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Climate change is leading to higher temperatures and altered rainfall patterns across Europe. These changes are likely to have major impacts on plant life. This is particularly relevant for livestock production systems which are dependent on grass and forage. Farmers need to know what they can expect in the future so that they can be well prepared and ensure that their livestock will have enough to eat. This thesis aims to quantify the impacts of rising atmospheric CO2 concentrations, higher temperatures and changes in water availability on the yield and protein content of European grasslands. The first approach used was a meta-analysis. Data from experiments in which the climate had been artificially altered was collected and divided according to geographic region (Alpine, Atlantic, continental, northern and southern) and plant type (graminoids, legumes, forbs and shrubs). Using Markov Chain Monte Carlo (MCMC) simulations, mixed models were developed to estimate the expected changes to plant yield and protein (i.e. nitrogen (N)) concentration under different climatic changes. The results showed that areas predicted to become warmer and wetter (i.e. northern Europe and parts of Alpine and continental Europe) will benefit from higher plant yields, but reduced plant N concentration. Areas which will become warmer and drier (i.e. southern Europe and parts of continental Europe) will see decreases in both yield and N concentration. The Atlantic region is the area where climate change is expected to be the least extreme and the effects on plant life will be relatively minor. Shrubs will particularly benefit from rising atmospheric CO2 concentrations, though will also suffer large decreases in N concentration, as will forbs. The next approach considered different methodologies for modelling grassland yield and N yield. One method involved developing a statistical model using data from long-term grassland experiments across Europe. Through stepwise linear regression, equations were developed to model grassland yield and N yield based on various weather and managerial variables. The other method used a pre-existing process-based model (Century), which was applied to six sites across Europe. Both approaches produced reasonable estimates of grassland yield and N yield. The prediction error was lower for the Century model while the regression methodology produced better correlations between observations and predictions. Both models were quite sensitive to uncertainties in weather parameters, particularly precipitation, with little sensitivity to soil properties. Overall, the regression approach was found to be suitable for considering general trends over large spatial scales, while the Century model was more appropriate for local-scale analysis. The two models described above were used to quantify the effects of two different climate change scenarios (one midrange and one more extreme) on the five European regions listed above. The two models generally produced similar predictions, indicating that grassland yields will increase in most areas though there may be slight decreases in southern Europe. Also, plant N concentrations will decrease. Generally permanent grasslands responded more positively to climate change than temporary ones. The impact of climate change tends to be less than the impact of fertiliser, geographic region or grassland type, suggesting that appropriate changes to grassland management practices should be able to mitigate the negative effects of climate change. The modelling described above was all performed using a monthly time-step. This is computationally efficient, but means that short-term extreme weather events are not accounted for. Extreme weather events such as heavy rainfall, droughts and heat waves are predicted to become both more frequent and more intense in the future and it is important to consider the impacts they will have on grasslands and therefore livestock. Two methodologies were used to quantify the effects of extreme weather events on grasslands. The first uses multiple regression analysis and incorporates terms such as 'number of days in a month with temperature greater than 30°' to account for weather extremes. The equations developed had a good fit with observed data. They were found to be predominantly sensitive to uncertainties in precipitation rather than in temperature or grassland species composition. Two projected future weather datasets were applied to the equations; both followed the same climate change scenario, but one included extreme events and the other was smoothed to reduce the extremes. Comparing the model outputs from the two datasets showed that smoothing the data increased the predicted yields and N yields, demonstrating that extreme weather events are detrimental to grasslands. In general, the yield of temporary grasslands decreased over time, while for permanent grasslands it increased. There was little change in N yield over time. The other methodology used the pre-existing process-based model DailyDayCent, which is very similar to the Century model, but is based on a daily rather than a monthly time-step. DailyDayCent was applied to six sites across Europe and was found to have reasonably good fit, though struggled to capture inter-annual variability. The model was predominantly sensitive to uncertainties in rainfall measurements rather than temperature. Two climate change datasets, with and without extreme events, were applied to the model for each of the six sites. Predicted yields and N yields were similar to those found with the Century model. The presence or absence of extreme events usually had little effect, but this may have been due to limitations of the model. The exception was for a site in southern Europe, where the presence of extreme events led to increases in yield and N yield in the short-term, but large decreases in the long-term. Overall, grassland yields are expected to increase in the future in response to climate change (except possibly in southern Europe), particularly for permanent grasslands, while plant N concentration will decrease. Increased yields are generally good for livestock, though reduced N concentrations indicate that grazing animals will need to have a higher intake in order to receive the same amount of protein. Extreme weather events are an important consideration, leading to reductions in grassland yield and N yield. Farmers need to be prepared to meet the challenges presented by such events, for example through using more resilient plant species or increasing plant species richness.

Life cycle assessment (LCA) has been increasingly applied to livestock production systems to estimate their environmental footprints, but the degree of uncertainties associated with these values is known to be generally high. This thesis explores novel methods of LCA modelling to reduce uncertainty associated with environmental footprints of meat production systems, with the view to contribute to objective and transparent debates about the role of livestock in global food security. Three innovative approaches are proposed in this thesis. First, as information on individual animals is often unavailable, livestock data are often aggregated at the time of inventory analysis. To investigate the level of bias caused by this aggregation, Chapter 3 uses primary data collected at the North Wyke Farm Platform in Southwest England and calculates emission intensities for individual animals and their intra-farm distributions, providing a step towards deriving optimal animal selection strategies based on livestock LCA. Second, the severity of greenhouse gas emissions from agricultural production is known to vary spatially and temporally, yet available LCA frameworks often fail to sufficiently consider these differences due to data constraints. To evaluate the degree of avoidable uncertainties attributable to this practice, Chapter 4 conducts an original field experiment to derive site-specific nitrous oxide emission factors, which are subsequently used in Chapter 5 to compare LCA results derived under these localised values and generic alternatives intended for the widest possible users. Finally, while LCA results are typically communicated in the form of environmental burdens per output of mass, it is gradually becoming recognised that product quality also needs to be accounted for to truly understand the value of each farming system to society. Using data from seven livestock production systems encompassing cattle, sheep, pigs, and poultry, Chapter 6 develops new methods to incorporate nutritional values of meat products into livestock LCA.

Livestock provide as much as one-third of all protein consumed by humans, but have a disproportionate and growing environmental impact. Livestock production occupies 50-75% of agricultural land, contributes 15% of anthropogenic greenhouse gas emissions, and drives agricultural expansion in the tropics through the global trade in animal feed. This thesis therefore evaluates two strategies for shrinking the environmental impact of the livestock sector. First, I evaluate the potential for food losses (i.e. foods which were intended for human consumption, but which ultimately are not directly eaten by people) to replace grain- and soybean-based pig feeds in Europe. While food losses have been included in animal feed for millennia, the practice is all but banned in the European Union, because of disease control concerns. Several East Asian states have in the last 20 years, however, introduced regulated systems for safely recycling food losses into animal feed. I combine data from multiple sources (including government reports, the animal science literature, and factory-floor data from South Korean swill-feed factories), and find that the introduction of East Asian practices for recycling food losses as animal feed could reduce the land use of EU pork (20% of world production) by one fifth, potentially saving 1.8 million hectares of agricultural land. This would also reduce 12/14 other assessed environmental impacts and deliver economic savings for pig farmers, as swill (cooked food losses) costs 40-60% less than conventional grain-based feeds. In a survey of pig farmers (n=82) and other agricultural stakeholders (n=81) at a UK agricultural trade fair, we found high support (>75%) for the relegalisation of swill. Support for swill feeding arose in part because respondents thought that swill would lower costs, increase profitability, and be better for the environment. Our results also confirmed the critical importance of disease control and consumer communication when considering relegalisation, as respondents who thought that swill would increase disease risks and be unpalatable to consumers were less supportive of relegalisation. Any new system for the use of swill will require careful design of regulation to ensure that heat-treatment is sufficient, and to reduce to a negligible level the risk of uncooked animal by-products entering feed. Our results suggest, however, that if such a system can be established, there would be multiple benefits and widespread support for its relegalisation. Second, I evaluated the potential to increase the productivity of cattle ranching in the Brazilian Amazon. While high hopes have been placed on the potential for intensification of low-productivity cattle ranching to spare land for other agricultural uses, cattle productivity in the Amazon biome (29% of the Brazilian cattle herd) remains stubbornly low, and it is not clear how to realize theoretical productivity gains in practice. I therefore (a) surveyed six on-the-ground initiatives which have been working with local farmers to improve cattle ranching, quantifying their farm practices, animal performance, and economic results; and (b) analysed the progress that has already been made in reconciling agriculture and forest conservation, by evaluating the impact of the flagship anti-deforestation policy, the priority list (Municípios Prioritários). The survey showed that cattle intensification initiatives operating in four states have used a wide range of technologies to improve productivity by 30-490%, while supporting compliance with the Brazilian Forest Code. Using two complementary difference-in-difference estimators, I then found no evidence for trade-offs between agriculture and forest conservation under the priority list; instead, reductions in deforestation in priority list municipalities were paired with increases in cattle production and productivity (cattle/hectare). The policy had no effect on dairy or crop production. Together, these results provide real-world evidence that increases in cattle production in Brazil do not need to come at the expense of the country’s remaining native vegetation.

This thesis places dung firmly at the centre of livestock farming. It tests the overarching hypothesis that intentional management of dung as a critical resource on-farm has multiple benefits that improve the resilience of beef production systems. Dung is a primary resource in beef production systems. This importance of dung as an organic fertiliser that recycles nutrients in agricultural systems is widely recognised and understood. The connection between disease, dung and its management through diet choice for beef cattle has received far less attention. In this study, the cattle diet, both intake and forage management, significantly influenced the rate of bulk and biochemical (fibre fractions, protein, lipids, carbohydrates, organic matter, ash and micronutrients) dung degradation over 84 days under three forage management treatments on the North Wyke Farm Platform. Site-specific factors were the primary drivers of bulk dung degradation; 70% of degradation was driven by field site and 4% by dung type. Non-target impacts of anthelmintics pose a risk to dung fauna that moderate dung degradation. A multiple-regression model predicted that targeted selective treatments (TST) created refugia for dung-breeding fly Scathophaga stercoraria and that proportions of treated cattle (55%) was more influential than effective dung drug concentrations (13%). Effective TST programmes rely on practical diagnostic tools. A non-invasive protocol was developed for the quantification of immuno-markers (immunoglobulins and lactoferrin) in dung for gastrointestinal health assessment. The anecdotal benefits of increasingly popular 'mob grazing' were supported by case studies of factors including pasture performance, reduced gastrointestinal nematode (GIN) burden, and soil organic matter content over a grazing season in a UK-wide study. The conclusion of this multidisciplinary study is that dung management has a critical role to play in a systems-level understanding of beef production and that optimisation relies on a quantitative understanding of the relationships between wider biological processes on farms.

Improving efficiency within the agricultural industry is vital to maintain the food demands of the increasing population, as well the current preference for a more protein rich diet. One avenue for addressing these issues is to study animal-based growth to determine if the efficiency of the production system can be improved by increasing lean muscle mass. The aim of this thesis is to provide an alternative exploration to experimental work to provide an insight into how muscle metabolism in pigs is altered by the administration of a beta-agonist which induces muscle hypertrophy. This will be incorporated into a wider body of work to determine specific pathways to target for improving feed conversion efficiency, contributing to the necessary research into global food security. We begin by compiling a selection of statistical methods to analyse muscle microarray data, which enables the identification of a selection of genes whose expressions are altered by the exposure to a beta-agonist. These differentially expressed transcripts are then grouped via a k-means algorithm, with log likelihood and the Bayesian Inference Criterion calculations providing an optimal selection of clusters. This results in selecting a group of 51 transcripts and partitioning them into 9 clusters, and identifying several pathways which appear key to the regulation of muscle metabolism in the presence of beta-agonist. We have proceeded to incorporate this information into a mathematical model for glycolysis and the TCA cycle, in an effort to analyse biological hypotheses about how the promoters work. The equations describe the concentrations of metabolites within the cytosolic and mitochondrial compartments of a cell using mass balance ODEs. An initial model is presented, which is then increased in complexity, to keep up with developments in the experimental side of the overarching project. We make use of a selection of methods to analyse the model in an attempt to determine the effects that the different parameters cause. Through steady state analysis, we determine parameter ranges which permit positive steady states. In finding these regions, we also determine the existence of time dependent solutions, which occur when critical values of certain parameters are exceeded, and result in the build up of specific metabolites. We use asymptotic analysis to generate approximate solutions when steady states do not exist. The model parameters of most interest are those which were identified through the microarray work, namely the upregulated transcripts of PCK2 and those within the serine synthesis pathway, the control mechanism for the first half of the TCA cycle, the proportion of GTP producing enzyme from the second half of the TCA cycle, and the flux into the glycolytic pathway. We find that critical values for the glycolytic flux, and the GTP production parameter exist, determining whether the model lies within the steady state regime. In a large number of cases, the parameters we choose to represent the beta-agonist case push the system into the time dependent state. The model does not exhibit any interesting behaviour when the parameter controlling the PCK2 pathway is studied, indicating that initial intuition of the key controlling reaction mechanisms were incomplete. Whilst there are shortfalls in the model, which highlight areas for investigation, the system is set up for validation and parameter fitting when appropriate experimental data become available. We have been able to determine specific metabolic pathways within the cell which may be of significance to improving feed efficiency.

The phasing out of popular chemical nematicides has led to increasing difficulties in plant parasitic nematode management, in particular the newly emerged root-knot nematode (RKN) Meloidogyne minor. Infestation by this nematode results in stunted development of turf-grass and consequently the appearance of chlorosis. This damage is largely the result of the nematodes invasive endoparasitic life-cycle. Although M. minor has been found in potato crops, its appearance is steadily increasing in sports amenity sites. Initially this study investigated the population dynamics of plant parasitic nematodes (PPN) on sports amenity sites in the UK and Ireland. The investigation suggests that PPN ecology within these Isles is somewhat different to what is observed in the USA. The availability of a turf naturally resistant to key pest M. minor, was investigated leading to the suggestion that the propensity to adopt USGA specification and trends may not be appropriate for our more temperate climate which appears to be a factor in the proliferation of M. minor and other genera. The study progressed to exploring the effects of natural nematicidial compounds, such as biostimulants and plant extracts on turf development, plant resistance and PPN control. The key trend to emerge from the data was that of hyper-vari"lbility, a trend also reflected in the current available literature. However the potential for a plant based nematicide could not be ruled out; the data indicated promising in vitro effects on PPN mobility follOWing treatment with natural plant extracts, but the need for further exploration is apparent. Overall the investigations outlined in this study indicate that PPN management within sports amenities will no longer be as straightforward as applying a quick-fix nematiticide . Further study is most ardently warranted and it would be suggested that successful control of PPN within sports amenities will involve a relatively complex program incorporating observation of PPN ecology, lessening of external stress opposed to turf and careful selection and application of approved nematicidal products.

California sea lions (CSLs) have an unusually high occurrence of urogenital cancer (UGC), with studies revealing metastatic carcinoma in 26 % of CSLs admitted to a rehabilitation centre between 1998 and 2012. It is likely that the aetiology of this disease is multi-factorial as genetics, viral infection and exposure to contaminants have been associated with this cancer to date. The goal of this study was to investigate the association of a number of factors using a case-control study design on animals admitted to a rehabilitation centre. The study additionally concentrates on two main areas; (i) genetic factors and (ii) the presence of herpesvirus. Previous investigations identified cancer to be more likely in animals with specific microsatellite alleles. In the present study genotyping of CSLs at three microsatellite loci revealed that homozygosity at one marker (Pv11) was significantly associated with the presence of the disease. Pv11 was found to be located within a gene called heparanase 2 (HPSE2) and investigations into the expression of its protein revealed differences according to Pv11 genotype. The presence of herpesvirus was investigated by two PCR methods and identified the gammaherpesvirus OtHV-1. The results of the two methods were contradictory with one method identifying a highly significant relationship between the presence of OtHV-1 and UGC whereas the other did not. Complicating factors such as potential differences in sensitivity of the tests along with the possible presence of closely related viruses or variants of OtHV-1 may explain this. The availability of necropsy data for the CSLs in the study allowed the inclusion of body condition data in the statistical analysis to evaluate other potential risk factors. Final analysis revealed the presence of three risk factors; Pv11 genotype, OtHV-1 presence and thinner blubber. This study is the largest study undertaken so far in order to investigate the involvement of risk factors associated with UGC in the CSL and supports a multi-factorial aetiology of this disease.

Neonatal mortality in grey seals on the Isle of May breeding colony and in a rehabilitation centre were investigated by detailed systematic post-mortem examinations (n=59), on-site bacteriology and advanced molecular diagnostic techniques for specific pathogens. Causes of death on the breeding colony included starvation (30%), omphalitis-peritonitis (26%), septicaemia (22%), stillbirth (10%) and trauma (4%) and in the rehabilitation centre starvation (44%) and septicaemia (22%). Detailed key gross and histopathological findings and pathogens are described and include the first report of Listeria monocytogenes in any marine mammal. Phocid herpes virus 1 nucleic acids were detected in nasal swabs of 58% live, free-ranging grey seal pups (n=90) and 28% yearlings (n=19), suggesting recrudescence in the latter. Previously undetected in Scotland, phocid herpes virus 2 nucleic acids were identified only in yearlings (15%); sealpox was detected in a single live stranded grey seal pup and phocine distemper virus was not detected. Given their unique characteristics and potential for acting as sentinels of coastal marine health several pathogens of putative anthropogenic origin were investigated: Toxoplasma gondii, Neospora caninum, Salmonella spp. and Campylobacter spp. Toxoplasma gondii DNA was detected in 6% dead free-ranging grey seal pups (n=50) but N. caninum was not found. Salmonella (20%) and Campylobacter (50%) were isolated from rectal swabs of live and dead grey seal pups and Campylobacter was significantly associated with moderate to severe colitis implying pathogenicity. These findings imply a land-sea-land transfer of T. gondii and early exposure of pups to this parasite. Extensive genetic fingerprinting suggested an exchange of Salmonella between grey seal, cattle and human populations and that the Campylobacter isolates may share the same origin as human clinical isolates. This work provides a solid base line study of diseases present in grey seal pups and demonstrates that they are useful indicators of coastal marine microbial contamination.

Rapid industrialisation of livestock farming since the 1950s has been accompanied by public and legislative concern directed towards a range of issues, including food safety and the negotiation of risk, and also the ethics attached to the care, slaughter and commodification of unprecedented numbers of animals in large scale production. Drawing on ethnographic data generated by long term fieldwork on intensive pig units, the thesis foregrounds the firsthand accounts of stockmen to explore in detail how pigs are produced now, and the reciprocal ways that pig production ‘makes’ people. Although these processes take place out of public view, pigs and people are nevertheless produced in response to external expectations, imaginations, and markets. The thesis shows how these influences, farmers’ attitudes, and the methods of pig production itself, are currently undergoing revision and change. By doing so, the thesis resists the idea that industrialisation and globalisation always and everywhere result in a flattening of space and time, arguing instead that what is produced is neither completely old or new, but rather an articulation between traditional forms of animal husbandry and new varieties of knowledge, technology and embodied practice.

Aquaculture is an essential developing sector for world food production, however the attainment of sexual maturity during commercial on-growing is a major bottleneck to industry expansion. Sexual maturation brings a commercial loss due to reduced growth performance as well as reduced immune function. Furthermore, serious concerns exist over potential genetic interaction with native stocks through broadcast spawning or spawning interaction by escapees. In the north Atlantic region, the Atlantic cod (Gadus morhua) and Atlantic halibut (Hippoglossus hippoglossus) are key aquaculture species in which industry expansion is limited by pre-harvest sexual maturation. However, through a species specific combination of modern technologies and refinement in management practices it is possible that this sexual maturation can be controlled and on-growing potential enhanced. Thus the overall aim of this thesis was to conduct novel research that will improve our understanding of the underlying mechanisms that regulate sexual maturation, whilst also advancing the optimisation of technologies for the management of maturation in cod and halibut. In Atlantic cod, owing to the inconsistent inhibition of maturation in commercial conditions, ever increasing intensities of light and in some cases narrow spectrum technologies are being used to try to combat this problem. Firstly, this PhD project investigated the potential welfare impacts of high intensity artificial lighting which have not been studied to date (Chapter 2). The work specifically investigated the effect of traditional metal halide and novel green cathode lighting on the stress response, innate immunity, retina structure, feeding activity and light perception of Atlantic cod. Results indicated that although acute responses to light were observed, there were no clear significant long term effects of any of the lighting treatments on these parameters. Regarding light perception, interestingly even when subjected to high intensity constant lighting (metal halide mean tank intensity: 16.6 watts m-2), cod still demonstrated a day/night rhythm in melatonin release which suggests perception of the overlying ambient photoperiod. The second trial of this PhD project investigated the efficacy of shading of ambient photoperiod in addition to constant lighting to inhibit maturation of cod outdoors (Chapter 3). This aimed at improving the performance of artificial lighting regimes in the open cage system during commercial on-growing by reducing the relative difference between day/night light intensities. The trial was conducted over a one year period where a low and high shade treatment were tested in outdoor tanks. Shading increased the relative night time illumination to 6.6% and 31.3% of daytime levels respectively, compared to <2% in an unshaded set-up. Both shading treatments were effective at suppressing sexual development in cod as confirmed through measurements of gonadosomatic index, histological analysis of gonadal development, oocyte diameter measurements and sex steroid profiles as well as measurements of growth. In addition to research at the applied level in Atlantic cod, this thesis has also extended to the fundamental level and explored one of the potential mechanisms relaying photoperiod signal to the endogenous regulation of sexual maturation in cod, namely the kisspeptin system (Chapter 4). Partial sequences for the signal peptide Kiss2 and its receptor Kissr4 were isolated and described showing similarity to other teleost species such as the medaka, Oryzias latipes and stickleback, Danio rerio. Novel molecular qPCR assays were designed and developed to measure the expression of both genes in male and female cod over a maturation cycle and compared to cod under constant lighting which remained immature. Interestingly, expression patterns of kiss2 and kissr4 did not reveal any clear association with season or photoperiod treatment. However, pituitary expression of gonadotropins (FSH, follicle stimulating hormone; LH, luteinising hormone) did show a differential expression in relation to treatment from early winter approximately 4-6 months after the photoperiod change. These new results are in contradiction with the hypothesis that the kisspeptin system would be involved in the initiation of gametogenesis, as shown in mammals. However, the FSH/LH data defines a window during which time kisspeptin or another GnRH stimulating mechanism must be active, this compels the need further investigation. In Atlantic halibut farming, all-female production removes the concerns of production losses through sexual maturation. Accordingly, this thesis investigated the potential/feasibility of generating monosex populations by FACS (fluorescence activated cell sorting) semen sexing based on cellular DNA content, as proven in terrestrial agriculture. Results however did not show any clear differences between the DNA of sperm in a range of species tested (Atlantic halibut, cod, sea bass, perch) suggesting that this technique may not be applicable in such species. The project also focussed on the production of a population of sex reversed halibut broodstock (neomales) that will generate, in the long term, a basis for traditional monosex population generation in the UK. Two in feed MDHT (17α-methyldihydrotestosterone) treatments were tested with the aim to reduce the use of hormone. Results were very successful with a hormone treatment of 5ppm MDHT generating a 97% phenotypic male population thus suggesting the presence of sex-reversed halibut which can be used for future monosex production. Overall, this work aimed to develop and/or refine potential remediation techniques for sexual maturation in two key commercially important farmed marine fish species, cod and halibut, as well as further our understanding on the regulation of puberty. The knowledge gained from this work provides a means to optimise the techniques employed in the industry and has the potential to increase production and profitability without compromising farmed animal welfare, thus ultimately promoting the sustainable expansion of the Atlantic cod and halibut aquaculture.

The use of maize (Zea mays) as a co-substrate with cattle slurry for the production of biogas was investigated in detail by running several long term digestion trials under different operational conditions in laboratory scale semi-continuous digesters. These conditions included varying the organic loading rate (OLR) from 2 to 6 g VS l-1 d-1, the proportion of cattle slurry from 25 to 100%, and the recirculating regime. Results indicated that the co-digestion of cattle slurry and maize was viable at all loading rates tested with the greatest volumetric methane yield, 1.46 l l-1 d-1, produced at a 5 g VS l-1 d-1 OLR consisting of 40% cattle slurry; this corresponded to a specific methane yield of 0.26 l g-1 VS added. Successful digestion was shown at retention times as low as 15 days where a volumetric methane yield of 1.26 l l-1 was produced. Co-digestion had a pronounced effect on the volumetric methane yield with improvements of up to 355% when compared to the digestion of cattle slurry alone. Additionally, the OLR could be doubled by the addition of an equal quantity of maize, on a VS basis, with the volumetric methane yield increasing by over 200% without a great loss of the methane potential of the maize. For each trial undertaken in this research the actual methane yield produced from co-digestion was compared to that calculated to be produced. Support for synergy was shown in the first two trials where the actual methane yield exceeded that predicted however, the method used to calculate the predicted yield was suggested to be an inaccurate determination. To address this inaccuracy a trial was designed testing the digestion of the two substrates alone and together under the same operational conditions and methodology. A comparison between the mono and co-digestion trials indicated that the addition of maize to cattle slurry produced a methane yield that more or less equalled that calculated from the sum of the cattle slurry and maize alone. This brought the early indications of synergy into doubt with suggestions that they were the result of an inaccurate determination of the predicted yield and of inhibition washout. In the final part of the research an attempt was made to improve the volumetric methane yield by introducing solids recirculation to the co-digestion process with the objective of maintaining the slowly degradable fraction of the maize and cattle slurry in the digester for longer periods. This proved not to be a viable option with the methane production showing a decline; at an OLR of 5 g VS l-1 d-1, consisting of 50% cattle slurry, a decline of 0.31 l l-1 d-1 occurred. Solids recirculation was also introduced to the mono-digestion process to determine whether the differences shown in the co-digestion trial were a result of recirculating the solids of the cattle slurry, the maize or a combination of the two. Results showed that both substrates produced unstable conditions indicating that the co-digestion trial was not the result of just one substrate failing. Liquid recirculation was also tested on the co-digestion of the substrates and while no decline was observed no improvement was produced. KEYWORDS: Anaerobic digestion, co-digestion, cattle slurry, maize, solids recirculation

Pork quality is an important issue for the whole meat chain, from producers, abattoirs, retailers through to costumers and is affected by a web of multi-factorial actions that occur throughout the pork production chain. A vast amount of information is available on how these diverse factors influence different pork quality traits. However, results derived from individual studies often vary and are in some cases even contradictory due to different experimental designs or different pork quality assessment techniques or protocols. Also, individual influencing factors are often studied in isolation, ignoring interacting effects. A suitable method is therefore required to account for a range of interacting factors, to combine the results from different experiments and to derive generic response-laws. The aim of this thesis was to use meta-analyses to produce quantitative, predictive models that describe how diverse factors affect pork quality over a range of experimental conditions.

This study investigated the effects of a seasonally variable forage resource on herbivore population dynamics. This involved estimating the relative importance of environmental conditions, and the accessible and used forage resources, at different stages of the seasonal cycle to herbivores in different life-stages and at different points in the reproductive cycle. This study was carried out in the Richtersveld region in South Africa, using goats kept by semi-nomadic Nama pastoralists. In the main study site, the Richtersveld National Park (RNP), herd movements follow a general seasonal migratory pattern: herds are based in the riparian zone of the Orange River during the dry season, and on plains away from the river in the wet season. Over 800 uniquely marked female goats in three life-stages (adults, yearlings and kids) were monitored over a three year period (2007 to 2009). These goats were weighed at 2 - 3 month intervals to provide an estimate of body condition. Browse availability in the riparian zone was estimated using measurements at an individual branch-level and a whole tree-level. FPAR satellite imagery was used to estimate forage abundance outside the riparian zone. Goat density was mapped for each week of the study using census data and the herd positions. Goat body condition, survival rates and fecundity rates for each life-stage were modelled as a response to forage availability, density and climatic conditions. The riparian zone in the RNP was found to function as the key resource of the RNP goat population. Forage depletion by goat browsing resulted in a negative feedback on goat body condition. This decline in body condition was directly related to lower adult survival over the dry season. Fecundity was also most influenced by dry season conditions through the negative effect of poor body condition on pregnancy rates and birth rates. Asymmetric competition between life-stages, resulting from the riparian browse profile being depleted from the bottom-up, was predicted to have a strong effect on goat demography by contributing to differences in body condition and survival rates between life-stages. Wet season conditions appeared to have little effect on goat population dynamics, either through increased neonate survival or through a mass carry-over effect influencing dry season survival. Goat body condition and vital rates were compared between the RNP and the neighbouring Kuboes rangeland, which does not have access to the Orange River, to assess the impact of differences in their dry season forage resource. The long-term size and variability of the livestock population in the RNP was also compared with livestock dynamics in Paulshoek, a rangeland 250 km south east of the RNP. The a priori predictions of relative population dynamics in each region, based on perceived differences in the nature of the key resource in each region, were largely supported.

An approach known as management strategy evaluation (MSE) provides a framework for identifying robust management strategies in the presence of multiple management objectives and system uncertainties, and has been increasingly used as a practical fisheries management framework in recent years. However, few examples exist that incorporate economics in MSEs. Meanwhile, there has been increased attention given to economic instruments for sustainable management of fishery resources, including the use of bioeconomic target reference points (RPs). However, investigation of the causes of errors and bias in the estimates of bioeconomic parameters is scarcely documented compared to their biological counterparts, and the implications of simplified assumptions concerning both the biological and economic parts of the bioeconomic models have not been adequately investigated. In this thesis, I used three case study fisheries to illustrate how economics can be explicitly integrated within the MSE framework, and demonstrated the usefulness of this flexible approach as a rigorous tool for the evaluation of the effect of uncertainties in key parameter estimates from bioeconomic fisheries models, as well as highlighting the merits of including economics in MSE in general. The interaction between life history characteristics, fisheries variables and economic systems strongly affect the behaviour and robustness of the bioeconomic target RPs for the case studies fisheries. It was clear from these examples that the MSE approach has the potential to radically improve the robust estimation of bioeconomic RPs as well as the construction, evaluation, and implementation of economically-oriented harvest strategies.

There is considerable opportunity to develop new modelling techniques within a Geographic Information Systems (GIS) framework for the development of sustainable marine cage culture. However, the spatial data sets are often uncertain and incomplete, therefore new spatial models employing “soft computing” methods such as fuzzy logic may be more suitable. The aim of this study is to develop a model using Neuro-fuzzy techniques in a 3D GIS (Arc View 3.2) to predict coastal environmental vulnerability for Atlantic salmon cage aquaculture. A 3D hydrodynamic model (3DMOHID) coupled to a particle-tracking model is applied to study the circulation patterns, dispersion processes and residence time in Mulroy Bay, Co. Donegal Ireland, an Irish fjard (shallow fjordic system), an area of restricted exchange, geometrically complicated with important aquaculture activities. The hydrodynamic model was calibrated and validated by comparison with sea surface and water flow measurements. The model provided spatial and temporal information on circulation, renewal time, helping to determine the influence of winds on circulation patterns and in particular the assessment of the hydrographic conditions with a strong influence on the management of fish cage culture. The particle-tracking model was used to study the transport and flushing processes. Instantaneous massive releases of particles from key boxes are modelled to analyse the ocean-fjord exchange characteristics and, by emulating discharge from finfish cages, to show the behaviour of waste in terms of water circulation and water exchange. In this study the results from the hydrodynamic model have been incorporated into GIS to provide an easy-to-use graphical user interface for 2D (maps), 3D and temporal visualization (animations), for interrogation of results. v Data on the physical environment and aquaculture suitability were derived from a 3- dimensional hydrodynamic model and GIS for incorporation into the final model framework and included mean and maximum current velocities, current flow quiescence time, water column stratification, sediment granulometry, particulate waste dispersion distance, oxygen depletion, water depth, coastal protection zones, and slope. The Neuro-fuzzy classification model NEFCLASS–J, was used to develop learning algorithms to create the structure (rule base) and the parameters (fuzzy sets) of a fuzzy classifier from a set of classified training data. A total of 42 training sites were sampled using stratified random sampling from the GIS raster data layers, and the vulnerability categories for each were manually classified into four categories based on the opinions of experts with field experience and specific knowledge of the environmental problems investigated. The final products, GIS/based Neuro Fuzzy maps were achieved by combining modeled and real environmental parameters relevant to marine fin fish Aquaculture. Environmental vulnerability models, based on Neuro-fuzzy techniques, showed sensitivity to the membership shapes of the fuzzy sets, the nature of the weightings applied to the model rules, and validation techniques used during the learning and validation process. The accuracy of the final classifier selected was R=85.71%, (estimated error value of ±16.5% from Cross Validation, N=10) with a Kappa coefficient of agreement of 81%. Unclassified cells in the whole spatial domain (of 1623 GIS cells) ranged from 0% to 24.18 %. A statistical comparison between vulnerability scores and a significant product of aquaculture waste (nitrogen concentrations in sediment under the salmon cages) showed that the final model gave a good correlation between predicted environmental vi vulnerability and sediment nitrogen levels, highlighting a number of areas with variable sensitivity to aquaculture. Further evaluation and analysis of the quality of the classification was achieved and the applicability of separability indexes was also studied. The inter-class separability estimations were performed on two different training data sets to assess the difficulty of the class separation problem under investigation. The Neuro-fuzzy classifier for a supervised and hard classification of coastal environmental vulnerability has demonstrated an ability to derive an accurate and reliable classification into areas of different levels of environmental vulnerability using a minimal number of training sets. The output will be an environmental spatial model for application in coastal areas intended to facilitate policy decision and to allow input into wider ranging spatial modelling projects, such as coastal zone management systems and effective environmental management of fish cage aquaculture.

A modelling framework is developed which transfers the uncertainty inherent in estimating the size of parr populations from electrofishing data into sub-models which predict the wealth of salmon biomass and age structure of such populations. The focus of much of this thesis is on data collected on the River Conon and we find here that such a model is able to account for 36.5% (posterior median, 95% credible interval (2.8%, 58.4%)) of the observed variation in the habitat “score” – a proxy measure for the estimated size of a population. Having looked at production, the next stage involves examining migrations of smolts within freshwater. Specifically, a methodology for using RJMCMC methods for model choice when considering a range of models for dealing with capture-recapture data with subsequent captures at a smolt trap, is developed. The smolt trap allows for estimates of a migration propensity for salmon parr by recasting migrations as recoveries of dead animals within the traditional capture-recapture-recovery framework. As a by-product, estimates for over-winter, over-spring and in-migration survival probabilities based on model-averaged posterior distributions can be achieved. This methodology is then extended to study the feasibility of incorporating highly variable time-dependent covariate histories into estimates of survival and migration. Despite the presence of a low capture probability, the data appears to hold sufficient information as to be able to identify a strong relation between migration propensity and fish length, which also appears to be positively correlated with in-migration survival.

Commercial fishing for Pecten maximus and Aequipecten opercularis has taken place in Shetland since the late 1960’s and early 1970’s, respectively, with fluctuations in landings of both species during this time. Recognition of the importance that shellfish fishing contributes towards maintaining a diverse economy in a rural area, coupled with concerns in the 1990’s about the potential for overfishing, prompted by reductions in the abundance of some shellfish species, the Shetland Shellfish Management Organisation Ltd. was formed, with a remit to implement local management of shellfish stocks, where necessary. The collection of biological data was started and the completion of log books begun in 1999 and 2000, respectively, to provide data to assess the species, with a view to their sustainable management. Von Bertalanffy growth parameters were determined for contemporary samples on both species and on historical samples of P. maximus. The asymptotic shell length, as a measure of growth, was examined in relation to the environmental variables of sediment composition and depth. Growth studies were carried out on juveniles to measure sub-annual growth. The gonadal condition through time in the adult stocks was assessed, changes in gonad condition were related to spawning activity by collection of spat on artificial collectors. Seasonal and spatial differences in yield of adductor muscle and gonad from experimentally derived, and commercial yield data, was analysed. The assessment of the fishery utilised fisher knowledge on the distribution of stocks. Catch Per Unit Effort and mortality rates data were calculated. The overall Spawning Stock Biomass was estimated for P. maximus using the swept area method. Long-term data from processing factories were incorporated into the fisheries assessment. The assessment indicates poor catches of A. opercularis for many years, and a recovery in abundance of P. maximus on some fishing grounds since the low catches experienced in 2000.

This thesis is concerned with acknowledging farm animals and their co-presence in the more-than-human space of the livestock farm, and with accounting for them responsibly in sustainability debates. The enrolment of farm animals as actors in political agendas for environmental sustainability, and farm animal welfare suggests that there are new ways of seeing and being with farm animals that permit their relational presence and recognise their subjectivity. Indeed geographers have in recent years acknowledged animals and their relations with humans, and they have begun to recognise the nature of animal subjectivies. However, within the fundamental rethinking of animals that has been provoked by these discussions, I suggest that farm animals have remained relatively invisible. Occupying ethically confusing terrain, farm animals have nonetheless been visible in a set of philosophical positions regarding their moral status, yet these debates present a rather confusing picture in which the farm animal as an individual is conspicuous by its absence. In seeking to redress the invisibility of farm animals within these debates, and recast them in relation to humans and the broader farm ecology, this thesis attempts to set out an epistemological and methodological framework through which farm animals might become visible as individual fleshy beings. Drawing on the concept of agricultural stewardship and new agendas in farm animal welfare science, it makes use of new methodological tools that have emerged in the social sciences to conduct a relational study of the livestock farm; a study in which farm animals themselves participate. It also considers how the divisions that have been constructed between humans, farm animals and the environment can be reconfigured as a more unified political science of the livestock farm.

In relation to hill sheep, the perception is that they live to a high welfare standard with minimal labour input per ewe, and that there is little reason for concern.  This perception has however not been confirmed by science to date, chiefly due to a lack of research interest into the hill sheep sector.  Meanwhile, extensive sheep farming faces increasing economic pressures, with low returns and falling government subsidy that may compromise animal welfare.  Labour has been shown to be a key input factor for both productivity and welfare in extensive production systems. Despite this, little research has been done to try and optimise the labour input for productivity and welfare. This study is a first attempt to link labour input, productivity and welfare in extensive sheep systems through empirical observation and computer modelling.  The fieldwork was undertaken from 2007 to 2009 on three research farms and three commercial farms.  Labour use was analysed within a number of defined tasks.  Linear programming (LP) modelling was then used to explore eight different scenarios with regard to sheep welfare, labour and productivity, and the potential impacts of specific management changes. Data analysis and model results showed hill sheep live to a high welfare standard according to the low incidence of welfare problems with low risks to productivity, confirming public expectations.  Farmers, are however, aware their attention to an individual sheep’s welfare brings poor returns in terms of flock productivity.  With this in mind, there is some scope for welfare-beneficial or –neutral reductions in labour, particularly if within-farm movement, e.g. between grazing areas, can be reduced.  However, larger reductions of labour, even within legal guidelines, could seriously endanger the welfare of individual sheep, though without great risks to productivity at flock or farm level.  Thus considerable savings in labour might, in some circumstances, reduce costs and hence improve profitability.

Cod, haddock and whiting are among the most economically important species in the Scottish demersal fishery. Juvenile settlement, the transition from pelagic to demersal habitat, has been identified as an important milestone for these species, but there is insufficient knowledge and data about this life stage. It is believed that the period of settlement has an impact on recruitment success, as important density-dependent processes may take place, such as competition for suitable substrate, refuge or prey. Also, knowledge of settlement timing and duration is relevant to understanding population connectivity and thus to the development of successful conservation measures. Sampling was conducted between April and August 2004, June and September 2005 and June and July 2006 at an inshore site off the east coast of Scotland. Over 4000 0- group cod, haddock and whiting were collected. Comprehensive morphometric and dietary analyses of the samples were carried out, followed by statistical analysis of the data. The results suggested clear differences in the patterns of settlement between the different species. Initially juvenile haddock favoured deeper, further offshore locations, while cod occupied shallower, inshore waters. Whiting settled much later in the season and over protracted period of time. Furthermore, cod showed an affinity for structured habitat, while haddock and whiting were found only over sand. The results also showed that the transition from the pelagic to the demersal habitat was associated with clear and progressive changes in the prey composition of the juvenile fish. The results also showed temporal, spatial and dietary niche segregation of settling juveniles, which is expected to reduce competition for resources and increase the potential for settlement success.

The sympatric occurrence of M. edulis, Mytilus trossulus, Mytilus galloprovincialis and their hybrids in cultivation has recently been reported and significant production losses attributed to the presence of M. trossulus. A molecular real-time PCR assay capable of identifying M. edulis, M. trossulus and M. galloprovincialis species-specific alleles was developed and applied to a large-scale survey of these species. We found M. trossulus distribution to be restricted to the south Highland and Argyll areas. Spawning asynchrony of M. trossulus and M. edulis was explored, aimed at favouring M. edulis production at mixed-species sites. However, the close similarity between these species and the impossibility of controlling important environmental and biological factors suggest strategies based on such differences would be too unpredictable for effective use by the industry. M. trossulus and its hybrids have also been noticed to be significantly more frequent on ropes in the upper 3-4 m of the water column, suggesting that changes in cultivation practices to avoid settlement in these depths are likely to reduce M. trossulus proliferation. At severely affected farms, the fallowing of sites and transfer of M. edulis unispecific seed is seen as the best long-term strategy towards the re-establishment of M. edulis stock. At all impacted farms area-specific solutions to managing the problem are being considered. Any management solutions will also be accompanied by an industry wide strategy and awareness, which will include the development of an industry supported code of good practice.

Food quality, including safety, is a major concern facing the food industry today. The effects of sanitary and phytosanitary (SPS) measures in the fisheries sector of The Gambia including the factors affecting the safety and spoilage of fish were investigated. Effects of SPS measures are important impediments for exporting fish and fishery products originating from The Gambia to the international food commodity trade. The inadequate scientific and technical expertise in addition to the general lack of information and finance are the major contributing factors to these impediments. The Government must build capacity, improve infrastructure and increase the number of trained personnel to adequately monitor and enforce fish safety and quality for both domestic consumption and exports. It is crucial that the seafood industry upgrade fish processing establishments and comply with the required hygiene and sanitary standards necessary. To minimise post harvest losses and improve fish quality, the use of ice along the production and supply chain must be applied. The effect of icing on colour and texture measurements of mackerel fish showed an increase in lightness of the eyes and gills during the initial 3 days of storage coinciding with a decrease in textural firmness. Deformation of the fish muscle over storage time was highly significant (p≤ 0 .01) for the upper and middle parts but not for the tail end of the fish. A comprehensive evaluation on the effect of storage temperature on sensory, chemical and microbiological assessment of mackerel fish was conducted. Whole un-gutted mackerel fish had a shelf life of 8 days during storage in ice. The average quality index (QI) was highly correlated (r=0.99) with days of storage. Both total volatile and basic nitrogen (TVB-N) and trimethylamine (TMA) increased during icing storage. The production of TMA and TVB-N as indicated by the correlation (r= 0.97; p< 0.001) was highly significant. A major increase in mean microbial count occurred at day 8; this indicated that the usefulness of total bacterial count as an indicator of spoilage was only clear from day 8. The effects of temperatures proved to be significant on the formation of biogenic amines and on the growth of microorganisms over storage time. Maximum contents of histamine, cadaverine and putrescine were obtained at 25°C. Histamine was not detected at 0°C despite the growth of the Enterobacteriaceae on the samples. Spermidine, spermine and tyramine cannot be used as suitable indicators of fish spoilage. The investigation on the effects of environmental conditions on the changes in microbial growth kinetics for Pseudomonas fluorescens, Shewanella putrefaciens and cultures of mixed bacteria from mackerel fish, showed a temperature effect which was highly significant. The maximum growth of the microorganisms was attained at 0 to 5% NaCI concentration and between pH 6.5 and 7. Overall, this study showed that the methods used proved important in evaluating mackerel fish freshness quality. The wider application of the sensory method will be useful for the fishing industry.

This research investigated the environmental impact of the pig production chain by modelling contrasting scenarios. Life Cycle Analysis (LCA) and scenario analysis methodologies were used to reveal the main opportunities to improve sustainability. Pig production systems were modelled in two countries (The UK and Mexico), each with a standard production system and on alternative system. This gave four scenarios which were different in the degree of integration that exist between pig and crop production and were then specified in detail to allow for comparison of environmental impact. This study used two strategies to analyse the four scenarios: A pre-assessment facilitated the construction of the system boundary and clarified the processes and commodities which should be included in the Life Cycle Inventory (LCI). A hybrid-LCA method combined a detailed collection of environmental burdens (e-burdens) from the main sources (process-LCA) and a broad compilation of e-burdens from indirect sources (Economic Input Output-LCA). The pre-assessment, conducted as a general LCA, explored novel techniques to construct the system boundary and explore the supply chains in detail. This step clarified the importance of the supply chains of different commodities that are used in the pig farm. The importance of previously reported commodities and processes that mainly contribute to the environmental impact, i.e. feed consumption and manure fermentation were confirmed. Novel findings included the importance of the environmental impacts of goods and services, i.e. machinery, equipment, disinfectants and medicines, that have negligible weight in the impact of environmental indicators that are traditionally analysed (global warming, acidification and eutrophication). The inclusion of novel indicators, such as ozone depression and ecotoxicity to water and soil, demonstrated the importance of including in the LCA those commodities and indicators that have been excluded in many previous studies on the sustainability of pig production. Subsequently, the hybrid-LCA method allowed the expansion of the system boundary of the LCA in a detailed evaluation of each scenario. Results showed the UK scenarios to be superior in management of nutrient flow, by manure management and good agricultural practice. Opportunities to capture methane and recycle nutrients for crop production in the Mexican scenarios were highlighted. In contrast, reduction in machinery and equipment use and fuel consumption were the main opportunities which emerged for the UK scenarios. In addition, specific opportunities to reduce the environmental impact of different pig supply chain sectors were identified in each scenario. In conclusion, the EIO-LCA method allowed for an extension of the traditional system boundary of the LCA, to encompass those e-impacts that have not been included in previous studies. The contrasting of different scenarios allowed emphasis to be placed on opportunities to reduce environmental impact of pig production by highlighting the main challenges in each case. This avoids the controversial issue of denoting a set of specific e-impacts that then favour one production system over another.

Kocuria SM1 and Rhodococcus SM2 were administered to juvenile rainbow trout as dietary supplements dosed at ~107–108 cells g−1 of feed for two weeks, and conferred protection against Vibrio infections. Thus, use of SM1 and SM2 led to a significant (P < 0.05) reduction in mortalities, i.e. 12–15% (relative percent survival, RPS = 81– 85%) and 15–20% (RPS = 73–80%) after challenge with V. anguillarum and V. ordalii, respectively, compared to the 80% and 74% mortalities among the respective controls. A two-week feeding regime, compared with 1–4 weeks, for SM1 led to the maximum reduction in mortalities after challenge with V. anguillarum. The use of an equi-mixture of SM1 and SM2 led to significantly enhanced survival against vibriosis, but the result was not better than the use of single cultures. Moreover, use of SM1 for two weeks led to protection for up to 4 weeks. Fish inoculated with cell wall proteins (CWPs) and whole cell proteins (WCPs) of SM1 and SM2 demonstrated better protection against challenge with V. anguillarum, although extracellular proteins (ECPs) fared less well. The mode of action reflected competitive exclusion (= antibiosis), nutrition (= positive effects on growth), and stimulation of cellular and humoral innate immunity, notably greater head kidney macrophage phagocytic, respiratory burst, peroxidase and bacterial killing activities, and elevation of leucocytes, globulin, protein, complement and lysozyme levels. These results demonstrate the efficacy of dietary bacteria as probiotics for the control of vibriosis in rainbow trout.

The research assessed the potential of developing a selective breeding programme for the UK rainbow trout industry. Levels of genetic variation at 12 microsatellite loci were first compared in seven different commercial strains. The Observed heterozygosity ranged from Ho = 48.1% in a gold rainbow trout strain (GTR) to Ho = 66.4% in a newly derived broodstock population constructed from a number of different sources (GIT). The Expected Heterozygosity (He) was highest in GIM1 (He= 79.5%) and lowest in the GTR strain (He = 56.9%). The Effective number of alleles (Mae) showed that the GIM1, GIM2, GIM3, and GIT strain (5.4; 5.2; 4.8; 4.2) were significantly more variable than the other strains and that GTR strain had the lowest value (2.5). There appears to be substantial genetic variability within the commercial United Kingdom rainbow trout strains surveyed in this study. This appears to be the case despite very different management histories and levels of record keeping. The strains appear to be genetically distinct (based on population genetic analyses), though the reasons for this remain unclear (and possibly unanswerable given the poor records kept by the different companies). The Glenwyllin farm strains (GIM) were chosen to form the base population for the project because of their high genetic variability, disease free status and because the farm produced around 20 million ova per year, so any genetic gains would have a widespread impact. The farm has an early (Strain A) and a late spawning (Strain B) and these were mated in a partial factorial design, 20 females and 20 neomales per strain (A & B) were chosen on the basis of maturity and gamete quality in November 2002 so that each male was crossed to 4 females (2 in the same strain and 2 in the other), a total of 160 families were created. All broodstock were biopsied to enable them to be genotyped. The families were reared separately up to the eyed stage at which point the eggs from each family were divided into three to generate three communal replicate populations. One of these was sent to a fingerling producer (Iwerne Spring) for ongrowing to fingerling size and formed the basis of a commercial production trial at Test Valley Trout farm (TVT) in Hampshire. When the fish reached an average weight of 5 g they were transferred from Iwerne Spring to TVT and 1500 were randomly selected, PIT tagged and biopsied to enable them to be assigned to their family using 11 multiplexed microsatellite loci. Parental assignment was based on exclusion (FAP) but the results were compared with another parental assignment based on likelihood (PAPA). Of the 1500 offspring (OIM) PIT tagged 1242 82.8% could be assigned to a single family utilizing different combinations of more than 6 loci (6 to 11). The growth of the 1500 OIM fish was tracked throughout the grow out period before they were finally harvested and fully processed. The results of OIM strain at the end of the trial period were mean weight of 415.5 g, and a mean length of 314.5 mm. The visual measurement of colour gave a mean flesh colour values of 26.01 on the 20-34 scale (SalmoFan™), and 11.0 with the colotimetry evaluation of colour (a*). The heritability results for the IOM strain were 43 ± 9% for weight, 42 ± 9% for gutted, and 28 ± 8% for length. The heritability estimates for the visual colour variables were 19 ± 7% and when using the colorimeter, the red chromaticity (a*) heritability was 14 ± 6%. Therefore, the heritability results of the IOM strain indicate that there are opportunities of substantial and rapid improvement of the growth rate and flesh colour traits. Also no line effects were observed or indications of non-additive genetic variation. In contrast to these last results, the overall survival of the GIM strain from the time of the physical tagging with PIT until harvest was 52.8%, and survival heritability was extremely low, 3 ± 2%, hardly significant.

This study reports on investigation of ways of improving the breeding programme for growth-related traits in common carp in Vietnam. The base population was synthesized following a single pair mating scheme from six carp stocks: (1) 2nd generation of family selection; (2) Hungarian 6th generation of mass selection; (3) Hungarian scaled carp; (4) Indonesian yellow 6th generation of mass selection; (5) Indonesian yellow carp; and (6) Vietnamese 6th generation of mass selection. The next two selected generations were produced using a partial factorial mating scheme, with each family being split and reared using communal early rearing (CER) or separate early rearing (SER) methods. The second generation (G2) was produced from selected fish from the CER G1 group. The total number of selection, control and reference families was 135 in the G1 and 101 in the G2 respectively. The control and reference (Hungarian P33 line) families were produced by single pair mating (reference families with the G2 only). Seven microsatellite loci were used for parentage assignment in the CER groups: 96.8% of the offspring (1284 individuals) and 96.2% offspring (1341 individuals) were unambiguously assigned to 113 families (selection, control) in the G1 and 99 families (selection, control and reference) in the G2 generations, respectively. Restricted maximum likelihood in the individual model was used to estimate phenotypic and genetic parameters. In CER, the estimated heritability values of common carp were from 0.20 ± 0.04 to 0.29 ± 0.05 for both weight and length at final harvest, indicating substantial additive genetic variation for selection on growth-related traits. The overall obtained maternal and common environmental effects were consistently close to zero. The average of direct response to selection for body weight was 15.0% per generation. In SER, the number of families in the G1 and G2 were 135 (selection and control) and 101 (selection, control and reference), respectively. The heritability estimates were from 0.20 ± 0.07 to 0.31 ± 0.08 at final measurement. Common environmental (full-sib family) effect were all lower at tagging and slightly higher at last measurement, ranging from 0.05 to 0.22. The response in each generation of selection as the difference between the selection and control lines was 8.1% on average for weight at final harvest, lower than under CER. The high genetic correlations of growth-related traits between the third (one year old, mature) and second (7 months old) measurements could allow selection to be based on the earlier assessment, reducing handling stress close to spawning. The benefits of using microsatellite markers to ascertain parentage, achieve greater growth rate (close to farming systems), shorten time to maturity and selection, and the overall relative merits of using CER v’s SER in this genetic improvement programme are discussed.

Scotland’s coastal environment has many areas which are potentially suitable for sustainable aquaculture development. However previous studies have shown that aquaculture may have a detrimental impact on sensitive environments. The main objective of this study is to develop a holistic management tool for sustainable coastal marine aquaculture in the Western Isles of Scotland through development of a multi-faceted holistic model that allows consideration of sensitive environments. As the Scottish Government promotes better collaboration and integration of all involved in coastal zone governance (Baxter et al, 2008) this study illustrates the benefits to be gained from harmonized management of information in a Geographical Information System. GIS models are strong support tools designed to aid decision-making. The main strengths are that GIS can generate easily understandable visual displays of results which are based on robust models capable of incorporating vast amounts of spatial data and which can be predictive and can simulate future coastal environment scenarios. Within this study it is demonstrated that GIS-based models can successfully manage and manipulate a wide range of datasets that are essential components in the determination and management of suitable aquaculture locations. The GIS decision support tools evaluated and integrated in this study were based on four main sub models. These were Cage Site Suitability, Particulate Dispersion, Sensitivity Biodiversity Indicators and Visual Landscape Capacity. Exploration of a combination of these sub-models into an overall decision support system was also completed. All sub models developed were flexible, instrumentally coherent and communicatively balanced for the management and planning of the coastal environment . A sub-model was designed to evaluate and optimize the location of marine cage systems. This required development of data layers and modelled sub-components relevant to the important environmental and engineering factors affecting cage designs which included wave climate, bathymetric and substrate profiles. Three cage types were explored; those designed for sheltered, semi-exposed and exposed areas. These environmental factor layers were combined through weighting and Multi criteria evaluation consideration for each cage type. The resulting three sub-models indicated that while the archipelago has quite restricted development potential for cages designed for sheltered environments (91km2), there is a limited development potential for cages designed for semi exposed environments (1543km2) and an optimal potential for aquaculture development with cages designed for exposed environments (3103km2). The greatest potential environmental impact from aquaculture comes from particulate dispersion. Currently, assessing footprints of effect from fish farms is carried out on an individual site basis mostly at ten metre resolution. The sub-model successfully developed in this work resulted in a partially validated multisite particulate sub model at one metre resolution which implemented maximum current velocity as the friction/force image. The sub-model was run on a range of coastal loch fjord systems and demonstrated the variation in particulate dispersion patterns in each fjord system. In all the fjord systems modelled, even where farm sites are close neighbours, there appears to be minimal interaction in the particulate dispersion. While the particulate sub-model is effective and rapid to deploy for multiple sites, it requires further development in order to incorporate the quantitative aspects of particulate dispersion. Aquaculture biodiversity sensitivity indicators were evaluated and five main sub-components were developed; Species sensitive to Aquaculture, Endangered species, Species important to the Western Isles, important spawning and nursery areas and Protected Areas. The sub-model was constructed by combining these layers through weighting and Multicriteria evaluation. The outcomes indicated that within the study area there are 1168km2 (4% of study area) which are highly sensitive to aquaculture activity, although 20595km2 (65% of study area) has a biodiversity that is much less sensitive to aquaculture. This sub-model, and some of its components, can operate as a “stand alone” tool or can be combined into a larger framework. Little modification and re-parameterisation would be required to enable models to be developed to cover the whole of the Scottish coastline, or other coastal locations. Aquaculture can visually affect landscapes, seascapes and can adversely affect visual capacity of different areas. GIS was successfully applied to investigate this contentious issue. This comprehensive and flexible sub-model successfully develops Seascape and Landscape sensitivity analysis of aquaculture structures and also incorporated a novel approach to visual assessment through use of proportional assessment. Combining the sensitivity layers, 6448km2 of the waters of the archipelago (20% of study area) were categorized as having high capacity to incorporate new aquaculture developments, whilst 3301km2 (10% of study area) have a moderate capacity for new aquaculture structures and 1324km2 (4% of study area) have a low capacity for new developments. An overall conceptual framework was designed to explore two methods for the combination of the major sub-models in order to identify the most appropriate areas for sustainable aquaculture with consideration of possible conflicts including conservation issues. Initial evaluations involved the extraction of information from the component GIS sub-models into a structured database. The extracted data provides a range of information that can be used for statistical analysis and decision support, but which leaves the evaluation of the optimal siting of aquaculture at any location in the Western Isles in the hands of the database interrogator. The second method involved combining the sub-models within GIS whole considering trade offs in relation to conservation. This GIS combination of models indicated that, taking many factors into consideration, the Western Isles has 748km2 (2.5% of study area) appropriate for aquaculture development when implementing the C315 and whilst considering the interactions with conservation areas. There were 498km2 (1.6% of study area) appropriate for development when implementing the intermediate C250 cage types but only 15km2 (0.04% of study area) were appropriate for development based on the LMS cage designs for sheltered environments. Both analytical approaches had strengths and weakness and clearly both need to be used in combination to maximise the benefit of the GIS model outcomes. This study has demonstrated the ability to apply scientific rigour to spatial modelling of aquaculture problems including site suitability, biodiversity, landscape capacity and multi-site particulate dispersion. The various sub-models and their components sub-models can be stand-alone decision-making tools or combined into a holistic model which incorporates a flexible method of trade-off management. The range of GIS-based coastal analytical tools developed form the core of a decision support system that can enable the objective management of the increasing demands on the coastal zone, while having the capacity to bring together stakeholders, multiple agencies and governing bodies that are responsible for management and use of these precious and sometimes threatened resources.

This thesis reports on an investigation of the association between muscularity and meat quality in Scottish Blackface (SBF) and Texel (TEX) lambs, and the in vivo assessments of these traits using X-ray computed tomography (CT) with a view to their possible inclusion in breeding programmes. The objectives of this work were: (i) to develop comprehensive in vivo assessments of muscularity using spiral CT scans; (ii) examine the relationship of the new muscularity indices with carcass and eating quality; (iii) explore the associations among CT assessments of carcass composition, muscularity and muscle density, and (iv) investigate the possibility of limiting the antagonism between selection for reduced fatness and maintaining eating quality by introducing a CT predictor of intramuscular fat (IMF) as an additional selection criterion for the breeding programmes using CT. The calculation of muscularity indices requires the measurement of the muscle mass and skeletal dimension of the regions of interest. Priority was given to the hind leg (HL) and lumbar region (LR), where high priced cuts are located. The utilisation of new novel imaging technology called spiral CT scanning, which captures detailed information on any specific region, was explored. An algorithm to automatically segment the spiral CT scans (SCTS), and procedures to assess the real dimensions of skeletal structures, were developed. Compared to previous CT m uscularity measurements, the accuracy was much higher with the new index in the HL (correlations with equivalent indices bases on dissection of 0.89 vs 0.51). The accurate measurement of femur length by CT used in the calculation of the new HL index made an important contribution to the higher accuracy of the index. The improvement in accuracy was smaller for the LR (0.55 vs 0.44). The association of CT muscularity indices and carcass traits by dissection in both breeds showed that improved muscularity is not phenotypically correlated with detrimental effects on other carcass quality traits. The correlation coefficients, after adjusting for carcass weight, were positive with meat yield and low and negative, or close to zero, with fatness. This is particularly relevant for the terminal sire breeds, in which the economically important traits included in breeding programmes tend to be carcass composition traits. In the case of SBF, the CT muscularity indices provide an opportunity to improve carcass conformation, a trait included in current breeding objectives. Differences in muscularity of the HL and LR, assessed by the CT muscularity indices, and eating quality were investigated between sexes (ram vs ewe lambs), breeds (SBF vs TEX) and progeny of high- and low-muscularity sires (HM, LM). TEX lambs had 16% greater muscularity than SBF in both regions, whilst differences between sire groups were 4%. Ewe lambs had slightly higher values of muscularity for the F1L than rams but no difference was found for the LR. Meat from SBF lambs was more tender, and had stronger lamb flavour and higher overall liking scores than TEX meat. Sex had a weak influence with ram lambs having a stronger abnormal flavour and lower overall liking in the LR only. No significant differences in meat eating quality were found between HM- and LM-sired lambs, suggesting that improved muscularity would not have unfavourable effects on sensory traits. Genetic parameters for the CT muscularity indices, predictions of carcass muscle and fat weights and CT muscle density were estimated. The estimates of heritabilities of the CT muscularity indices showed they were at least moderately heritable (from 0.38 to 0.92) in both breeds. CT muscle density, measured in the LR, had a moderate to high heritability in both breeds, and strong negative genetic and phenotypic associations with IMF and carcass fat weight. Little association was found between muscularity indices and CT muscle density, implying that improved muscularity would not have a negative effect on CT muscle density. These results suggest, overall, that the effect of selection for improved muscularity of sheep is likely to be favourable for carcass quality and neutral with respect to meat eating quality. Because of the strong phenotypic and genetic associations with IMF, CT muscle density may be a promising selection tool to counteract possible negative effects of decreasing fatness on IMF and therefore eating quality. The inclusion of CT muscle density as a selection criterion allowed more favourable genetic responses in IMF, without further unfavourable increases in carcass fat weight or detrimental effects on leanness. Because increased economic values for IMF led to different expected gains in IMF and other traits in the breeding goal, the definition of the specific values depends on the desired gains in all traits by the industry. Positive returns for the industry from using CT muscle density at the second stage of selection can be obtained for all economic values included in this simulation. The economic benefits were maximised when the proportions of ram lambs CT scanned were 0.15.

The bottom mussel industry in Northern Ireland is threatened by a number of issues arising due to overfishing and variable settlement success of mussel seed. Investigations on the Skullmartin mussel seed bed showed ~gative impacts of dredging. However, as Skullmartin is a sink: for mussel larvae, fishing ofthe bed is likely to be sustainable as long as the source ofthe larvae is maintained. The biodiversity of Skullmartin was adversely affected by dredging. Species richness and diversity decreased after dredging. However, these effects were short-lived, with species richness recovering once dredging had ceased. The transport ofstarfish from seed. bed to relaying site is a problem facing all bottom mussel growers. The mostefficient method to reduce the transport of starfish is to submerge the contents ofthe hold with freshwater. This led to 100 % mortality of starfish after 12 hours. Desiccation ofstarfish, which is used in the 1'.Torthern Ireland industry, was found to be inefficient as it required 48 hours to cause 100 % mortality, with . large mussel mortality also occurring after this time. As mussel seed is a limited resource it is imperative that it is managed efficiently. Relaying trials found that although meat content and shell length are adversely affected by an increasing relaying density, it is the marketable yield which is most affected, ,with a density of75 tha-l exceeding the carrying capacity of the study site. Spat collectors, were examined as a sustainable source ofmussel seed. Peaks in settlement appeared in the summer and Belfast Lough was found to have a significantly larger settlement than Carlingford Lough due to the larger coverage of licensed mussel relaying plot in Belfast Lough which can directly attribute to the larval supply in the Lough.