Environmental factors such as chemical contamination can have immunomodulatory effects on the immune response of fish and may be contributing to the decline in salmonid populations by augmenting disease susceptibility. Xenobiotics can interfere with the immune system at several levels of complexity, and different immune cells and processes have variable sensitivity to pollutants. For this reason, a suite of tests is required to evaluate immunomodulatory mechanisms. In this thesis, I formulated and calibrated an assay for the detection of humoral immunity for chinook salmon (Oncorhynchus tshawvtscha). Subsequently, I used this technique in conjunction with other immune and endocrine assays to detect effects of embryonic exposure to o,p'-DDE, a known environmental estrogen. The technique combines exposure of whole animals or leukocyte cultures to immunomodulatory agents/conditions with in vitro mitogenic activation of B-lymphocytes. The proportion of leukocytes undergoing blastogenesis following in vitro stimulation with lipopolysaccaride (LPS) was quantified by flow cytometric analysis of forward and side scatter properties. In addition, I used a fluorescein isothiocyanate labeled anti-rainbow trout surface immunoglobin monoclonal antibody (anti-RBT SIgM-FITC) to determine the ability of the lymphoblasts to express surface immunoglobin (SIgM) through flow cytometry. I used the assay to evaluate the effects of short-term exposures to o,p'-DDE during early life history stages on the long-term immune competence of fall chinook salmon. Immersion of chinook salmon eggs in 10 ppm o,p'-DDE for 1 h at fertilization followed by 2 h at hatch caused significant reductions in the ability of splenic leukocytes to undergo blastogenesis and express SIgM upon in vitro stimulation with LPS one year after treatment (ANOVA, P<0.05). The concentration of o,p'-DDE in fry treated with 10 ppm o,p'-DDE was 0.92 ��g g����� lipid one month post first feeding. The chemical persisted through development and, one year after exposure, levels in juvenile muscle tissue were 0.94 ��g g����� lipid. Mortality rate, time to hatch, fish size, sex ratios, gonadal development, plasma estradiol and 11-ketotestosterone concentrations were not affected by treatment with o,p'-DDE. In addition, neither plasma lysozyme concentration, nor mitogenic response of splenic leukocytes to concanavallin A or polyinosinic-polycytidylic acid were influenced by the treatment. A short period of exposure to an estrogenic chemical during early periods of development induced long term effects on humoral immune competence of chinook salmon. I discuss the possibility that the xenobiotic is exerting its activity through steroid-mediated pathways. / Graduation date: 2002

The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Further investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Traditional spawning habitat models could be improved if they: used spawning area-specific, rather than river-specific; spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. / Graduation date: 1999

Three experiments were designed to determine if and how steelhead trout, Oncorhynchus mykiss, may affect chinook salmon, O. tshawytscha, when they are confined together as in a raceway or on a barge. We observed groups of chinook and steelhead together and groups of only chinook in a behavioral experiment to determine if steelhead are aggressive and if their presence changed the behavior of chinook. Two physiological experiments were completed to determine if the loading of steelhead on top of chinook and if the introduction of odor from rainbow trout (steelhead not available) caused a change in plasma cortisol levels in chinook. It was found that chinook showed characteristics of a schooling species, while steelhead exhibited territory holding characteristics. Behavioral changes in chinook were observed when steelhead were present. Chinook grouped with steelhead reduced their movements, darted less, were attacked up to 16 times more often, and were found less frequently in the shade than groups of only chinook. Steelhead were found to establish territories and defend them with chases, charges, and nips. In attempts to establish territories and defend them, steelhead attacked chinook as often as they attacked other steelhead even though chinook showed little aggression toward steelhead. In a physiological experiment, chinook experienced the loading of salmonids into their tank. Chinook had higher levels of plasma cortisol at 2 and 32 hours after the loading of steelhead than chinook that were loaded with chinook or controls (no loading). A second physiological experiment with odor showed that chinook that received rainbow odor and those that received chinook odor had similar levels of plasma cortisol. Cortisol levels (two hours after the odor was introduced) were higher in chinook receiving either of the scented waters than in those that did not receive any odor. In conclusion, all three experiments indicated that the presence of juvenile steelhead trout affect juvenile chinook salmon behavior and physiology. / Graduation date: 1998

Graduation date: 1996

I examined habitat electivity and movement patterns of adult spring chinook salmon at microhabitat and channel unit spatial scales, and seasonal to annual temporal scales in seven streams in the Grande Ronde, John Day, and Imnaha basins. The objective was to compare habitat use and availability among streams, channel units, and microhabitats, and to assess chinook salmon fidelity to those habitats using radio-telemetry. The analyses showed that habitat quality and availability in the seven study streams varied. Each stream posed different physical constraints on adult chinook salmon habitat; this was reflected by the differential use of habitat by salmon among streams. Salmon elected pools almost exclusively in the John Day Basin, whereas pools and riffles were elected in near equal proportion in the Grande Ronde and Inmaha basins. Within streams, use was similar between years. Almost all salmon were observed in association with cover, but the type of cover largely reflected availablity. Chinook salmon elected the deepest depths within channel units (microhabitat scale), but not necessarily the deepest channel units among streams (channel unit scale). Chinook salmon did not elect cooler stream temperatures within channel units in any study stream, except the Middle Fork John Day River. Radio-tagged chinook showed a high fidelity to habitats, except when stream temperatures approached lethal limits. Due to stream specific differences in habitat availability and use, multiscale habitat assessments for individual streams are recommended to increase the success of watershed restoration activities. / Graduation date: 1999

Graduation date: 1991

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 364-378).

I investigated juvenile coho salmon (Oncorhynchus kisutch) distribution and habitat utilization in an agricultural/urban watershed, the Salmon River, Langley, B.C. The results of my empirical work confirmed the importance of instream woody debris and undercut banks in coho distribution. I examined experimentally how juvenile coho select among patches that differ in foraging profitability and in cover availability. Ideal free distribution (IFD) models were used as the practical basis for hypotheses about habitat choice by coho salmon. My experiments were conducted in artificial stream channels and involved two different types of cover, instream and overhead, and two spatial scales. The two scales (patches within individual pools and pools within stream reaches) were used to detect the effect of different levels of sampling and information processing by the fish. Juvenile coho responded positively to food abundance both within and between pools, but they did not do it as predicted by the IFD model. Cover presence further deviated coho distribution from an IFD. Within pools, coho foraged in open patches away from cover, but preferred pools with cover when choosing between separate units. None of the alternative dispersion models that I considered, derived from the IFD, fully explained the observed dispersion patterns. Coho's ability to maximize food intake rate was not only affected by the physical complexity of their habitat, but also by intraspecific competition and interference. Subsequently, I investigated experimentally coho's response to food and different densities of woody debris in natural stream reaches. If food was abundant, coho favoured pools with sparse cover, which offers accessible refuge and leaves unobstructed foraging patches where prey and perhaps also predators are easy to detect. Pools with either high densities or total lack of woody debris attracted proportionately less fish. Earlier in the summer, fry were indifferent towards cover, but as they became older their association with instream woody debris increased. Experiments I conducted during winter indicated that water velocity and temperature affected juvenile coho downstream movement. The proportion of fish that tried to leave the experimental channels increased with water discharge and decreased with water temperature. Based on the results of my empirical and experimental work, and on information derived from comparative case studies, I evaluated the potential impact of agriculture and urbanization on coho salmon habitat. Activities associated with these types of land developments tend to: a) reduce stream channel complexity; b) eliminate off-channel fish habitat; c) increase both the magnitude and the frequency of peak flows; d) augment water sediment transport; e) alter riparian vegetation; and, f) degrade water quality. A multilayered management plan, aimed at increasing coho salmon production, was developed. The plan's management strategies were devised reflecting on the different spatial scales that watershed components have and on the connectivity processes that exist among them.

Prior to the construction of the dams, migrating salmonid species accessed the upper reaches of the Capilano, Seymour, and Coquitlam watersheds as an integral part of their natural lifecycle. There are multiple initiatives being undertaken by BC Hydro and the stakeholders to re-introduce sockeye salmon (Oncorhynchus nerka) to one of their natural habitat in the upper Coquitlam watershed. Concerns have been raised that the restoration may be in conflict with the drinking water mandate of Metro Vancouver’s watershed management policies. The research objective of this project was to investigate and assess the social, economic, and environmental aspects of restoring an extirpated sockeye salmon population. Through an exploratory case-study approach, the research concluded that the existing fish passage constraints and reliance upon re-anadromy to restore the population are limiting factors in sustaining the Coquitlam Reservoir sockeye.

Pacific salmon (Oncorhynchus spp.) are key elements of ecological systems, and play an important role in the cultural foundation of human societies. All species of wild salmon face multiple, simultaneous threats, with habitat degradation likely playing a key role in survival. Open net-pen salmon farms can degrade important nursery marine habitat for wild juvenile salmon by disrupting natural salmonid host-parasite dynamics. The first two chapters in this thesis examine louse parasitism of wild juvenile chum (Oncorhynchus keta), pink (O. gorbuscha), and sockeye salmon (O. nerka) in relation to their marine migration past salmon farms. I compare sites of low and high exposure to salmon farms, and include two areas without farms on British Columbia’s central and north coasts to assess baseline infection levels. Louse prevalence and abundance were lowest and most similar to natural baseline levels at low exposure sites, and highest at high exposure sites in all farm regions. A significantly greater proportion of the lice infecting juvenile chum and pink salmon were Lepeophtheirus salmonis at high exposure sites. Caligus clemensi was the principal louse species infecting all juveniles in areas without salmon farms, and at low exposure sites within salmon farm regions; C. clemensi was also the dominant louse to infect juvenile sockeye that migrated past farms. Mixed-effects modelling results showed that exposure to salmon farms was the most consistent factor to explain the variation in louse infection levels, and support my hypothesis that salmon farms are a major source of sea lice on juvenile wild salmon in regions with salmon farms. I discovered that juvenile sockeye at one particular location within the Georgia Strait hosted unusually high lice levels; this location was situated at a distance from salmon farms, but near a farm salmon processing facility. Upon further investigation, I found live sea lice, Lepeophtheirus salmonis, mucus, and fish tissue in effluent discharged from the processing facility. Sea lice transmitted from this source may pose a threat to wild salmon populations, and the release of potentially untreated offal, including blood water, is of considerable concern. These results form the third chapter in my thesis. Given the challenges facing juvenile salmon in general, and sockeye from the Fraser River in particular (i.e., 2009 was the lowest return on record), and because poor habitat conditions within Georgia Strait are considered the major cause of the recent decline in Fraser River sockeye, this raises the question as to whether food limitations are a factor. The final chapter in my thesis examines the prey assemblage, diet composition, and foraging selectivity of juvenile sockeye, and investigates whether food limitations can be detected during early migration through Georgia Strait. Juvenile sockeye demonstrated high prey diversity, with preference for particular prey. Prey were more concentrated in the north, which may help explain migratory behavior of juveniles through the study region, and temporal similarities in sockeye foraging success may reflect short-term food resource stability. Moreover, I could not find evidence of food limitations that might suggest juvenile sockeye were strongly food deprived during the years of this study. Finally, my thesis explores how best to conserve salmon populations given the multitude of stressors. Because stressors often interact to produce compound effects and unpredictable results, ranking the overall threats in order of severity may not be useful. Instead, the most successful ranking system may be in terms of reducing harm where possible. For juvenile salmon during their early marine migration, risks posed by salmon farms can be more easily mitigated than the far-reaching effects on ocean productivity of climate change and ocean acidification, or predator removal. I recommend we begin here. / Graduate