River flow regime is fundamental in determining lotic fish communities and populations, and especially of salmonid fishes. Quantifying the effects of human induced flow alteration on salmonids is a key question for conservation and water resources management. While qualitative responses to flow alteration are well characterised, a more intractable problem is quantifying responses in a way that is practical for environmental management. Using data drawn from the Environment Agency national database, I fitted generalised linear mixed models (GLMMs) using Bayesian inference to quantify the response of salmonid populations to the effects of impounding rivers, flow loss from rivers due to water abstraction, and the mitigating effects of flow restoration. I showed that in upland rivers downstream of impounded lakes, the magnitude of antecedent summer low flows had an important effect on the late summer abundance of 0+ salmonids Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). In contrast, the abundance of 1+ salmon and brown trout appeared to be largely unresponsive to the same flows. I demonstrated that short-term flow cessation had a negative impact on the abundance of 1+ brown trout in the following spring, but that recovery was rapid with negligible longer-term consequences. I further established that flow restoration in upland streams impacted by water abstraction provided limited short-term benefits to salmonid abundance when compared with changes at control locations. However, while benefits to salmonid abundance were limited, I detected important benefits to the mean growth rates of 0+ and 1+ brown trout from flow restoration. I discuss the implications of my findings for salmonid management and conservation and propose a more evidence-based approach to fishery management based on robust quantitative evidence derived using appropriate statistical models. The current approach to flow management for salmonids requires revision and I recommend an alternative approach based on quantitative evidence.

The safety of migrating salmon, especially salmonids, in the Pacific Northwest has been a concern for decades. With the advent of fish bypass systems, and safer turbines the focus of salmon safety has turned to total dissolved gases. Produced by entrainment of air into tailrace waters, total dissolved gases (TDG) can cause gas bubble disease, a harmful and potential lethal disease in fish. Avian predators are another danger for migrating salmon. In some areas of the world birds common in the Pacific Northwest can account for as much as 65% of salmon smolt losses. The goal of this thesis is to determine the effects of changing operational conditions at McNary dam on fish exposure to predator habitats and TDG. Computational fluid dynamic models were implemented to predict the hydrodynamics, TDG distribution and inert particle trajectories in the tailrace of McNary dam for varying operational conditions. A 3D volume of fluid (VOF) model was used first to capture the free surface shape in the tailrace. A rigid-lid model was then used to simulate the hydrodynamics and TDG distribution within the tailrace using the free surface shape from the VOF model. This 3D two phase model utilized an anisotropic Reynolds Stress turbulence model. All grids were generated using the commercial Gridgen software. A lagrangian particle tracking model that followed Newton's laws of motion were used to track inert particles throughout the domain. Validation of the model was performed. A grid refinement study with four different refinement levels was performed. Velocities for each grid type were compared against field data taken in 2004, and TDG was compared amongst the four grids. It was determined the medium level of refinement could accurately predict the velocities, and the TDG was relatively independent of grid density; TDG averages at the grid outlets were within 1.435% of one another. The TDG distribution was then compared, using the grid of medium refinement against field data measured in 1997and were between 1.5 and 3% of error depending on the transect. After validation of the model 16 predictive simulations were run with varying levels of total river flow and operational conditions. Tailrace hydrodynamics along with TDG production and distribution were compared for simulations with comparable total river flow rates. Fish trajectories were tracked using the particle tracking model. Inert particles were injected into the domain and properties such as velocity, distance to the shore and depth about each were recorded. Statistics were then generated for the particles based on criteria that defined dangerous predation zones within the tailrace. After completion of the simulations, it was determined that existing operations consistentlyproduced higher levels of TDG due to increased entrainment of the powerhouse flows into the spillway regions. It was also found that with increasing total river flows, TDG levels increased. On average, summer operations had lower TDG than spring due to the lower total river flows. Predation zones were similar for all simulations, but particle statistics varied depending on operational conditions. In general, particles were safer for higher flowrates as fewer low velocity eddies where particles could be trapped formed in simulations with high flowrates.

Utility companies and regulatory agencies are interested in understanding juvenile salmon swimming patterns as they approach hydropower dams because it can allow them to assess fish bypass efficiency and conduct fish survival studies. A model capable of predicting juvenile salmon swim paths can assist in the design of fish bypasses and diversion structures. This thesis presents a mechanistic model tailored to simulate swimming patterns of juvenile salmon swimming in forebays, tailraces, and free-flowing rivers. The model integrates information on juvenile salmon behavior at both field and laboratory scale and literature on juvenile salmon swimming capabilities. Simulated fish swim paths are determined by solving Newton's Second Law. Most of the model parameters are represented by probability distributions. Behavioral responses are triggered for the most part by the flow acceleration and pressure. The model uses conditional probability distributions of thrust magnitude and direction, given flow acceleration. Simulated fish select a swimming direction referenced to the flow velocity vector. To consider juvenile salmon's tendency to coast with the flow, the model intersperses periods of active swimming and gliding. Chinook salmon measured swim paths were analyzed. The flow variables at the fish locations were obtained from CFD simulations. Juvenile salmon mean thrust was determined from solving Newton's Second Law at every measured location. Results show that as flow acceleration increases, the juvenile salmon average thrust increases and the probability of gliding decreases. Chinook salmon tend to migrate tail-first as flow acceleration increases. For the flow accelerations of 5x10-4 m/s2 and 1x10-2 m/s2, approximately 85% and 95% of the analyzed fish migrated tail-first, respectively. The model capacity to predict fish migration route selection, fish-like trajectories, and residence times was tested at two hydropower dams. On average, migration routes were predicted with 17 percent of relative error. Model predictions for fish average residence times were within 10 percent of measured values.

Graduation date: 2002

Stocks of salmon are declining in the Pacific Northwest. Based on region-wide studies that list and categorize the status of salmon stocks (Nehlsen et al., 1991; Huntington et al., 1994; and Nawa, 1995), I analyze the watersheds where stocks of salmon spawn for several anthropogenic variables, most of which are known to affect salmon. A total of 202 watersheds (stocks of salmon) in Washington, Oregon, California, and Idaho are coded for 13 anthropogenic variables such as dams, forest, agriculture, human population, hatcheries, Indian tribes, and watershed organizations. Most variables are ordinally coded 1 to 5 with the help of maps, some survey results, and visual assessment. Hypotheses are that the human activities that are detrimental to the health of salmon are associated with the poor status of salmon stocks in watersheds where they spawn. Salmon watersheds are also analyzed according to ecoregions and salmon management regions. Principal components analysis is performed to reduce the number of anthropogenic variables into factors. Kendall's tau, partial correlation, multiple linear regression, logistic regression, and discriminant analyses are performed separately for five species/races of salmon (coho, spring chinook, summer chinook, fall chinook, winter steelhead) and for the watershed average for salmon stock status, against the anthropogenic variables and factors. Statistical results using both variables and factors support most of the hypotheses relative to salmon and anthropogenic activities in watersheds. Results suggest that the 5 species/races of salmon are associated differently with most anthropogenic activities. The greater the amount of dams below watersheds where salmon spawn, the less healthy the salmon stocks. Summer chinook are least healthy where hatcheries are absent, while wild and scenic rivers are associated with healthier spring chinook. Coho are least healthy where there is more agriculture, more human population, and less forest. Fall chinook are least healthy where there is more US Forest Service land. Winter steelhead are least healthy where hatcheries are absent and less Indian tribal land. Ecoregional differences coupled with the absence of dams on the Coast compared to the Columbia Basin are associated with healthier coastal stocks. / Graduation date: 1998

Although differences between selective pressures in hatcheries and streams have been theorized to cause genetic divergence between hatchery and wild salmonids, evidence of this is lacking. This study was initiated to document the presence or absence of genetic change in hatchery and wild stocks by characterizing genetic traits in fish of various life history stages within a single generation. Nine biochemical traits (enzyme loci) and 12 meristic traits were characterized for adult fall chinook and one or more juvenile stages of their progeny of the 1984 brood year. Study groups consisted of hatchery-reared and naturally-reared subunits of populations in two tributaries of the lower Columbia River: Abernathy Creek and the Lewis River. Parents of both groups from Abernathy Creek were primarily of hatchery origin, whereas parents of both groups from the Lewis River were primarily of wild origin. The experimental design thus included reciprocal comparisons of hatchery and wild-reared groups from each of two stocks: one that has been propagated under hatchery conditions for at least five generations and one that has evolved in a stream environment. Both biochemical and meristic traits varied among adult and juvenile stages within hatchery and wild groups. Changes in some of these traits appear to have been caused by natural selection. This was true even for Abernathy hatchery and Lewis wild groups, which have been in the same environment for many generations. The direction and/or degree of change in some biochemical and meristic traits differed between hatchery and wild groups from a given stream, suggesting that selective pressures of the hatchery and wild environments differed in those cases. However, it could not be determined from these data whether the observed divergence of traits reflects general differences in hatchery and stream environments, or if it reflects population-specific responses to site-specific environmental conditions. The extent to which patterns of genetic change within a single generation might vary among year classes or generations is likewise unknown. Evidence of temporal changes in biochemical and meristic traits of hatchery and wild fish within a single generation has important implications regarding the use of those traits to characterize stocks. Assumptions of temporal stability of biochemical or meristic traits within or between year classes should be applied with caution. Sampling strategies of studies involving these characters should account for the possibility of temporal heterogeneity. Finally, these results suggest that workers using allozymes as genetic tags should test the assumption of selective neutrality of the particular allozyme markers being used. / Graduation date: 1991

This study was designed to provide information about the juvenile life history of coho salmon, Oncorhynchus kisutch, in the Tenmile Lakes in Oregon by 1) classifying scales of spawning fish and outgoing smolts (1+), 2) assessing the contribution of juvenile life history types to the returns of adults (3₂) and jacks (2₂), and 3) comparing growth rates and survival of different types. Scales of outmigrating smolts from one brood year, jacks from two brood years, and scales of adults from four brood years were classified into juvenile life histories and examined for several scale characters. A linear discriminant function analysis was used to show the separation of the types and to determine the most distinguishing scale characters. Length of smolts at ocean entry back-calculated from scales of jacks and adults was compared with the length of the observed group of emigrating smolts. Based on variation in numbers and spacing of circuli and the size of the freshwater scale zone, believed to represent different residence time in the tributaries and the lakes, four types of juvenile life histories were defined. Fish classified as type 1, stream-reared, are believed to have reared in the tributaries until migrating as smolts in the following year. Type 2, stream-lake-reared, fish are thought to have reared in the tributaries for almost a year but then moved down to the lakes, where rearing continued until smolt migration in spring. Type 3, stream-lake- reared, are believed to have reared for a short time in the tributaries, then moved down to the lakes sometime in their first year of life. Rearing continued in the lakes until spring of the following year. Type 4, lake-reared, are thought to have moved down to the lakes shortly after emergence from the gravel, where they reared until migrating as smolts in the following spring. Scales of smolts, jacks, and adults were sorted into these four types. Presently, coho salmon fry and yearlings appear to be moving out of tributaries in late spring and from March to beginning of May, respectively. Migration of smolts out of the lake system to the ocean occurs mostly within the month of May. Recent habitat surveys show that dramatic seasonal changes occur in use of rearing habitat by juvenile coho salmon in the Tenmile Lakes tributaries from summer to winter. In winter juveniles appear to be using more low gradient, low velocity, off-channel areas than in summer. Fish of type 4 represented 90%, 43%, and 74% of the returns of adults in 1957- 58, 1963-64, and 1971-72, respectively, and 90% of the returns of jacks in 1962-63 and 1970-71. However, no type 4 fish was represented in the returns of adults in 1985-86, whereas type 1 fish represented 89% of the returns. Type 4 appeared to have grown better in fresh water, reached a larger size at outmigration, and have a greater relative survival than fish of type 2, when compared among the observed group of smolts, returning jacks, and adults. The large proportion of the escapement returning as jacks for some of the years may indicate good growing condition for juvenile coho salmon in fresh water. According to the classification of jack scales a large proportion of fish returning as jacks were lake-reared and were found to be larger at migration to ocean than fish returning as adults. This may suggest that fish that reared well in the lakes and reached a large size at outmigration had the tendency to mature early and return as jacks. Based on the analysis of scales, lake-reared juvenile coho salmon formerly contributed well to adult returns. The former high returns of jacks and adults reflect the importance of the lake habitat for the coho salmon populations of this system. In order to enhance this stock to a higher level, management strategies should be focused on making the lake habitat available to juvenile coho salmon for at least some part of their freshwater life. / Graduation date: 1992

Experiments were carried out in fall and winter, 1990 and spring and summer, 1991 , to determine growth and mortality of juvenile Pacific oysters {Crassostrea gigas) in effluent from cultured coho salmon {Oncorhynchus kisutch) , and effluent from salmon in which the red macroalga Palmaria mollis was cultured. Ambient sea water from Yaquina Bay was used as a control. Juvenile Manila clams {Tapes japonica) were also tested in summer, to compare the growth response of clams with that of Pacific oysters. Measured growth parameters included: increase in mean individual live weight, specific growth rate (% increase of mean live weight per day) and mean individual organic (ash-free) weight. Temperature, chlorophyll a, phaeopigment, carbon and nitrogen concentrations and C/N ratio for all treatments were also recorded during spring and summer, 1991. The oysters grew significantly faster in effluent from salmon and salmon conditioned by macroalgae than in the control during the Fall Experiment (September 7- 0ctober 31, 1990). Mean water temperature was 13-16°C. Growth rates were significantly greater in oysters cultured in salmon effluent than in the control during the Winter Experiment (December 7, 1990-February 15, 1991). However, growth was very poor due to low water temperatures (7-10°C). Growth of oysters was significantly greater in the control than in effluent from salmon and salmon conditioned by macrolagae in the Spring Experiment (March 7-May 24, 1991). Mean water temperature was 12°C. In the Summer Experiments, (June 3-July 4 and July 19-August 17, 1991) growth of oysters was more rapid in treatments with macroalgae as compared to treatments without macroalgae Comparative experiments with juvenile Manila clams gave similar results. Percentage mortality for both oysters and clams ranged from 0 to 5% and was highest during winter and lowest during summer. Mean chlorophyll values ranged from 1 μg/1 in spring, 1991 to 11 μg/1 summer, 1991. / Graduation date: 1992

Dietary proteins from Atlantic salmon and cod have previously been shown to have antidiabetic effects. Since dietary proteins are digested into small peptides before being absorbed through the intestinal mucosa, it is reasonable to deduce that the antidiabetic effect is due to enzymatically-digested peptides rather than the proteins themselves. The aim of this study was to develop a protocol to recover peptides with antidiabetic effects from salmon and cod protein digests and then scale up and optimize the salmon protein hydrolysate production process for industrial-scale production. The peptide mixtures were screened using cell culture assays for insulin-modulating activities and were further fractionated and purified for the final identification. Total yields of salmon and cod protein hydrolysates (<1 kDa) as measured by Kjeldahl nitrogen were 16.9% and 40.1%, respectively. The production process used for the salmon protein hydrolysate (<1 kDa) showed good reproducibility and potential for the industrial-scale production.

Untersucht wurde, wie hoch die Schädigungsrate abwandernder Lachssmolts bei der Passage einer Francisturbine in einer für Sachsen typischen Kleinwasserkraftanlage ist. Die Untersuchungen belegen, dass die Fische bereits am 20 mm-Rechen der Anlage und durch Scherkräfte der Leitschaufeln und am Turbinenrad erhebliche Schädigungen erleiden. Um diese zu vermeiden bzw. zu verringern, werden Maßnahmen und bauliche Veränderungen an der Wasserkraftanlage vorgeschlagen.