying selection and increased functional divergence of HoxA13a copies in the Corydoradinae compared with teleosts that have not undergone additional rounds of WGD. The RAD data set confirmed significant genome-wide shifts in duplicate, multi-haplotype regions across the Corydoradinae, and indicates that several species from lineages 6-9 are functionally polyploid, whereas species that underwent earlier WGDs have largely diploidized and are likely paleopolyploids. An increase in paralogous genes was noted, with Gene Ontology suggesting that gene retention in the Corydoradinae mirrors previously described retention in Tetraodon following the fish-specific genome duplication in the Teleostei. Intriguingly, the RAD data also identified a significant expansion of Transposable Elements (TEs), driven by a DNA TE superfamily (Tc1-Mariner). This expansion significantly contributed to the genome size variation, though to a lesser degree than the WGD events identified within this thesis.

Farmed fish display genetic differences from wild fish in a variety of morphological, behavioural and physiological traits as a result of the domestication process and selective breeding. Farmed salmon typically outgrow wild salmon by large ratios under hatchery conditions, although observed growth differences are much less in the wild. It is possible that farmed salmon have become adapted to regulated domestic environments, while concurrently they are unable to perform as well in more variable wild environments. Escaped farmed salmon interact with wild salmon through resource competition and disease transmission, and can interbreed with wild salmon. The introduction of mal-adapted domestic genotypes into wild populations can lower their productivity. Comparative studies that assess the effects of hybridisation on life-history traits linked to fitness are important in understanding how interbreeding will affect the resilience of wild populations. The present thesis investigated the freshwater growth and survival of multiple families derived from various farmed, wild and F1 hybrid salmon populations when reared at contrasting (1) temperatures, (2) densities and rearing conditions, (3) food availabilities, and (4) diets. In all experiments farmed salmon outgrew wild and hybrid salmon, and their hybrids displayed intermediate growth. Relative growth differences detected at contrasting temperatures were population-specific; indicating that the competitive balance between conspecifics may depend upon genetic background and river temperature. Findings highlight the merits of adopting a more spatially resolved approach to risk management of wild populations. In all other experiments the relative growth differences among groups did not differ across treatments, indicating that farmed fish have retained their plasticity in response to respective experimental treatments. Although experiments were conducted under controlled conditions, findings suggest that the investigated treatments are not individually responsible for elevated growth differences observed in hatchery conditions or the lower growth differences observed between farmed and wild salmon in the wild.

Overfishing on coral reefs is a key threat to the structure, function and resilience of coral reefs and the well-being of dependent human populations. Despite their global socio-economic importance and biodiversity value, knowledge of sustainable management of coral reef fisheries remains poor. I use an interdisciplinary approach to explore the consequences of exploitation of reef fisheries by integrating global-scale island nation landings statistics with local-scale social knowledge. Globally, catches of reef fishes on islands varied considerably, and increased with human population density. High-yielding fisheries were sustained by greater proportions of lower trophic level taxa, had overexploited fisheries exploitation status, and tended to be found within the Indian and Atlantic Oceans. Islands with overexploited fisheries tended to be larger, with smaller reef area: land area ratios, greater dependence on reef resources, and higher levels of socioeconomic development (GDP). Conversely, sparsely-populated Pacific islands were underexploited with larger reef area: land area ratios and lower levels of GDP. Maximum sustainable yield for island coral reef fisheries was estimated using surplus production methods, and ranged from ~8.2-22.7 mt●km-2●yr-1, depending on the exploitation status of islands incorporated into the models. Results suggest yields > ~8mt●km-2●yr-1 may lead to overexploitation, highlighting the need to set conservative targets for their sustainable use. In contrast to global-scale spatial analyses, local social knowledge of fishers on the island of Anguilla revealed temporal declines in reef catches in recent decades, despite Anguillian reef fisheries being described as underexploited. This suggests that official landings statistics are highly conservative and highlights the importance of fisheries- independent information in understanding local-scale resource use and management on coral reefs. Sustaining reef fisheries for future generations requires an interdisciplinary approach combining ecological and societal knowledge that seeks to address the multiple underlying causes of reef degradation.

No description available.