For this dissertation I studied groundwater and surface water interactions in the Kenai Lowlands, Alaska. In particular, I examine two important aspects of groundwater and surface water interactions: 1) Groundwater's influence on surface-water temperature; and 2) Groundwater's role in forming hydrologic flow paths that can connect uplands to streamside wetlands and streams. Chapter 2 investigates the controls on stream temperature in salmon-bearing headwater streams in two common hydrogeologic settings: 1) drainage-ways, which are low-gradient streams that flow through broad valleys; and 2) discharge-slopes, which are high gradient streams that flow through narrow valleys. The results from chapter 2 showed significant differences in stream temperatures between the two hydrogeologic settings. Observed stream temperatures were higher in drainage-way sites than in discharge-slope sites, and showed strong correlations as a continuous function with the calculated topographic metric flow-weighted slope. Additionally, modeling results indicated that the potential for groundwater discharge to moderate stream temperature is not equal between the two hydrogeologic settings, with groundwater having a greater moderating effect on stream temperature at the low gradient drainage-way sites. Chapter 3 examines the influence of groundwater on juvenile coho salmon winter habitat along the Anchor River. Two backwater habitats were selected from the larger set of 25 coho overwintering sites from a previous study for an in-depth hydrologic analysis. The results from chapter 3 showed that the type of groundwater discharge (i.e., focused versus diffuse groundwater discharge) can play an important role in determining habitat suitability in these backwater sites. During winter, focused discharge from a local groundwater seep maintained higher surface-water temperatures and higher concentrations of dissolved oxygen compared to the site with more diffuse groundwater discharge. Chapter 4 investigates the linkages along hydrologic flow paths among alder (Alnus spp.) stands, streamside wetlands, and headwater streams. Chapter 4 tested four related hypotheses: 1) groundwater nitrate concentrations are greater along flow paths with alder compared to flow paths without alder; 2) on hillslopes with alder, groundwater nitrate concentrations are highest when alder stands are located near the streamside wetlands at the base of the hillslope; 3) primary production of streamside wetland vegetation is N limited and wetlands are less N limited when alder stands are located nearby along flow paths; and 4) stream reaches at the base of flow paths with alder have higher nitrate concentrations than reaches at the base of flow paths without alder. The results from chapter 4 showed that groundwater nitrate concentrations were highest along flow paths with alder, however no difference was observed between flow paths with alder located near versus alder located further from streamside wetlands. Vegetation had a greater response to N fertilization in streamside wetlands that were connected to flow paths without alder and less when alder stands were near. Finally, higher nitrate concentrations were measured in streams at the base of flow paths with alder. The combined results of this dissertation showed that, in the Kenai Lowlands, groundwater and surface water interactions have a direct influence on the local ecology and that a fundamental understanding of the hydrology can aid in the successful management and protection of this unique and important ecosystem.

Approaches for the evaluation of plant protein ingredients for salmonid feeds were investigated in a series of four trials. The first trial compared the apparent digestibility coefficients (ADC) of crude protein (CP) and amino acids (AAs) of two novel products - Indian mustard protein concentrate (IMC, 62% CP) and Indian mustard protein meal (IMM, 42% CP), to a commercially available soy protein concentrate (SPC, 57% CP) for two salmonid species, rainbow trout and Atlantic salmon. The second trial involved assessment of relative bioavailability of arginine (Arg) from IMC, IMM and SPC compared to that of a crystalline Arg (L-Arg) in rainbow trout using slope-ratio assay. In the third trial, the effects of phytic acid (PA) and lignin on nutrient utilization and partitioning in rainbow trout were assessed. Finally, a series of experiments was conducted in the final trial to establish the evaluation criteria for pellet quality assessment. The ADC of CP and most AAs in IMC and IMM were high (>90%). Differences in the ADCs of some AAs can be attributed to the high PA intake by fish fed 30%-IMC diet. The significantly higher (P<0.05) bioavailability of Arg from IMC (123 to 187%) and IMM (116 to 211%) relative to that of L-Arg, as determined by various regression approaches, reaffirmed the findings of the first trial that these ingredients are of excellent protein quality and can readily be used in compounded fish feeds. It can be inferred from the lack of effects of PA, lignin or PA plus lignin on most indices of physiology, performance, and nutrient utilization in the pair-fed fish, that like any other animal, controls feed intake when in the presence of one or more dietary ANF. It was also shown in the pellet quality assessment trial that minor changes in dietary composition can significantly alter physical properties of aquaculture feed. This study highlighted the importance of a comprehensive assessment for the effective evaluation of the nutritive value of plant protein ingredients for use in aquaculture feeds. / Ontario Ministry of Natural Resources; BIOEXX Specialty Proteins Ltd.; Martin Mills Inc.; MITACS

In boreal streams, stream salmonids typically face low water temperatures and variable ice conditions during winter, and thus stream salmonids are expected to use different behavioural strategies to cope with these environmental conditions. The studies presented in this thesis explore how temperature, light intensity, and surface ice affect salmonid behaviour, with focus on drift-feeding and ventilation rates. The first paper reports results from a laboratory study designed to measure prey capture probabilities and reaction distances of drift-feeding Atlantic salmon, brown trout, and European grayling at light intensities simulating daylight and moonlight at seven temperatures ranging from 2 to 11°C. There was a positive relationship between water temperature and prey capture probability for all three species at both light levels, but the temperature-dependence did not scale according to the Metabolic Theory of Ecology. Reaction distance was also positively related to temperature for the three species, which may explain the temperature effects on prey capture probability. The results from this study should be of interest for those working with energetic-based drift-foraging models. In the second paper, the effects of ice cover on the diel behaviour and ventilation rate of brown trout were studied in a laboratory stream. Ice cover is believed to afford protection against endothermic predators, and thus the need for vigilance should be reduced under ice cover. This hypothesis was tested by observing ventilation rates at night, dawn, and during the day in the presence and absence of real, light-permeable surface ice. Further, trout were offered drifting prey during the day to test if ice cover increased daytime foraging activity. Ice cover reduced ventilation rates at dawn and during the day, but not at night. Moreover, trout made more daytime foraging attempts in the presence of ice cover than in its absence. These results suggest that ice cover affects the behaviour of brown trout and presumably has a positive effect on winter survival. Global warming, by reducing the extent or duration of surface ice, may therefore have negative consequences for many lotic fish populations in boreal streams. / BAKSIDESTEXT In boreal streams, salmonids typically face low water temperatures and variable ice conditions from autumn to spring. The studies presented in this thesis explore how temperature, light intensity, and ice cover affect salmonid behaviour, with focus on drift-feeding and ventilation rates. In Paper I, drift-foraging was studied at light intensities simulating daylight and moonlight at seven temperatures ranging from 2 to 11°C. There was a positive relationship between temperature and foraging success at both light levels, but the temperature-dependence did not scale according to the Metabolic Theory of Ecology. Moreover, reaction distance was positively related to temperature. In Paper II, the effects of ice cover on behaviour and ventilation rate of brown trout were studied. Ice cover is believed to afford protection against predators, and thus the need for vigilance should be reduced under ice. This hypothesis was tested by observing ventilation rates at night, dawn, and during the day in the presence and absence of surface ice. Ice cover reduced ventilation rates and increased daytime foraging activity, suggesting that ice cover presumably has a positive effect on winter survival.

Le développement du sexe est un processus fondamental et versatile qui forme la morphologie, la physiologie et le comportement des animaux. Le processus de développement sous-jacent est composé de la détermination et de la différentiation du sexe. Les mécanismes de détermination du sexe sont souvent génétiques et nommés gènes de détermination du sexe. A l’heure actuelle, parmi les gènes de détermination connus, trois familles de gènes nommément sox, dmrt and les facteurs TGF-ß gouvernent ce processus de développement.Comme exception à cette règle, sdY « sexually dimorphic on the Y » n’appartient à aucune de ces familles puisqu’il provient d’une duplication/évolution d’un gène ancestral de l’immunité, c’est-à-dire d’un facteur lié à l’interféron, irf9. sdY est le gène maître de la détermination du sexe chez les salmonidés, un groupe de poissons incluant des espèces tel que la truite arc-en-ciel et le saumon Altantique. L’étude présentée avait pour but de premièrement caractériser les propriétés de la protéine SdY. Deuxièment, l’étude a pour but de comprendre comment SdY pouvait entraîner la différentiation testiculaire. Les résultats pris dans leur ensemble proposent que SdY pourrait entraîner la différentiation testiculaire chez les salmonidés en interagissant avec un facteur prédominant de la voie femelle. / Sexual development is a fundamental and versatile process that shapes animal morphology, physiology and behavior. The underlying developmental process is composed of the sex determination and the sex differentiation. The initial triggers are often genetics called sex determining genes. To date, among the known sex determining genes, three gene families namely sox, dmrt and TGF-ß factors govern this developmental program. As exception to this rule, sdY “sexually dimorphic on the Y” does not belong to one of these families as it comes from the duplication / evolution of an ancestor gene related to immunity, i.e., the interferon related factor 9, irf9.sdY is the master sex determining gene in salmonids, a group of fishes that include species such as rainbow trout and Atlantic salmon. The present study was aimed to firstly characterize the features of SdY protein. Results indicate that SdY is predominantly localized in the cytoplasm, composed of a ß-sandwich core surrounded by three a-helices as well specific characteristics conferring a putative protein-protein interaction site. Secondly, the study was aimed to understand how SdY could trigger testicular differentiation. Altogether results propose that SdY would trigger testicular differentiation in salmonids by interacting with a prominent female factor.

De l’éclosion à l’abattage, le saumon Atlantique et la truite arc-en-ciel d’élevage sont soumis à divers événements inducteurs de stress. Le stress influe directement sur la physiologie, le comportement et les performances zootechniques des animaux. Ainsi, l’intérêt grandissant du public pour le bien-être des animaux nous a amené à améliorer les connaissances sur le stress des salmonidés d’élevage pour en proposer des méthodes d’évaluation et de contrôle. Partant de ce constat, nous avons étudié les conséquences de deux situations inductrices de stress et proposé une méthode d’évaluation du bien-être de la truite arc-en-ciel d’eau douce. Nous avons ensuite étudié l’interaction entre stress et pathologie à travers l’exemple du parasite du saumon Lepeophtheirus salmonis. Après avoir mis au point un test d’attractivité du saumon pour ce parasite, nous avons étudié les conséquences du stress aigu puis chronique sur l’attractivité des saumons. Le stress de manipulation augmente l’attractivité des saumons pour le parasite, alors qu’il n’y a pas de différence entre les saumons stressés chroniquement et les témoins. Nous avons ensuite proposé une méthode de contrôle de ce parasite en isolant un sémiochimique issu du mucus de saumon et inhibant l’attachement du parasite. L’ensemble de nos travaux ouvre des perspectives intéressantes quant à l’amélioration des méthodes d’évaluation et de contrôle du stress en élevage des salmonidés. L’étude des conséquences du stress est importante pour mesurer l’impact, à la fois sur le bien-être de l’animal, mais aussi sur les coûts de production. Le sémiochimique inhibiteur de l’attachement du parasite sur le saumon promet de nombreuses études pour comprendre ses mécanismes d’action et son éventuelle utilisation en élevage. / From hatching to slaughter, Atlantic salmon and Rainbow trout are subjected to several stressful events. Stress impairs physiological, behavioral and zootechnical performances of animals. The public interest in animal welfare brings us to study the assessment and control methods of stress in farmed salmonids. To do that, we studied the consequences of two different stressful events and proposed a method for assessing welfare of freshwater Rainbow trout. We also studied the interaction between stress and pathology with the salmon louse Lepeophtheirus salmonis. After developing an attractiveness test of salmon for the parasite, we investigated the influence of shortand long-term stress on salmon attractiveness for the parasite. Handling stress increased attractiveness of salmon for the parasite, while there was no difference between chronically stressed and control salmon. We proposed then a method to control this parasite by isolating a semiochemical which inhibit the hooking behavior of the parasite on the host. These results open interesting prospects for improving the assessment and control methods of stress in farmed salmonids. The investigation of stress consequences on animal welfare and on production performances is crucial. The semiochemical inhibiting the hooking behavior of the parasite on the salmon needs more studies to identify its mechanisms of action for use in farms.

Abstract The degradation of rivers and streams has led to world-wide efforts to restore freshwater habitats. A good understanding of the social-ecological context is considered key to successful restoration. In this thesis, a multidisciplinary framework was applied to study ecological and social dimensions of restoration success. First, the long-term performance of in-stream restoration measures was examined by conducting repeated cross-sectional surveys in restored streams up to 20 years post-restoration. Next, nationwide electrofishing data were used to assess the density responses of juvenile salmonids to habitat restoration and factors influencing restoration success were examined. Finally, changes in the provision of ecosystem services were evaluated by comparing the perceptions of restoration outcomes between two user groups and three study rivers. The results indicated that the restoration-induced increase in habitat heterogeneity persisted over time, initiating an overall positive development also in biological metrics (i.e. juvenile salmonids and aquatic mosses). However, overall substrate variability in restored streams remained lower than in near-pristine streams, with a shortage of gravel beds. Fish responses varied strongly between rivers, which was explained mainly by watershed scale (e.g. river basin size, dominant geology) and local (potential interspecific competition) factors. Site-specific differences were also observed in the delivery of ecosystem services, mainly reflecting stakeholder perceptions of landscape value and fish provisioning. Overall, the results show that setting indicators and target levels for restoration success is grounded on perspective. Socially conscious ecological restoration that acknowledges local specialities and needs in priority setting, planning and implementation has the potential to provide multiple benefits for river ecosystems and society. / Tiivistelmä Virtavesien ekologisen tilan heikentyminen on johtanut maailmanlaajuisiin toimiin niiden elinympäristöjen kunnostamiseksi. Usein ekologisen kunnostuksen onnistuminen edellyttää kuitenkin ihmisen ja ympäristön vuorovaikutussuhteiden laaja-alaista ymmärtämistä. Tässä väitöskirjatutkimuksessa käytettiin monitieteistä viitekehystä virtavesikunnostusten ekologisten ja sosiaalisten vaikutusten tutkimiseen. Ensimmäisessä osatyössä arvioitiin kunnostustoimenpiteiden kestävyyttä sekä uoman rakenteellisen monimuotoisuuden kehittymistä pitkällä aikavälillä (10-20 vuotta kunnostusten jälkeen). Toisessa osatyössä tehtiin valtakunnallisen sähkökalastusaineiston avulla meta-analyysipohjainen yhteenveto suomalaisten virtavesikunnostusten vaikutuksista taimenen ja lohen kesänvanhojen (0+) poikasten tiheyteen sekä tutkittiin kunnostustulokseen vaikuttavia ympäristötekijöitä. Kolmannessa osatyössä selvitettiin kunnostusten onnistumista ekosysteemipalvelujen näkökulmasta vertaamalla kahden eri käyttäjäryhmän kokemia muutoksia kolmen tutkimusjoen välillä. Väitöskirjan tulokset osoittivat, että kunnostukset lisäsivät jokiuoman rakenteellista monimuotoisuutta sekä lyhyellä että pitkällä aikavälillä ja vaikuttivat myönteisesti myös biologisiin indikaattoreihin (lohikalojen poikastiheys ja vesisammalet). Vaihtelu pohjan laadussa oli kuitenkin luonnontilaisia uomia vähäisempää ja erityisesti kutuun soveltuvaa soraa oli niukasti. Lohikalojen tiheysvaste vaihteli voimakkaasti jokien välillä, mikä selittyi pääasiassa valuma-alueeseen liittyvillä (esim. valuma-alueen koko ja geologia) ja paikallisilla (mahdollinen lajien välinen kilpailu) tekijöillä. Paikkasidonnaisia eroja havaittiin myös vaikutuksissa ekosysteemipalveluihin ja ne heijastivat etenkin maisemassa ja kalasaaliissa koettuja muutoksia. Tutkimus osoitti, että erilaiset taustat ja odotukset vaikuttavat vahvasti siihen, millaisten kriteerien perusteella kunnostusten onnistumista arvioidaan. Jotta kunnostuksilla saavutettaisiin hyötyjä sekä jokiekosysteemeille että yhteiskunnalle, on tärkeää tuntea paikalliset erityispiirteet ja -tarpeet ja ottaa ne huomioon kunnostuskohteiden valinnassa sekä toimenpiteiden suunnittelussa ja toteutuksessa.

Sammanfattning Användningen av korttidsreglering av vattenkraftverk kommer troligen öka då det är kostnadseffektivt och efterfrågan av förnybar energi är hög. Jag undersökte effekten av habitatkomplexitet och flödesändringar på simaktiviteten hos harr (Thymallus thymallus) i experimentella vattenrännor. Två olika habitat användes, ett beståendes av bara en grusbotten och en med större stenar placerade på grusbotten. I experimentet användes en behandling där flödet var stabilt och en där flödet varierade. Det fanns en signifikant interaktionseffekt mellan en ändring i flödet och habitat, som visade att simaktivitet ökade i samband med flödesändring, men endast i habitatet utan större stenar. I jämförelse av två konstanta flöden visade också studien att simaktivitet minskade med högre vattenhastighet. Effekter som dessa bör uppmärksammas för att bättre förstå påverkan korttidsreglering kan ha på fiskar i rinnande vatten. / Abstract The use of hydropeaking by hydropower plants will probably increase due to it being cost-effective and the demand for renewable energy being high. I examined the effect of habitat complexity and changes in flow on the swimming behaviour of graylings (Thymallus thymallus) in experimental flumes. Two types of habitats were used, one consisting only of a bed of gravel and the other with large stones added to the gravel bottom. In the experiment, one treatment with stable flow and one with variable flow were used. There was a significant interaction effect between change of the flow and type of habitat, indicating that swimming activity increased in changing flow, but only in the habitat without large stones. When comparing two constant flows the study also showed that swimming activity decreased with increased water velocity. Effects such as these should be considered when trying to understand how hydropeaking affects riverine fishes.

A mechanistic model is developed to determine the habitat needs of drift-feeding stream salmonids from the direct cause-and- effect relationships of environmental and physiological variables on net energy intake (NEI). The model determines NEI by subtracting energy costs (basal metabolism , swimming cost, digestion cost) and losses (egestion and excretion) from the gross energy intake obtained as a result of simulated prey capture. The prey capture portion of the model utilizes components o f the predation model of C.S. Holling and the prey capture model of N.F. Hughes and L.M. Dill to determine the rate of prey capture (gross energy intake) as a function of fish size, water velocity, water depth, water temperature, and the amount of drift. Physiological input parameters for the model are estimated from the literature. Two separate validation tests of the model's ability to predict stream habitat use of trout, primarily cutthroat trout (Oncorhynchus clarki), in St. Charles Creek, Idaho, are presented. In both cases, the NEI model closely predicts the stream habitat that different size classes of fish utilize. The validation tests provide strong evidence that drift-feeding fish utilize stream habitats that provide high rates of NEI as determined by the model. Sensitivity and simulation analyses of the model are used to identify the most important input parameters and to illustrate in terms of energetics why drift-feeding fish utilize various habitats. Model simulations explain why fish utilize deeper and faster habitats as they get larger and why they utilize slower habitats in the winter. In addition, it is shown that streams with high drift rates should theoretically provide more usable salmonid habitat than similar streams with lower drift rates.

Invasions from coho salmon were first reported in the Cape Horn Biosphere Reserve (CHBR) in 2019 which is the most southern distribution registered to date. The CHBR is known for its high number of endemic species and unique biodiversity, such as the native fishes Galaxias maculatus and Aplochiton taeniatus. There are now three invasive salmonid species in the rivers of CHBR and are a potential threat to the native fish taxa. Stable isotope and gut content analysis were used to understand resource utilization by both native galaxiid and invasive salmonid taxa, as well as aquatic macroinvertebrates and riparian spiders. The natural laboratory study approach applied to this research, allowed for comparisons of differences within streams that contain conditions in which fish do not occur naturally, to sites in which high densities of invasive salmonid exist. Analysis of the trophic niche and diet in this study showed the importance of marine resource use by the native galaxiid and coho salmon juveniles supported with elevated δ15N and δ34S ratios. Diet analysis also confirmed there was the highest similarity between the coho salmon juveniles and the native fish. Altered behavior and habitat use was shown through the isotope and diet analysis for the galaxiid in snow melt streams which could be due to the high density of invasive salmonids in these streams. The invasive salmonids were found to impact aquatic macroinvertebrate populations, specifically larger bodied Trichoptera abundance. Aquatic insect emergence was negatively correlated to salmonid densities. The aquatic insect emergence revealed alterations with significantly higher biomass of aquatic insect emergence in upstream sites without invasive fish. Lastly, aquatic insect predator (Hydrobiosidae: Rheochorema sp.) exhibited a suppressed trophic position in rivers with invasive salmonids. An unexpected finding from the study was the refugium stream habitat conditions that has been shown to be important for conserving the native fish in the CHBR. We conclude that the impacts from invasive species are significant enough to disrupt lower trophic levels especially aquatic insects. The altered aquatic emergence and insect behavior have the potential to disrupt food webs and ecosystem functioning in the southernmost protected ecoregion in the world.

Background: The Atlantic salmon, Salmo salar L., is a prominent member of the Salmonidae family, and has been the focus of intense research because of its environmental and economic significance as an iconic sporting species and its global importance as an aquaculture species. Furthermore, salmonids constitute ideal organisms for the study of evolution by gene duplication as they are pseudotetraploid descendants of a common ancestor whose genome was duplicated some 25 to 100 million years ago. Whole-genome duplication is considered a major evolutionary force capable of creating vast amounts of new genetic material for evolution to act upon, promoting speciation by acquisition of new traits. Recently, large-scale comparison of paralogous genes in Atlantic salmon suggested that asymmetrical selection was acting on a significant proportion of them. However, to elucidate the physiological consequences of gene and genome duplications, studies integrating molecular evolution and functional biology are crucial. To this end, sequence and molecular analyses were performed on duplicated Elovl5 fatty-acyl elongases of Atlantic salmon, as they are responsible for a rate-limiting reaction in the elongation process of long-chain polyunsaturated fatty acids (LC-PUFA), critical components of all vertebrates. The aim of the research presented here was to investigate the role of gene duplication as an evolutionary process capable of creating genetic novelty, and to identify the potential ecological and physiological implications. Results: Linkage analyses indicated that both fatty-acyl elongases segregated independently and located elovl5 duplicates on different linkage groups. Genetic mapping using microsatellites identified in each elovl5 locus assigned elovl5a and elovl5b to chromosomes ssa28 and ssa13, respectively. In silico sequence analysis and selection tests indicated that both salmon Elovl5 proteins were subject to purifying selection, in agreement with previous results showing indistinguishable substrate specificities. Gene expression and promoter analysis indicated that Elovl5 duplicates differed in response to dietary lipids and tissue expression profile. Lipid biosynthesis and metabolic gene expression profiling performed in Atlantic salmon SHK-1 cells, suggested that the control of lipid homeostasis in fish is similar to that described in higher vertebrates, and revealed the particular importance of Lxr and Srebp transcription factors (TFs) in the regulation of LC-PUFA biosynthetic enzymes. Sequence comparison of upstream promoter regions of elovl5 genes showed intense differences between duplicates. Promoter functional analysis by co-transfection and transcription factor transactivation showed that both elovl5 duplicates were upregulated by Srebp overexpression. However, elovl5b exhibited a higher response and its promoter contained a duplication of a region containing response elements for Srebp and NF-Y cofactors. Furthermore, these studies indicated an Lxr/Rxr dependant response of elovl5a, which was not observed in elovl5b. Analysis of the genomic sequences of elovl5 duplicates by comparison to various sequence databases showed an asymmetrical distribution of transposable elements (TEs) in both introns and promoter regions. Further comparison to introns of the single elovl5 gene in pike indicated much higher TE distribution in salmon genes compared to the pike. Conclusions: Although not conclusive, the most parsimonious origin for the salmon elovl5 duplicates is that they are derived from a WGD event. This conclusion is also supported by the close similarity of two elovl5 paralogs in the recently available rainbow trout genome. Regardless of their origin, Atlantic salmon elovl5 genes have been efficiently retained in the genome under strong functional constraints indicating a physiological requirement for both enzymes to be functionally active. In contrast, upstream promoter regions have strongly diverged from one another, indicating a relaxation of purifying selection following the duplication event. This divergence of cis-regulatory regions has resulted in regulatory diversification of the elovl5 duplicates and regulatory neofunctionalisation of elovl5a, which displayed a novel Lxr/Rxr-dependant response not described in sister or other vertebrate lineages. Promoter analysis indicated that the observed elovl5 differential response to dietary variation could be partly attributed to varying transcriptional regulation driven by lipid-modulated TFs. The distribution of TEs in elvol5 genes of Atlantic salmon shows a clear increase in TE mobilisation after the divergence of esocids and salmonids. This must have occurred after the elongase duplication and thus the salmonid WGD event and contributes to the observed regulatory divergence of elovl5 paralogs.