Thesis (M.S.)--Oregon State University, 2006. / Printout. Includes bibliographical references (leaves 90-96). Also available on the World Wide Web.

Thesis (Ph. D.)--Oregon State University, 2006. / Printout. Includes bibliographical references (leaves 284-312). Also available on the World Wide Web.

Thesis (M.S.)--Oregon State University, 2006. / Title from metadata title field (viewed Nov. 13, 2006). Includes bibliographical references (p. 90-96).

Thesis (Ph. D.)--University of Washington, 1986. / Vita. Bibliography: leaves [173]-183.

49 leaves ; 29 cm Typescript Thesis (M.S.)--University of Oregon, 1974 Includes bibliographical references (leaves 45-49) Unif. Title University of Oregon theses, Dept. of Biology, M.S., 1974

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Freshwater ecosystems and the species that reside therein are disproportionately imperiled compared to terrestrial systems. Over the past 150 years, the Columbia River basin in the western United States has gone from one of the most productive and abundant salmon watersheds in the world, to having just a small fraction of its former salmon abundance. The cause of declines in salmon productivity and abundance are related to overlapping and confounding stressors including changes in large-scale climatic patterns and anthropogenic alterations within and adjacent to the Columbia River. Four main anthropogenic stressors have been identified as the leading causes of salmonid declines: commercial harvest of adult salmon, hydroelectric power generation and associated reservoirs, habitat loss due to impassible dams and restricted access to historical habitat, and hatchery production. My dissertation broadly examined how salmon ecology and population dynamics have been influenced by anthropogenic alterations occurring within the Columbia River basin. This dissertation addresses three main questions: Do the hydroelectric dams on the Lower Columbia River represent a pulse- or press-type ecological disturbance to migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) and what are the biotic and abiotic factors that most influence the survival of fish passing multiple dams? How do wild and hatchery fish differ in regards to the precocious life-history strategy, and which variables influence this strategy across environments (freshwater to marine) and life stages (egg to adult)? What are the morphological differences between wild and hatchery salmonids and how much of that variation is attributable to rearing-environment? I found that high outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to an ecological press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids during this life stage. Both biotic and environmental factors affect precociousness in hatchery and wild Chinook salmon, across freshwater and marine environments. Wild fish are influenced by density-dependent processes in freshwater, as well as marine conditions that promote growth. Wild Chinook have the highest probability of precocious maturation when large smolt (>150 mm) experience productive marine environments within the first several months of ocean residence. Precocious hatchery fish are broadly influenced by conditions experienced during freshwater residency, outmigration, and in marine habitats. There was no interaction between the size of hatchery fish and environmental variables, suggesting that these fish attained the size required to mature precociously prior to migration. These results indicate that hatchery Chinook salmon do not respond to the same environmental cues that determine life history transitions as wild Chinook salmon, likely as a result of different physiological conditions and environmental exposures during early life stages. There are ecological and economic consequences to the precocious life history strategy including reduced marine-derived nutrients entering freshwater ecosystems and a loss of investment for fish intended for the adult fishery. There are significant differences in body shape between wild and hatchery origin Chinook salmon and steelhead that can be partially explained by rearing environment and variables influenced by smoltification. Hatchery fish of both species are significantly larger (i.e. centroid size, length, weight) than wild fish but have comparable or lower condition factor. In general, hatchery fish have smaller heads and longer, thinner tails (i.e. fusiform) compared to wild fish. Allometric trajectories (i.e. shape change with size) indicate that the shape of wild and hatchery fish are significantly different at small and large sizes. Wild and hatchery Chinook salmon became more morphologically different as size increased, while steelhead became more similar. The overall amount of shape variation was not significantly different between wild and hatchery Chinook salmon. This finding suggests that regardless of significant differences in the way shapes vary, hatchery Chinook have not lost overall shape variation. Total amount of shape variation was significantly greater in wild compared to hatchery steelhead, indicating that hatcheries may have a homogenizing effect on steelhead shape. I recommend a coordinated effort between federal, state and tribal hatcheries to incorporate elements of the natural rearing environment into conventional hatcheries. These elements include in-water structure that promotes the burst swimming mode, increased water velocities to increase dorsal-ventral distance, under-water feeding apparatus that reduce surface feeding behavior, overhead cover and mimicked predators to teach escape behavior. Major advancements have been made in identifying and ameliorating negative effects of anthropogenic alterations within the Columbia Basin, however, many wild populations continue to decline. My research suggests that the physical (i.e. weirs and bypass structures) and operational alterations (i.e. voluntary spill) to the lower Columbia hydrosystem have substantially improved conditions for migrating smolt compared to past years, but involuntary spill during years of high flow continue to create deleterious conditions for migrating smolt. Riverscape-scale management strategies that recognize biotic and abiotic connectivity between dams (i.e. press disturbance) will benefit migrating smolt. My research indicates that hatchery fish are not currently equal or adequate replacements for wild fish. Hatcheries vary greatly in their stated goals and desired outcomes and several coordinated changes to general hatchery practices may help produce fish that are more similar to wild fish in morphology and life histories: 1) Change the goals of production away from producing as many, large individuals as possible, to producing fish that resemble the target wild populations they are intended to support; 2) Alter the hatchery environment to reflect the rearing environments in which salmon evolved and into which they will be released; and 3) Reduce the annual number of hatchery fish released into the Columbia Basin for the sole purpose of harvest. Recovering and rehabilitating critical and diverse habitats utilized by salmonids at each life stage (spawning, rearing, migration, estuary and marine) remains crucial for wild population success into the future.

Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex stream habitat to potentially support a diverse salmonid assemblage. The materials deposited by debris flows would otherwise be inaccessible to streams, and thus deposits may play an important role in creating and maintaining complex salmonid habitat over time. Despite the potential of deposits for increasing habitat complexity, most fish studies have focused on the destructive effects of debris flows and short-term recovery and re-colonization in scour zones. Debris-flows that occurred during the record-setting winter storms of 1996 in western Oregon, USA, provide an opportunity to study intermediate-term effects of debris-flow deposits on abundances and habitat for juvenile salmonids. In this setting, I surveyed salmonid abundance and habitat in three Oregon Coast Range streams that contained several debris-flow deposits from the 1996 storms. I explained fish abundance using hierarchical models, accounting for heterogeneous detection probabilities with repeated counts from multiple-pass snorkeling. The "best" hierarchical model of detection probability and abundance was selected (QAIC) from pool and snorkel-pass characteristics separately for juvenile coho salmon (Oncorhynchus kisutch), age 0+ trout, and age 1+ trout (Oncorhynchus spp.) in each stream. Adding distance to the nearest 1996 debris-flow deposit (DDF) produced a significant drop-in-deviance for four of nine "best" models, including at least one in each stream and for each species/age-class. In these four models, salmonid abundance decreased with increasing distance from deposit. As a potential explanation, several pool habitat characteristics were correlated (Spearman's rank) with DDF. Results varied across streams, but generally, percent of substrate as bedrock was lower and boulder density and percent substrate as gravel were higher closer to deposits. Although repeat counts are increasingly used in hierarchical modeling of heterogeneous detection probabilities and abundance for other wildlife species, studies of fish often rely on uncalibrated, single-pass snorkel counts. When exploring the value of repeat counts, I found that juvenile salmonid abundance decreased with increasing distance from debris-flow deposits in more multiple-pass hierarchical models that accounted for heterogeneous detection probabilities than for single-pass models that did not. Thus, modeling heterogeneous detection probabilities with repeated snorkel counts may be beneficial in other situations, addressing limitations of uncalibrated indices without relying on methods such as electrofishing, which may be difficult or impossible for remote study areas, longer surveys, or sensitive species. My findings suggest that debris-flow deposits may influence salmonid abundances after 15 years, and support management of debris flow-prone hillslopes and low-order channels to deliver elements of stream habitat complexity. / Graduation date: 2013

Photoperiod manipulations are widely used throughout the Atlantic salmon (Salmo salar) farming industry as a means of producing a product of uniform quality all-year round. However, farmers still remain sceptical over their effectiveness to regulate growth and maturation during the on-growing stage. Furthermore, reports of a characteristic growth-dip following light exposure suggest that light may negatively affect the physiological performance of fish in the short-term. Thus, this thesis investigates the effects of light characteristics (spectral quality, intensity and photoperiod) on growth and maturation of salmonid fish and addresses some of the uncertainties surrounding photoperiod use currently reported within the industry. Rainbow trout (Oncorhynchus mykiss) are seemingly an ideal model species for examining photoperiod effects on growth. Consequently, the application of constant light exposure (LL) at two different intensities (28W and 16W) during two different thermal conditions (summer and winter) was examined on individually tagged fish. Feed intake and growth appeared to be related to the ambient water temperature and did not appear to be affected by intensity or photoperiod, although the onset of constant light did appear to initially affect growth rate. This may indicate that LL has a limiting effect on the growth of trout or that the prevailing water temperature at which light is applied may override the photoperiodic effect. Furthermore, the lack of enhanced growth in trout exposed to LL, unlike that demonstrated for other salmonids, suggest that there may be a species-specific response to environmental variables. Thus, questions regarding photoperiod effects should be limited to the species in question. The main source of variation in results observed under photoperiod manipulations stems from the salmon industry. Atlantic salmon post-smolts were reared in seawater tanks and either maintained under a natural photoperiod (NP) or exposed to a simulated natural photoperiod (SNP), constant light superimposed on the natural light (NPLL) or constant light only (LL). Artificial light onset, irrespective of photoperiod, resulted in an apparent trend for a reduced appetite lasting up to 60 days. Furthermore, the onset of constant light resulted in a significant chronic elevation of plasma cortisol levels and changes to growth and thyroid hormone levels, providing direct evidence that constant light exposure induces stress. In addition, fish exposed to SNP failed to exhibit a stress response despite a low feed intake. However, differences in the plasma melatonin levels during twilight times, as compared to NP, suggest that gradual changes in the natural light intensity throughout the day, particularly around dawn and dusk, may be important for synchronizing daily events. No differences in growth were observed between the NP and NPLL regimes, although fish reared in an enclosed regime (SNP and LL) exhibited a significantly lower weight gain than fish in an open environment (NP and NPLL). This further highlights the impact that the rearing environment has on the growth performances of fish and the need for commercially run trials. Advances in lighting technologies and a greater understanding of how light is transformed through the water column have focussed research on the spectral sensitivity of fish. Therefore the lighting efficiency of novel blue narrow bandwidth LED lighting units through the water column and their effects on growth and maturation performances of salmon reared in commercial production cages were compared against the standard metal halide units currently utilized throughout the industry. LL application, irrespective of intensity or spectrum, reduced the numbers of fish maturing as compared to fish reared under a natural photoperiod. However, this was greatest under the standard metal halide units reflecting a greater light penetration and perception as determined by plasma melatonin levels. The metal halide groups exhibited the greatest relative weight gain over the trial period as compared to control fish. No evidence was observed for a growth-dip under metal halide light, although blue lit treatments exhibited an initial significant reduction in food consumption, suggesting a possible welfare issue. Nevertheless, the prototype blue LED units showed possible potential for commercial application by penetrating the water depth at half the distance of the metal halide units for only one eighth the power and one fifth the brightness. However, further tests of these prototype spectral units are required to examine the potential welfare and physiological growth and reproductive effects. These studies have shown that the efficacy of artificial light regimes is largely dependent upon the effectiveness of the light source through the underwater environment and its perception by fish, providing a sufficient intensity is emitted exceeding the physiological threshold level for the species cultured. Moreover, whilst the onset of artificial light may elicit a stress response and demonstrate a trend for a suppression of appetite for salmon reared in experimental tanks, no compelling evidence for a suppression of appetite or growth was found under normal commercial cage conditions. This suggests that the growth-dip observed within the industry may in part be a combination of a physiological response to the onset of light further exaggerated by the farmer’s perception and altered judgement in feeding. In addition, the results obtained from this study have helped to standardize the use of light regimes within the industry. Nevertheless, further studies are necessary to fully elucidate the underlying mechanisms which may govern growth and maturation in fish following the onset of light exposure.

La pollution croissante des milieux aquatiques nécessite la mise au point de nouvelles technologies permettant d’optimiser la surveillance de la qualité de l’eau. Dans ce contexte, nous avons développé un biomarqueur de susceptibilité du degré de la pollution globale des milieux aquatiques intitulé « Sentinelle ». Le principe du biomarqueur Sentinelle est basé sur le niveau de coexpression de deux protéines « Multidrug Resistance » (MDR), la protéine ABCG2-like et la P-gp, dans les érythrocytes de la truite Salmo trutta fario. Le biomarqueur sentinelle a été validé en conditions in vitro grâce au développement des cultures primaires d’érythrocytes de truite. Après l’exposition des globules rouges de truites à des concentrations croissantes d’un polluant modèle, le Benzo-a-pyrène, l’expression de la protéine ABCG2-like et de la P-gp augmente d’une manière dose dépendante. Le biomarqueur Sentinelle a ensuite été validé en milieu naturel sur des truites fario en provenance de différents cours d’eau d’Auvergne. En milieu naturel, les deux protéines MDR sont exprimées différemment dans les érythrocytes de truites fario selon le degré de contamination du cours d’eau. En effet, dans une rivière où la pollution est faible voire nulle, seule la protéine ABCG2-like est exprimée, alors que dans une rivière présentant une contamination plus importante, la P-gp et l’ABCG2-like sont toutes les deux coexprimées par une réponse de type relais. Les expériences menées en conditions in vitro et en milieu naturel, laissent supposer que la protéine ABCG2-like assure une fonction de garde alors que la P-gp assurerait une fonction de protection défensive. En conséquence, selon le niveau d’expression de la protéine de garde et de la protéine de défense, le degré de contamination de la rivière pourrait être évalué. L’intérêt de l’utilisation du biomarqueur Sentinelle a aussi été validé sur des Salmonidés en provenance de pisciculture. Ce nouvel outil biologique apporte des informations plus intégratives et plus précoces sur la qualité des milieux aquatiques, informations essentielles pour une meilleure gestion des ressources en eau. / Increasing aquatic pollution requires the development of new technologies for to optimize the monitoring of water quality. In this context, we have developed a “biomarker of susceptibility” designating the degree of global pollution in aquatic medium, entitled "Sentinel". The Sentinel biomarker is based on the co-expression level of two major "Multidrug resistance" (MDR) proteins, such as ABCG2-like protein and P-gp, in erythrocytes of brown trout’s in response to aquatic pollution. After developing a primary erythrocyte culture, the Sentinel biomarker was validated in a controlled medium. Trout erythrocytes exposure to increasing concentrations of Benzo-a-pyrene, a model pollutant, induced an increase expression of ABCG2-like protein and P-gp by a dose-dependent response. The Sentinel biomarker was then developed in a natural environment, using the erythrocytes of brown trout collected from the various rivers located in the Auvergne region of France. In the natural environment, both MDR proteins are differentially expressed in the erythrocytes of brown trout depending on the degree of contamination of rivers. Indeed, wild brown trout erythrocytes in an uncontaminated river, expressed only the ABCG2-like protein, whereas, in a river presenting a higher contamination, P-gp and ABCG2-like were both coexpressed with a relay response. Experiments in vitro conditions and natural environment, suggest that ABCG2-like protein acts as a vanguard protective protein, in complement to P-gp which acts as a “defensive” protective protein. Consequently, according to the expression level of the vanguard and defense proteins, the degree of contamination of the river could be evaluated. The use advantage of the Sentinel biomarker has also been validated on Salmonidae erythrocytes form farmed fish. This new tool provides biological information more early and integrative on the quality of aquatic environments. These informations are essential for better management of water resources.