Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 92-102). Also available on the World Wide Web.

Thesis (Ph. D)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 140-146).

Thesis (Ph.D.)--Memorial University of Newfoundland, 1999. / Bibliography: leaves 212-224.

No description available.

Over the past few years one of the major concerns in the Atlantic salmon (Salmo salar) farming industry has been the increasing incidence and severity of inflammatory viral diseases. Heart and skeletal muscle inflammation (HSMI) and cardiomyopathy syndrome (CMS) are currently two of the most prevalent viral diseases in commercial Atlantic salmon farms in Norway. Mortality levels in both diseases are generally low but morbidity can be very high with the associated chronic inflammatory response lasting for several months. The consequent reduced growth performance is causing considerable financial impact as HSMI has become increasingly widespread in recent years. The impact of CMS is further exacerbated as it generally affects large fish close to harvest. HSMI lesions occur in the atrium and ventricle in the heart including inflammation and necrosis in epi- endo- and myocardium along with myositis of red skeletal muscle. CMS lesions are commonly observed in the spongy myocardium in the atrium and ventricle of the heart with severe mononuclear inflammation and necrosis. Furthermore, circulatory disturbances associated with reduced cardiac function cause multifocal liver steatosis and necrosis in both diseases. Currently there are no vaccines or any other effective treatments for these diseases and so alternative therapies that could potentially modulate the intensity of the inflammatory response could be crucial to improve the clinical manifestation of the diseases. Therefore, the overall aim of the present study was to evaluate the concept of “clinical nutrition” to improve the clinical symptoms of both viral diseases, HSMI and CMS, through the use of functional feeds formulated with reduced lipid content and increased proportions of anti-inflammatory fatty acids to moderate the apparently uncontrolled inflammatory response in the heart tissue associated with both diseases and also alleviate the secondary hepatic lesions. The experimental work consisted of three major dietary trials in Atlantic salmon in seawater. Two large trials investigated the effects of functional feeds in Atlantic salmon challenged with Atlantic salmon piscine reovirus (ASRV) and piscine myocarditis virus (PMCV), the causal agents of HSMI and CMS, respectively. In both trials, heart transcriptome, heart and liver histopathology and tissue lipid and fatty acid compositions and metabolism were determined post-infection in fish fed with the functional feeds in comparison with fish fed with a standard commercial feed formulation considered as a reference diet. All the functional feeds were formulated to have reduced digestible energy through lower dietary lipid and higher protein contents, and increased levels and proportions of anti-inflammatory long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic acid (EPA) compared with the reference diets. Histopathology, fatty acid composition and gene expression of heart were assessed over a long time-period of 16 weeks and 14 weeks post-challenge with ASRV and PMCV, respectively. Viral load in heart tissue, hepatic histopathology and fatty acid composition of liver and head kidney along with expression of the genes involved in the eicosanoid and LC-PUFA and eicosanoid biosynthesis pathways were also determined in the HSMI trial. The third trial was a nutritional trial evaluating the effects of dietary digestible energy content on lipid and fatty acid metabolism in salmon fed diets containing graded amounts of lipid. Fatty acid composition of liver and heart were assessed over 12 weeks, along with the hepatic expression of genes of lipid and fatty acid metabolism. The results of this research are presented in four chapters (Chapters 2-5) as four paper manuscripts. The manuscripts/Papers are either published (Chapter 2), in review (Chapter 3 and 4) or drafted for submission (Chapter 5) in appropriate peer-reviewed international journals. Chapter 2 and 3 correspond to the HSMI trial, Chapter 4 to the nutritional trial, and Chapter 5 to the CMS trial. Chapter 2 showed that viral load and histopathology scores were lower in fish fed the functional feeds, especially diet FF1, which displayed better performance. Diet strongly influenced the expression of genes related with the immune and inflammatory responses, with delayed expression in fish fed the functional feeds. Up-regulation of pro-inflammatory genes was correlated with the higher viral load observed at early-mid stages of the disease in fish fed the reference diet (ST). Expression of genes related with the immune response at 16-weeks post challenge reflected the differences in immunomodulation between the functional feeds, with fish fed diet FF1 showing lower expression. Therefore, severity of the heart lesions was correlated with the intensity of the immune response and could be associated with tissue anti-inflammatory LC-PUFA levels. Chapter 3 was focused on liver histopathology, fatty acid composition and LC-PUFA biosynthesis, along with phospholipid fatty acid composition and eicosanoid production in head kidney and heart tissue at early and late stages of ASRV infection. Liver was severely affected by the virus at the beginning of the infection in fish fed the reference ST diet, but the level of lesions were similar in all dietary groups at the end of the trial. Hepatic expression of fatty acyl desaturases was significantly depressed in fish fed the ST diet compare with fish fed the functional feeds despite the lower levels of dietary LC-PUFA in that feed. Thus endogenous production and bioavailability of anti-inflammatory LC-PUFA was potentially enhanced in fish fed the functional feeds. Changes in tissue lipid content, mobilization of fatty acids involved in inflammatory responses and changes in expression of transcription factors and genes involved in eicosanoid biosynthesis were more prominent in head kidney, confirming the important role of this organ in dietary immunomodulation after viral infection. To a lesser extent similar changes were observed in heart tissue, suggesting in situ production of eicosanoids could also be important. The unexpected effects of diet on expression of genes of LC-PUFA biosynthesis were specifically investigated in the trial described in Chapter 4. One aim of this study was to clarify whether dietary lipid content or viral infection was the cause of altered expression of desaturase genes between the different diets. Hepatic expression of other genes of lipid and fatty acid metabolism were also determined to evaluate metabolic changes associated with dietary lipid/energy level. In general, reduction of dietary energy and lipid contents while maintaining similar proportions of dietary fatty acids, led to a general up-regulation of genes involved in lipid biosynthetic pathways. Thus salmon fed lower energy diet showed increased liver expression of fatty acyl desaturases in comparison with fish fed higher energy levels. Heart transcriptomic data in Chapter 5 showed a similar delay in the inflammatory response in fish fed the functional feeds after PCMV infection as observed in the HSMI study. Modulation of inflammatory responses, similar to that previously described after ASRV infection, was also observed in fish fed the functional feeds. However, the differences in the expression of immune related genes and the level of heart lesions were not as prominent at mid-late stages of the disease as in fish fed FF1 in the HSMI trial. The present study demonstrated the beneficial effects of a clinical nutrition approach via functional feeds in two viral inflammatory diseases, HSMI and CMS, currently affecting farmed Atlantic salmon.

Atlantic salmon (Salmo salar L.) has been domesticated since the 1960s and has undergone over 10 generations of artificial selection for economically important traits. As a result, domesticated salmon have diverged with respect to a number of phenotypic, genotypic and behavioural traits from their wild counterparts. Since the selection pressures that are present in the wild differ greatly from the ones that shape salmon under culture conditions, domesticated salmon stocks are considered to be maladapted to natural conditions. Despite strict regulations, insoluble issues pertaining to large-scale cage rearing of farmed fish mean that there is a continuous presence of farm escapees in the wild. Gene flow from escapees has been perceived as a factor in the decline of wild populations, suggested to occur through disruption of local adaptation. This study aims to improve understanding of the genetic differences between wild and domesticated stocks by comparing the transcriptomes of Figgjo (wild) and Mowi (domesticated) strains. A series of common garden experiments have been performed, utilizing pure and reciprocal hybrid crosses of the wild and domesticated stocks, reared under two different conditions and sampled at four time points and three distinct life stages (embryo, sac-fry and feeding fry). Microarray interrogations were performed employing a 44K custom microarray design to identify genes and gene pathways that are differentially expressed between the stocks. KEGG-based functional analyses have been implemented using different gene set enrichment packages, and dominance and additive parameters were calculated from normalized expression values to predict the mode of heritability of the genes identified as differentially expressed between stocks. Most biological functions represented in wild and domesticated crosses were consistent across life stages and environments. The transcriptomic differences detected between stocks in multiple developmental stages likely reflected adaptations to selection pressures differing between natural and aquaculture environments. Down-regulated environmental information processing and immune and nervous system functions in domesticated vs. wild fish may be due to local adaptation to captivity. These included reduced information acquisition and processing systems, altered stress responsiveness and changes in feeding behaviour. In line with the resource allocation theory of production trait animals, reduced immune function was coupled with increased expression of growth and development related pathways in domesticated salmon, compared to wild counterparts. Although there is support for this trade-off in all life-stages, resource allocation showed a shift over time; possibly reflecting variation in the utilization of energy sources during the transition from endogenous to exogenous feeding. Differences in cell communication and signalling pathways between wild and domesticated stocks, associated with organogenesis during the embryo stage, reflect sampling time and are indicative of altered organ development in response to domestication. Stress responses common across stocks included the down-regulation of cellular processes, including cell cycle and meiosis, and genetic information processing, such as replication and repair, transcription and translation pathways, probably reflecting the reallocation of energy resources away from growth and towards the restoration of homeostasis. Moreover, the mobilization of energy to cover the increased demands of maintaining homeostasis was indicated by the up-regulation of some metabolic pathways, mostly involved in energy, lipid and carbohydrate metabolism in response to stress. The analysis also revealed cross-specific stress responses, including indicators of a non-additive stress response in hybrid crosses. Most differentially expressed transcripts exhibited additive (31-59%) or maternal dominant (19-33%) inheritance patterns, although maternal over-dominance (23-26%) was also significant in the embryo stage. The mode of heritability of some immune transcripts was suggestive of maternal environmental influence having been affected by aquaculture. This study has demonstrated that biological functions affected by domestication include those associated with allocation of resources, involve reduction of information acquisition and processing systems and may lead to loss of local adaptation to wild conditions. Since such changes may affect key systems, such as immunity and responsiveness to stress, they can potentially have serious negative consequences under natural conditions. Transcriptomic differences observed between wild and domesticated stocks primarily exhibited additive and maternal dominant inheritance modes. Since gene-flow from farmed fish can be frequent and primarily concerns farmed females, this suggests that introgression due to repeated large scale escape events has the capacity to significantly erode local adaptation.

The rapid 1980's development of the salmon farming industry in British Columbia has been called "a poorly defined experiment in a poorly understood coastal environment", and the main impetus behind it described as "the chaotic, bottom-line orientation" not only of the industry itself but also of relevant government policy. The purpose of this thesis is to elaborate on these themes by identifying and delineating the most significant reasoning models underlying government development policy; and to offer an evaluation of the policy's 'rationality'. Throughout the development of the industry, but particularly in the early stages, two major areas of uncertainty have been prevalent. First, detailed government policy towards salmon farming has been far from clear - an inarticulation that is characteristic of the philosophy of laissez faire, which was particularly influential in Canadian government policy in the early 1980's. Secondly, a variety of possible ecological impacts have been suspected from the outset. A heuristic approach, both for the basic method employed in the thesis and for the normative model set up to evaluate government policy, is advanced for addressing these different uncertainties. In order to identify relevant policy, it is hypothesized that systems of ideas expressed formally in 'core' models of neoconservative and neoclassical economics were particularly important policy influences. It is argued that the core concept of neoconservative theory (as defined) is the adaptive efficiency of the autonomous market. The theory's fundamental adaptive ideas - economic information 'discovery' by competitive trial-and-error selection, and consumer 'regulation' via the price system - are to be found in representative federal and provincial economic policy documents from the early 1980's, as well as in the occasional government elucidations of B.C. salmon farming policy (scattered in heterogeneous historical sources). An examination of (inferred) specific decisions relevant to ecological aspects of salmon farming reveals the influence of trial-and-error - deliberate omission of government planning - on early salmon farm siting policy; and the influence of the presumption of consumer 'sovereignty', which was assumed to obviate the need for government ecological regulation. The relevant core concept of neoclassical economics (as defined) is the rational model derived from the conception of homo economicus. The model and its derivations are visible in the same early 1980's economic policy documents, which outline public sector 'restraint' criteria, as well as in salmon farming policy elucidations. It is argued that the maximizing 'solution' prescribed by the model is without operational significance in complex, uncertain situations, where ostensible use of the formal technique may be to legitimate decisions taken on other grounds. The normative model set up to evaluate government policy is drawn from three sources: Friedrich Hayek's rationalization of the adaptive market process, C.S. Holling's prescriptions for "adaptive environmental assessment and management", and Herbert Simon's development of "procedural rationality". These models support the conclusion that acquisition of information by the agency that mediates actions and goals - which, in the case of ecological regulation, must be government - has major value as the basis of more rational decisions. But acquiring conclusive evidence by trial-and-error learning involves risk of serious error, particularly irreversible ecological harm, and it is rational to utilize the inconclusive evidence that is always available for making general predictions, in order to guide search and select lesser risks. Incorporating the important constraint of search costs - particularly significant in the economic recession of the early 1980's - the requirements for rational adaptation become minimal, procedural ones of 'reasonableness': lack of bias towards any class of information relevant to social welfare; lack of denial of uncertainties, and thus of development risks, in the complex and little-known salmon farming environment; and timely response to uncertainties subsequently, adequately resolved by experience. It is suggested that all three requirements were infringed by government policy towards salmon farming development. / Science, Faculty of / Resources, Environment and Sustainability (IRES), Institute for / Graduate

Digestible carbohydrate is commonly encountered by chinook salmon {Oncorhynchus tshawytscha) in practical culture diets, although little is known regarding its utilization. This study was undertaken to examine (1) the effects of a high carbohydrate diet and (2) glucose tolerance in chinook salmon of selected British Columbia strains. Yearling chinook salmon of three strains were fed to satiation either a high or a low carbohydrate diet for 63 days. The diets were isonitrogenous, and contained respectively 30 % gelatinized wheat starch or an equicaloric amount of herring oil. There was an overall reduction in growth of chinook fed the high-carbohydrate diet over the 63-day feeding period. Although specific growth rates declined initially in the high carbohydrate-fed groups, they were comparable to those of control groups in the final third of the trial, indicating an adaptation response. Chinook fed the high carbohydrate diet had increased carcass protein and ash, and decreased carcass fat levels relative to controls. Feed intake was generally lower in these groups, and differences in feeding response were observed between diets and strains. Although feed and energy efficiencies were reduced in chinook fed the high carbohydrate diet, protein utilization was comparable on the two diets, indicating a protein-sparing effect of the carbohydrate. Consumption of the high carbohydrate diet led to significant elevations in hepatosomatic indices (HSI) and liver glycogen (LG) concentrations. In Quesnel chinook, LG levels exceeding 10 % did not appear to have any detrimental effects on feeding, growth or health. LG concentrations and HSI fell to basal levels in all groups 21 days after feed withdrawal. Some strain differences were evident. For example, Big Qualicum chinook fed the high carbohydrate diet exhibited the lowest liver glycogen accumulation, highest rate of carcass fat deposition, and best energy efficiency ratios relative to control groups, suggesting a difference in carbohydrate metabolism in this strain. On the other hand, Quesnel chinook exhibited the highest relative growth on the high carbohydrate diet. Mortality, although unaffected by diet in the Quesnel and Robertson Creek chinook, appeared to be higher in high carbohydrate-fed Big Qualicum chinook. In the second part of the study, chinook salmon subjected to an oral glucose tolerance test displayed pronounced and persistent hyperglycaemia, indicative of poor glucose tolerance. Strain differences were evident in the magnitude of response. Acclimation to a high carbohydrate diet prior to testing resulted in a significantly reduced elevation of blood glucose, indicating an adaptation response. While plasma glucose concentrations approached 500 mg/dl in some trials, plasma insulin concentrations exhibited a two-fold rise, with indistinct peaks. Plasma glucose and plasma insulin concentrations were poorly correlated, indicating that glucose is a poor insulin secretagogue in chinook salmon. / Land and Food Systems, Faculty of / Graduate

The genetic relationship of anadromous (sockeye salmon) and non-anadromous (kokanee) Oncorhynchus nerka was examined in conjunction with the breeding behaviour of the two forms to determine: (1) if there is evidence of genetic divergence between the forms where they spawn sympatrically; (2) if such divergence is associated with significant premating isolation between the forms and; (3) if premating isolation results directly from the size difference between the forms (sockeye are much larger than kokanee at maturity). Both sexes exhibit spawning territoriality; females establish and defend particular nest sites until death or displacement, males defend access to specific females from other males until the female has spawned out, they are displaced, or leave to compete for additional mates. Size and prior access to resources (mates and/or specific areas) are significant factors in intrasexual aggression in both sexes, with size the major factor in males and prior access the major factor in females. Females accompanied by males larger than themselves lose weight at a faster rate than those accompanied by males smaller than themselves. Weight loss is related to egg loss, indicating females spawn at a faster rate when accompanied by large males. Male mate preference depends on the size of the male. Males of various sizes prefer females of their own size or larger over females smaller than themselves. In contrast, all sizes of males tested demonstrated no preference between females of their own size and those larger. Large males, which have the widest range of potential mates (because of male intrasexual competition and female choice), are the most selective and small males, which have the narrowest range of potential mates, are the least selective. There were significant differences in allele frequencies between sympatrically spawning sockeye and kokanee. However, there were no consistent differences between sockeye and kokanee at any of five polymorphic loci examined. The extent of genetic differentiation between sympatric forms appears to be less than that between neighbouring populations of the same form, judging from an examination of allele frequencies and/or allele compositions. There was extensive assortative mating by form between sockeye and kokanee, which was not totally accounted for by the large size difference. In the two systems examined, males preferred to mate with females of their own form. In sockeye, such preferences are expected because of the size difference between forms. In kokanee, such preferences are not expected based on size alone, suggesting the evolution of premating isolating mechanisms. The degree of premating isolation was positively correlated with the extent of genetic divergence between sympatric forms. The results of this study are related to existing models of sympatric speciation to hypothesize that sockeye and kokanee have diverged in sympatry. The probable differences in selection between the marine and freshwater environments coupled with the assortative mating resulting from their size difference may have caused subsequent genetic divergence. This divergence appears to have been followed by the evolution of premating isolation. / Science, Faculty of / Zoology, Department of / Graduate

This study was conducted to satisfy three objectives. The first was to provide a detailed description of the differences between the prey contents of rainbow trout (Salmo qairdneri) and kokanee (Oncorhynchus nerka) compared either to each other or to the prey contents of the natural environment. The second was to determine how elements of anatomy, physiology and behaviour interact to promote the acquisition of species specific diets by trout and kokanee. The third was to precisely identify the foraging strategies of the two predators by assessing how different anatomical and behavioural characteristics serve as interrelated adaptations that suit each species to effectively use a specific habitat-prey complex. Matched samples of trout and kokanee from Marion Lake exhibit only modest A dietary overlap (mean of C λ = .462, range.136 to .881). Although kokanee appear to track the environmental abundance of prey more closely than trout, both predators exhibit pronounced patterns of "density independent" acquisition of prey from the total complex of prey that is apparently available in the lake. To test hypotheses about the factors that control these dietary patterns, I conducted a series of studies concerning where trout and kokanee choose to forage, when they choose to forage, how they search for prey, how they attack prey, and how experience in encountering various prey alters the predator's foraging behaviour. Temporal segregation of trout and kokanee foraging activities is not well-developed under field conditions and appears unlikely to promote strong patterns of food-resource partitioning. By contrast, spatial segregation is well-developed and clearly plays a major role in promoting the acquisition of relatively large numbers of nearshore benthic prey ( eg. planorbid snails or odonates ) by trout and of relatively large numbers of offshore, water-column prey ( eg. chironomid pupae ) by kokanee. Close inspection of the details of predator and prey distributions indicates that many aspects of food-resource partitioning are not logical outcomes of spatial segregation. Differences in predator search-techniques do not determine the presence or absence of various prey types in predator diets, however, differences in predator search behaviours do bias them to obtain different quantities of particular classes of prey. Kokanee search procedures allow them to detect prey in both exposed and concealed locations while trout detect only exposed prey. While searching for benthic or lake-surface prey, kokanee maintain search positions which allow them to detect prey of smaller sizes than trout. This clearly favours the trend for kokanee to include greater quantities of small prey (eg. Hyalella sp.) in their diets than trout. Differences in search procedures do not explain why kokanee obtain a greater proportion of their diet than trout from small zooplankton (≤ 1 mm ) in late summer or why kokanee seldom exploit any of the relatively large ( > 4 mm ), armoured prey that are common in the diet of similar sized trout. Differences in both behavioural and morphological characteristics involved in the attack phase of foraging by trout and kokanee serve as the basis for explanations of a number of differences between the diets of free-ranging predators. These differences include: the greater utilization of aerial prey by trout, the inclusion of large numbers of copepods in the diet of kokanee but not of trout, the generally greater utilization of zooplankton by kokanee compared to trout, and the relative-scarcity of large ( > 4 mm ), armoured prey, in the diet of kokanee. A series of laboratory experiments was used to examine the extent to which short term experience might influence food-resource partitioning by trout and kokanee. These experiments offered convincing evidence that differential effects of experience will amplify the trends in resource partitioning already set in motion by differences in habitat selection, search procedures, and attack procedures. I argue that the morphological and behavioural traits that control food "selection" by trout and kokanee in Marion Lake are a consequence of the evolution of mutually exclusive foraging strategies. Trout are portrayed as D-strategists that concentrate on relatively large, dispersed prey for the bulk of their energy requirements. Adaptations which enable trout to differentially exploit large prey include: procedures for area-extensive search; a predisposition to attack relatively large, armoured-prey; large mouth-size; and persistent responses to opportunities to attack large prey. An inability to sustain high attack rates on small prey ( < 1 mm ) at high density ( 35 per liter ) and a tendency to ignore or reject such prey suggest that trout are not well-adapted to exploit relatively small, morphologically-uniform,prey. Kokanee are portrayed as C-strategists which concentrate on relatively small, contagiously-distributed prey for the bulk of their energy requirements. Adaptations which enable kokanee to differentially exploit small prey include: procedures for area-intensive search; a predisposition to attack relatively small, morphologically-uniform prey; small mouth-size; well-developed gill-rakers; and an ability to sustain high attack rates on small planktonic prey. Low ingestion success with a variety of large benthic prey and a tendency to ignore or reject such prey under laboratory conditions where they serve as the sole source of food are evidence that kokanee are not well adapted to exploit large, armoured-prey. Adaptations associated with the search, capture, manipulation and ingestion phases of the foraging cycle appear in each instance to be evolutionary responses to specific features of a given habitat-prey complex. C-selected or D-selected foraging strategies appear to be mutually exclusive evolutionary avenues down which trout and kokanee have been directed by the fundamental nature of a given habitat-prey complex. / Science, Faculty of / Zoology, Department of / Graduate