The main source of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA) in our diet is supplied by fish, and an ever-increasing proportion of these are being produced by aquaculture. The drive for the growing market demand and production from sustainable sources has led to the use of high-energy (fat) diets and, recently, to the replacement of fishmeal and fish oil with non-marine components, such as plant meals and vegetable oils that are devoid of n-3 LC-PUFA. Both changes impact greatly on lipid and fatty acid metabolism in fish, with health implications for the fish and the human consumer. This impact highlights the need to investigate the basic molecular mechanisms underlying the regulation of lipid and fatty acid metabolism in fish, specifically focussing on the pathways of lipid homeostasis and LC-PUFA synthesis. The aim of this study was to develop and utilise Chinook salmon embryo (CHSE-214) cell line as a model for Atlantic salmon, Salmo salar L., to enable an integrated approach to study the biochemical and molecular regulation of lipid metabolism in fish. In particular, α-linolenic acid (LNA, 18:3n-3) and linoleic acid (LOA, 18:2n-6), which are essential fatty acids abundantly found in vegetable oils, and are precursors of LC-PUFA, were supplemented in combination with other fatty acids, to explore the effect of these on total lipid content, lipid class, FA composition and gene expression of CHSE-214 cell line. Total lipid content was extracted, followed by determination of lipid class and fatty acid analyses. Gene expression analyses of transcription/nuclear factors and various target genes in Atlantic salmon, including those involved in pathways of LC-PUFA synthesis and fatty acid oxidation, were carried out. The results demonstrated that CHSE-214 cell line, under experimental conditions, is able to convert LNA to eicosapentaenoic acid (EPA, 20:5n-3), and LOA to arachidonic acid (ARA, 20:4n-6), but not LNA and/or EPA to docosahexaenoic acid (DHA, 22:6n-3), highlighting the activity of elongase and desaturase enzymes during the conversion process. Changes occurring on the fatty acid profile and also at molecular level were observed. Understanding the role that transcription factors play in the regulation of lipid biosynthesis in fish will allow endogenous LC-PUFA synthesis to be optimised. The results from this study could be used to improve the efficiency of alternative, sustainable diets in aquaculture, while maintaining the nutritional quality of farmed fish for the final consumer. CHSE-214 cell line can therefore be used as a model to study the molecular mechanisms involved in the LC-PUFA biosynthesis, particularly in the conversion of LNA to EPA, which can then be reproduced in vivo, saving time and money.

Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts.

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.

Ceratomyxa shasta infects salmonids in the Pacific Northwest (PNW) of North America, occasionally causing losses in wild and captive populations. Host-specific parasite genotypes (O, I, II, III) were previously characterized molecularly using markers in the ribosomal DNA and phenotypically by type host in the Klamath River, CA/OR. This thesis sough to re-examine the composition of the parasite population elsewhere in the PNW and to further evaluate the host specificity of each genotype. I surveyed salmonids native to the PNW primarily from the Fraser, the Columbia and the Sacramento River basins. I also conducted sentinel studies on the Willamette and Deschutes Rivers that exposed native and non-native salmonids to parasite populations above and below migration barriers. These studies expanded upon the known host range of each genotype: O was specific to rainbow/steelhead (Oncorhynchus mykiss) and coastal cutthroat trout (O. clarkii); I was specific with Chinook salmon (O. tshawytscha); II was non-specific, being detected in six species, but predominating in coho (O. kitsuch), chum (O. keta), and pink (O. gorbuscha) salmon; and III was also non-specific infecting many native and non-native salmonids. Hosts infected with genotype III were considered “adequate” if myxospore development occurred, and included brook char (Salvelinus fontinalis), brown (Salmo trutta), rainbow, cutthroat, and steelhead trout; but Chinook, kokanee/sockeye (O. nerka) and Atlantic salmon (Salmon salar) were less suitable. The distribution, life history, and phylogenetic traits of each salmonid host are factors that potentially explain the host specificity and the spatial and temporal patterns of each genotype. Data collected in this thesis provide evidence that host-specific C. shasta coevolved with Pacific salmonids, adapting unique host-parasite relationships over time. / Graduation date: 2012

The freshwater polychaete Manayunkia speciosa was identified as an obligate host of the salmonid parasite Ceratomyxa shasta in 1997, prompting increased research on the small benthic invertebrate. Ceratomyxa shasta infection in fish can cause mortality, and presents a disease risk for both hatchery and wild salmon and trout. Ceratomyxa shasta is endemic to rivers of the Pacific Northwest, and its effects have been particularly well documented in the Klamath River, Oregon and California. One option for managing C. shasta impacts is by decreasing densities of M. speciosa through habitat manipulation, thus decreasing amplification of the parasite. The Klamath River is regulated by irrigation and hydropower dams, thus manipulating the hydrograph to destabilize habitat is a possibility. Decreasing habitat through flow manipulation requires a thorough understanding of the hydraulic environment of polychaete habitat, and how that environment changes with discharge. This thesis proposes an influence diagram of physical variables driving M. speciosa density, and investigates several of them. Samples were collected for enumerating M. speciosa density from nine sites in the Klamath River over 15 months, and seasonal density changes were examined, as were the relationships between density and hydraulic variables (depth, average velocity, substrate size, Reynolds number, Froude number). Density increased directly with depth and inversely with velocity, and was greater on small (silt, sand) and large (boulder, bedrock) substrate relative to medium substrate (gravel, cobble). Density was highest in the summer (July, August, September), and there was evidence that summer densities were influenced by spring discharges through the mechanism of substrate mobilization. Differences in infection prevalence among seasons and habitats were also investigated; however, very low overall incidence of infection limited any conclusions. Based on these results, it is recommended that habitat modeling for management of M. speciosa populations include a habitat stability component that incorporates s whether peak discharge the previous year surpassed a stability threshold. / Graduation date: 2013

Stream channelization is a common form of anthropogenic disturbance, whose impacts on cold water salmonid communities have received little attention in comparison to the body of work demonstrating its negative effects on low land, warm water systems. Here, I compared the effects of stream channelization on fish and invertebrate communities and their habitats in disturbed and undisturbed cold-water mountain streams in southern Alberta. I demonstrate that stream channelization has imposed significant alterations to stream habitat, most notably a loss of deep habitat, and that these alterations have led to a statistically significant decline in abundance and biomass of Rainbow Trout and Mountain Whitefish, as well as a significant decline aquatic invertebrate biomass. Because of the importance of monitoring fish abundance in deep pools, I used snorkel surveys instead of electrofishing. In shallow, disturbed streams, however, snorkel surveys may be less effective and should be used with caution. / ix, 104 leaves : col. ill., col. maps ; 29 cm

The Pacific Coastal ecoregion contains large tracts of economically important forest lands that also serve as critical stream habitat for endangered Salmonids. Excessive fine sediment deposition in streams of this region is a major environmental concern in the region but difficult to measure directly. The use of stream invertebrates to monitor fine sediment conditions in streams requires careful consideration of several important factors that complicate their use as bioindicators including high spatial and temporal variability and covariance with other environmental variables. To evaluate the use of stream invertebrates as bioindicators of excessive fine sediment, three hypotheses were tested. The first hypothesis was that invertebrates would be related to broad-scale climate variables (Chapter 2). The second hypothesis was that functional aspects of the invertebrate community would serve as useful indicators of excessive fine sediment condition (Chapter 3). The third hypothesis was that invertebrates in streams with naturally high levels of sediment would be tolerant to fine sediment (<2 mm, Chapter 4). Hypotheses were tested using a temporal data set at two streams in western Oregon, spatial data from 214 sites across the Oregon Coast Range, and in-situ experiment conducted in streams with erosive or resistant geologies. In the temporal study, both invertebrate density and functional traits were positively related to El Nino strength (R2 range = 0.22-0.36, ρ range = 0.008-0.04) and air temperature (R2 range = 0.32-0.49, ρ range = 0.002-0.01). The spatial study identified several environmental and hydrological factors that exhibited strong negative controls on both fine sediment (Mantel r range 0.14-0.25, ρ range = 0.001-0.01) and invertebrate Scrapers (R2 range = 0.11-0.14, ρ range = 0.001-0.04). The result of the experimental study provide evidence that invertebrates in streams with erosive geologies exhibit tolerance to sediment addition when compared to invertebrates in resistant geologies (mean loss=15%, ρ <0.01) and that invertebrate grazing traits were most strongly associated with fine sediment dosing frequency (ρ <0.05). The findings of this research demonstrate the role of geology in shaping invertebrate communities and their functional response to fine sediment addition and identify functional indicators that may be useful in different geologic settings. For environmental managers in the Pacific Coastal ecoregion, these findings are of potential value in assisting with the identification of biologically-relevant changes in stream fine sediment conditions and support efforts to balance economic needs in the region while protecting critical Salmonid habitat.

Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus) nest in large colonies on East Sand Island in the Columbia River estuary, the largest known colonies for the two species in the world. Both species of piscivorous colonial waterbirds have been identified as predators with a significant impact on the survival of juvenile salmonids (Oncorhynchus spp.) listed under the U.S. Endangered Species Act. To better understand and address issues related to seabird-fisheries interactions in the Columbia River estuary, I conducted studies related to the ecology, conservation, and management of these two species of piscivorous waterbirds. I evaluated the demographics and inter-colony movements of Caspian terns belonging to the Pacific Coast metapopulation, with special emphasis on two breeding colonies, one on East Sand Island in the Columbia River estuary and the other on Crescent Island in the mid-Columbia River, based on re-sightings of color-banded individuals. Apparent annual adult survival at both colonies was high, and age at first reproduction was greater than previously reported for the species. Colony site philopatry of breeding adults at both colonies was high; however, some individuals prospected for breeding colonies over much of the Pacific Coast region and moved to other colonies over distances of up to 3,000 km. Some terns from the large colony in the Columbia River estuary responded quickly to the availability of new colony sites as distant as 550 km from the estuary, and established successful breeding colonies within less than a year of the new sites becoming available. The Caspian tern colony on East Sand Island appears to be an important source colony for a number of smaller, less productive colonies distributed over an extensive area from the Salton Sea, California to the Copper River Delta, Alaska, an area with limited and ephemeral nesting opportunities. Environmental contaminants have been a conservation concern for wildlife in the Columbia River estuary, especially species that consume fish and are therefore likely to bioaccumulate persistent organic pollutants. I measured and compared levels of polychlorinated biphenyls (PCBs) in eggs and chicks of Caspian terns and doublecrested cormorants, as well as their primary prey fish types, at colonies on East Sand Island and farther up-river. Based on differences in tern and cormorant diet composition at the various study colonies, higher PCB levels in eggs and chicks were associated with diets dominated by resident freshwater and estuarine fishes. PCB levels in prey fish were positively correlated with lipid content; however, PCB levels in the livers of chicks were negatively correlated with chick fat scores, suggesting that chick fat reserves are a sink for ingested PCBs. Lower PCB levels in terns and cormorants from East Sand Island compared to colonies farther up-river reflected diets with a higher proportion of marine forage fishes at East Sand Island; marine forage fishes had lower average levels of PCBs than their resident freshwater and estuarine counterparts. In order to explore non-destructive techniques for managing nesting colonies of double-crested cormorants, I evaluated habitat enhancement and social attraction, two techniques that have proven effective for relocating Caspian tern colonies to sites where impacts on fish stocks of conservation concern would be minimal. Cormorants were attracted to nest and successfully raised young at test plots on East Sand Island and on islands in the estuary with a previous history of cormorant nesting or unsuccessful nesting attempts. On an island with no history of cormorant nesting or prospecting, however, no cormorants were attracted to nest. My results suggest that attraction of nesting cormorants using these techniques is dependent on the previous history of cormorant nesting or nesting attempts, the frequency and intensity of disturbance by potential predators, and the presence of breeding cormorants nearby. While habitat enhancement and social attraction have potential as methods for redistributing nesting cormorants away from areas where fish stocks of concern are highly susceptible to predation, successful establishment of new colonies using these techniques will likely require a focus on sites with a history of cormorant nesting. Findings from this dissertation raise some concerns over the management of Caspian tern and double-crested cormorant colonies on East Sand Island in order to redistribute parts of these colonies to alternative sites and mitigate the impact of those piscivorous colonial waterbirds on ESA-listed salmonids. East Sand Island has supported source colonies of piscivorous colonial waterbirds for many smaller colonies throughout the region and is close to an abundant and relatively uncontaminated food supply. Also, alternative colony sites that can substitute for East Sand Island are not readily apparent, especially for double-crested cormorants. Therefore, management of Caspian tern and double-crested cormorant colonies on East Sand Island to benefit Columbia Basin salmonids needs to proceed cautiously and reversibly because of the implications for the region-wide populations of these piscivorous colonial waterbirds. / Graduation date: 2012