Signal crayfish (Pacifastacus leniusculus) is important invasive species in European freshwaters. Its influence on other freshwater organisms is well known from the literature, as well as direct and indirect impact on fish assemblages. This work was focused on the experimental evaluation of non-indigenous signal crayfish as a predator of salmonids compared to indigenous noble crayfish (Astacus astacus). Moreover, the possible importance of young-of-the-year signal crayfish as a prey for salmonids was assessed. There were carried out experiments using eggs and hatchings of grayling (Thymallus thymallus) as a prey for adult and subadult specimens of both, signal and noble crayfish. Next experiment used young-of-the-year signal crayfish as a prey for young-of-the-year of brown trout (Salmo trutta). Results showed that the danger of signal crayfish for grayling eggs is slightly higher. However, detected differences were surprisingly lower and in the majority of parameters even insignificant. In the case of grayling hatchings, was not detected any significant difference at all. The abilities of both tested species to prey on eggs and hatchings are therefore very similar, comparable. Even so, the effect of signal crayfish can be importantly higher in natural conditions because of its more dense populations, higher growth rate and fast maturation. In accordance to our findings, it is evident that brown trout has no so high effect of crayfish juveniles compared with crayfish effect on salmonids early developmental stages. Crayfish are therefore more likely able to limit salmonids than conversely.

In the management of threatened and endangered species, informed population estimates are essential to gage whether or not recovery goals are being met. In the case of Pacific salmonids, this evaluation often involves sampling a small subset of the population and scaling up to estimate larger distinct populations segments. This is made complicated by the fact that fish populations are not evenly distributed along riverscapes but respond to physical and biological stream properties at varying spatial extents. We used rapid assessment survey methods and the River Styles classification to explore fish-habitat relationships at a continuous network scale. Semi-continuous surveys were conducted across nine streams in the upper Middle Fork John Day River watershed and increased the number of sites surveyed eight-fold over other monitoring methods within the watershed. Using this increased sample size and continuous habitat metrics we improved watershed-wide steelhead (Oncorhynchus mykiss) abundance models. We first validated the distinctions among River Styles through a classification analysis using physical metrics measured at the rapid assessment sites. Overall classification accuracy, using a combination of reach and landscape scale metrics, was 88.3% and suggested that River Style classification was identifying variations in physical morphology within the watershed that was quantifiable at the reach scale. Leveraging the continuous River Styles classification of physical habitat and a continuous model of primary production improved the prediction of steelhead abundance across the network. Using random forest regressions, a model that included only habitat metrics resulted in R2 = 0.34, while using the continuous variables improved the model accuracy greatly to R2 = 0.65. Random forest allowed for further investigation into the predictor variables through the analysis of the partial dependence plots and identified a gross primary production threshold, below which production might be limiting steelhead populations. This method also identified the rarest River Style surveyed within the watershed, Confined-Valley Step Cascade, as the morphology that had the largest marginal effect on steelhead. The inherent physical properties and boundary conditions unique to each River Style has the potential to inform fish-habitat relationships across riverscapes and improve abundance estimates on a continuous spatial scale.

Le changement climatique devrait induire une augmentation des précipitations pendant l'hiver et le printemps dans les régions tempérées et la côte nord de l'Europe. Dans les écosystèmes fluviaux, les précipitations affectent directement le débit des eaux courantes et les rivières subiront des crues plus sévères. En outre, la température de l'air et de l'eau augmenteront à travers le monde. Ces nouvelles conditions environnementales vont avoir des conséquences sur la phénologie des espèces et les interactions prédateurs/proies. Les jeunes truites fario (Salmo trutta L.) commencent leur alimentation exogène en mars/avril. Cette étape critique de leur cycle de vie induit d’importants changements aussi bien physiologiques que comportementaux. Pour permettre un bon développement des individus et un taux de survie élevé, les proies doivent être disponibles et abondantes, en particulier à ce moment de l’ontogénèse où les juvéniles sont vulnérables au manque de nourriture et à la prédation. Des expériences en milieux contrôlés ont été menées pour quantifier la sensibilité à différentes modalités de vitesses de courant de trois espèces d’invertébrés couramment consommées par les salmonidés et pour évaluer l’effet de la température sur le métabolisme d’alevins en situation de jeûne. Des expériences en milieu semi-naturel ont été mises en place pour mieux comprendre les effets d’une crue sur la communauté d’invertébrés et sur la survie, le comportement et la croissance des alevins en première alimentation. Il apparaît que la crue impacte différemment les truites en fonction du moment de la saison auquel elles commencent à s’alimenter (au début ou à la fin du printemps) et de la productivité du système. / Global Climate Change will increase precipitations in the temperate and Northern coast of Europe during winter and spring. In riverine ecosystems, precipitation affects directly the discharge of running waters and, thus, it is predicted that streams will face more severe floods. Additionally, air and water temperature will increase all over the world. These new environmental conditions can alter the phenology of species and predator/prey interactions. Newborns of brown trout (Salmo trutta L.) start their exogenous feeding in March/April. This stage is a critical step as individuals undergo huge physiological and behavioral changes. To allow a good development and a high survival rate, prey has to be abundant, particularly during early ontogenesis when they are most vulnerable to food scarcity and predation. In this thesis, experiments in controlled-environment were conducted to estimate the effect of water velocity on the preferred prey taxa for salmonids and to understand the effect of temperature on the metabolism of alevins facing starvation. Experiments in semi-natural conditions were set up to better understand the effects of floods on invertebrate communities and on survival, behavior and growth of first-feeding alevins. Our data support that floods affect trout differently depending on when they start feeding (early or late spring) and the availability of prey in their environment.

Aquaculture is the fastest growing food industry in the world and it accounts for roughly half of the world's fish supply. The majority of global aquaculture production occurs in freshwater systems that are increasingly subject to multiple uses by different stakeholders. Given the overall scarcity of freshwater on a global scale, freshwater aquaculture will face increasing environmental constraints that will demand an ever better understanding of its potential impacts on the aquatic environment and human health. This thesis consists of a series of studies that, collectively, contribute to further our understanding on the effects of freshwater aquaculture effluents on aquatic ecosystems, on the effects and environmental safety of antibiotics used in freshwater aquaculture on aquatic bacterial communities and on the link between antibiotic pollution and antibiotic resistance. Chapter 2 reviews the effects of freshwater aquaculture effluents on stream ecosystems using land-based salmonid farms as a case study. In this chapter I discuss relevant considerations related to the temporal and spatial scales of effluent discharge and ecological effects that highlight the need to characterize the patterns of stressor discharge when assessing environmental impacts and designing ecological effects studies. I also discuss the potential role of multiple stressors - with an emphasis on veterinary medicines - in disrupting ecosystem structure and function. Overall, the critical analysis presented in this chapter indicates that further research on the effects of veterinary medicines using relevant exposure scenarios would significantly contribute to our understanding of their impact in relation to other effluent stressors. Chapter 3 is a general methods chapter that describes the stream microcosm system used to assess the effects of erythromycin thiocyanate (ERT) and florfenicol (FFC) on bacterial communities of stream biofilms. This chapter presents the results of preliminary experiments whose results provided relevant information on the overall operation of the microcosms and on the variability of major physical and biological variables. This information guided the experimental designs used to assess the effects of FFC and ERT on the bacterial community structure of stream biofilms. Chapter 4 presents the results of the experiment conducted to assess the effects of FFC on the bacterial community structure of developing biofilms. The objective was to assess changes in bacterial community structure along a gradient of FFC concentrations that could provide insight into the type and magnitude of effects that could be expected from episodic exposure of stream biofilms to FFC in headwater streams. At 10 and 20 days of biofilm development, bacterial community structure differentiated in a pattern consistent with the FFC concentration gradient and there was a positive relationship between bacterial richness and bacterial diversity with FFC concentration. At 15 days of biofilm development there was also a positive relationship between FFC concentration and the surface coverage of bacteria and extracellular polymeric substances. These trends declined as the biofilm developed a more complex architecture, in terms of thickness and in the surface coverage of algae. The results are consistent with an initial stimulatory effect of FFC on biofilm formation that triggered changes in bacterial community structure that were gradually compressed as the development of a complex biofilm architecture increased the relative importance of autogenic ecological processes. The results suggest that the co-occurrence of FFC with bacterial pathogens in effluents and wastewaters may favour their persistence in the environment by enhancing biofilm formation. Chapter 5 presents the results of the experiment conducted to assess the effects of ERT on the bacterial community structure of developing biofilms. Currently, Aquamycin® 100 - a Type A medicated article (i.e., Premix) containing 100 g ERT lb-1 and used to produce a Type C medicated feed - is a candidate drug for approval by the US FDA to control mortality associated with bacterial kidney disease in freshwater salmonids. The objective of this experiment was to assess the effects of ERT on the bacterial community structure of stream biofilms using an exposure period consistent with the 28-day treatment regime suggested for Aquamycin® 100. The results provide no evidence to suggest that a 30-day exposure to ERT concentrations in the range of 10 μg L-1 (i.e., 7.3 ± 3.9 μg L-1) would lead to changes in the bacterial community structure or overall bacterial abundance of stream biofilms, while they suggest that these effects may occur at concentrations in the range of 100 μg L-1 (i.e., 87.2 ± 31.1 μg L-1). Chapter 6 attempts to determine whether environmental concentrations of antibiotics and concentrations representing action limits used in environmental risk assessment may exert a selective pressure on clinically relevant bacteria in the environment. In this chapter I use bacterial inhibition as an assessment endpoint to link antibiotic selective pressures to the prevalence of resistance in bacterial populations. Species sensitivity distributions were derived for three antibiotics by fitting log-logistic models to endpoints calculated from minimum inhibitory concentration (MIC) distributions based on worldwide data collated by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Bacteria represented in these distributions were placed in a broader context by performing a brief phylogenetic analysis. The potentially affected fraction of bacterial genera at measured environmental concentrations of antibiotics and environmental risk assessment action limits was used as a proxy for antibiotic selective pressure. Measured environmental concentrations and environmental risk assessment action limits were also directly compared to wild-type cut-off values. Results suggest that measured environmental concentrations of antibiotics and concentrations representing environmental risk assessment action limits are high enough to exert a selective pressure on clinically relevant bacteria that may lead to an increase in the prevalence of resistance. Chapter 7 presents the results of an exploratory analysis conducted to assess the abundance of class 1 integrons in stream biofilms exposed to FFC and ERT. There was no pattern in the abundance of intI1 genes consistent with the treatment of FFC and ERT, suggesting either the absence of gene cassettes involved in dealing with selective pressures caused by these antibiotics or that the concentrations tested were below those required to give them a selective advantage. Chapter 8 is a brief general discussion that brings together the findings of the thesis and makes suggestions for future research. Key areas identified for future research include assessing in further detail the stimulatory effect of FFC on biofilm formation in complex bacterial communities, the interactive effects of multiple aquaculture effluent stressors on aquatic bacterial communities and their potential effects on the development of antibiotic resistance, the fate of FFC and ERT in stream ecosystems, and further developing the analysis based on MIC distributions presented in chapter 6 to assess the potential effects of antibiotic pollution on the selection of multi-drug resistance in the environment.

This work addresses two areas of computational biology: automation of sequence processing and an assessment of the evidence for a hypothesized salmonid genome based on an analysis of a set of expressed sequence tags. Three problem areas in sequence processing are addressed in the first half of the work. Chapter 3 describes an accurate technique for trimming of vector, adapter and poly(A) sequence. Chapter 4 suggests methods for verifying the accuracy of assembled mRNA transcripts despite a large number of chimeras in the cDNA clone libraries. Chapter 5 is concerned with the problem of estimating the number of transcripts in a tissue or cDNA library, concluding that computational and statistical techniques are inadequate to estimate the quantity accurately. The hypothesized salmonid genome duplication has been widely accepted since 1984. If it occurred, it should have left evidence in the form of many paralogous pairs of genes, all at approximately the same degree of sequence divergence. To assess this question, several hundred thousand ESTs were assembled into transcripts, compared to each other to find homologs, and the evolutionary distances of the homologs represented as a histogram. Evidence of a single evolutionary event was not seen. The same procedure was applied to Xenopus laevis, which has a well-established recent genome duplication, and Danio rerio, which is known not to have had one. In those cases, the evidence for or against a genome duplication appeared exactly as predicted. The conclusion is that if the salmonid genome duplication occurred, some force altered its evolutionary development subsequently to mask the duplication, but also that a genome duplication is not necessary to explain the observed pattern of homolog distances.

A multi-scale approach for restoration site selection is presented and applied to an upland catchment, the River Ure, North Yorkshire. Traditional survey methods, advances in remote sensing, Geographical Information Systems (GIS) and risk-based fine sediment modelling using the SCIMAP module are combined to gather data at the catchment-scale through to the in-stream habitat-scale. The data gathered have been assessed against spatially distributed brown trout fry populations using Pearson’s correlation and multiple stepwise regressions. Fine sediment was shown to have a positive correlation with fry populations when upland drainage channels (grips) were added to the SCIMAP model. This suggests risk from peatland drainage is realised further down the catchment where eroded sediments are deposited. Farm-scale SCIMAP modelling was tested against farmers’ knowledge with variable results. It appears there is a cultural response to risk developed over generations. Management of meadows and pasture land through sub-surface drainage and stock rotation resulted in the risk being negated or re-routed across the holding. At other locations apparently low-risk zones become risky through less sensitive farming methods. This multi-scale approach reveals that the largest impacts on brown trout recruitment operate at the habitat-adjacent scale in tributaries with small upstream areas. The results show a hierarchy of impact, and risk-filters, arising from different intensity land management. This offers potential for targeted restoration site selection. In low-order streams it seems that restoration measures which exclude livestock, and provide bankside shading, can be effective. At such sites the catchment-scale shows a reduced signal on in-stream biota. Thus, brown trout stocks could be significantly enhanced by targeting restoration at riffle-habitat zones and adjacent land in order to disconnect the stream from farm-derived impacts and through adding structure to the stream channel.

Les changements globaux provoquent une disparition accélérée des espèces endémiques. Il apparait crucial de quantifier les risques potentiels d’extinction en relation avec les changements climatiques liés à l’activité anthropique, et particulièrement pour les espèces dont l’aire de répartition est restreinte. Dans ce travail de thèse je me suis intéressé aux effets des changements globaux sur le complexe de la truite du Mexique qui vit dans le nord-ouest du Mexique. Ce complexe représente le groupe des salmonidés avec la distribution la plus méridionale au monde, avec seulement deux taxa décrits : la truite dorée mexicaine (Oncorhynchus chrysogaster) et la truite de San Pedro Mártir (O. mykiss nelsoni).En tant qu’espèce montagnarde d’altitude, ces salmonidés sont très vulnérables aux effets des changements globaux, et particulièrement au changement climatique et à l’introduction d’espèces exotiques pour l’aquaculture, comme la truite arc en ciel. Les objectifs généraux de cette thèse étaient de déterminer les relations entre les processus micro-évolutifs chez la truite mexicaine dorée, ainsi que la structure spatiale de leur habitat qui définissent les risques d’extinction engendrés par les changements globaux.Afin de répondre à ces questions, j’ai appliqué aux écosystèmes de rivières une approche de génétique du paysage intégrant différentes échelles spatiales à différents niveaux taxonomiques, ainsi j’ai appliqué des analyses de génétique des populations, des analyses de système d’information géographique et de modélisation de la distribution des espèces, ainsi que des simulations démo-génétiques.Initialement, les analyses de génétique des populations réalisées sur 11 loci microstallites nous ont permis de mettre en évidence une structure génétique spatialisée pour l’ensemble du complexe des truites mexicaines, ainsi qu’une introgression génétique chez la truite endémique. Ces résultats ont été confirmés par d’autres analyses utilisant un plus grand nombre de microsatellites et de marqueurs SNP. Une étude plus fine centrée sur O. chrysogaster et combinant simulations génétiques et distribution de l’espèce a permis de définir les caractéristiques des paysages de rivières comme les principaux déterminants de la structure génétique des populations natives, voire comme des barrières aux flux de gènes. Pour cette espèce, j’ai également généré une base de données de 9676 SNP grâce aux techniques de séquençage de nouvelles génération et mis en évidence une structure génétique cryptique chez O. chrysogaster. Une approche de génomique du paysage a révélé une influence significative des variables physiques des rivières sur la structuration génétique neutre et adaptative de la truite dorée mexicaine. / The combined effect of different threats has caused an accelerated loss of biodiversity in endemic species. Then, it is crucial to quantify potential extinction risks as consequence of global change related with human activities, especially in range restricted species. An example of that situation is represented by the native Mexican trout complex inhabiting the highlands of northwest Mexico and representing the group of salmonids with the southernmost distribution in the world, with the Mexican golden trout (Oncorhynchus chrysogaster) and the coastal nelson trout (O. mykiss nelsoni) as the only described species for this complex.However, as mountaintop species, these salmonids are highly vulnerable to global change effects, mainly by climate change and the introduction of the exotic rainbow trout for aquaculture purposes. The overall aim of this PhD project is to assess the possible relationships between microevolutionary processes of the Mexican golden trout, as well as the spatial structure of their habitat defining extinction risks derived by global change.To address those questions, a riverscape genetics approach was applied at different spatial scales and taxonomic levels including population genetics analyses based on neutral microsatellite markers and Next Generation Sequencing (NGS), G.I.S. (Geographic Information Systems; riverscape characterizations), species distribution modeling and demo-genetic simulations.Initially, population genetics analyses of 11 microsatellite loci revealed a spatial genetic structure for the entire Mexican trout complex as well as genetic introgression for native trout collected in aquaculture farm proximities, these results were corroborated by other using more microsatellite and SNPs markers. Moreover, focusing on O. chrysogaster, species distribution models and demogetic simulations defined riverscape as the main factor driving native population genetic structure, and as a boundary against exotic introgression. Additionally, 9,676 SNP’s were generated by NGS techniques defining a cryptic genetic structure for O. chrysogaster. Finally, landscape genomics approaches revealed a significant influence of riverscape factors on the neutral and adaptive genetic structure of the species.

Abstract My main objectives in this thesis were to explore general patterns and mechanisms driving salmonid invasions globally and, more specifically, to examine the invasion dynamics and impacts of the North American brook trout in North European stream systems. Non-native salmonids have often spread extensively and caused many harmful impacts on their native counterparts. Among the three globally introduced salmonids, the European brown trout appeared as the 'worst' alien species (strongest impact on native fish), followed by the North American rainbow trout and brook trout. Brook trout, which is widely established in European streams, was found to be a non-aggressive species. Moreover, the growth of brown trout was unaffected by brook trout, indicating negligible interspecific interactions between the two species. Habitat niche segregation between brook trout and brown trout was evident, with brook trout occupying mainly low-velocity pool habitats, whereas brown trout resided in fast-flowing riffles. At the river-wide scale, brook trout occurred mainly in small, slightly acid headwater streams, whereas brown trout was found primarily in larger downstream river sections. Evidently, North European streams with a very low number of native fish species offer underutilized niche space for tolerant headwater specialists such as brook trout. However, the habitat niche filled by brook trout was not completely vacant, as brown trout co-occurred with brook trout in numerous small and mid-sized (3–16 m wide) streams. In these streams, brown trout reproduction was negligible presumably related to the presence of brook trout. Brook trout had also increased in density relative to brown trout during the 10-yr study period (1994 vs. 2004). Moreover, the growth rate and population densities of brook trout were high and the species had spread extensively towards the upmost headwater streams during the 10-yr study period. Thus, harmful effects on the native brown trout by brook trout are likely to occur in the core habitat of the invader, i.e. headwater streams, leaving populations of the native species unaffected elsewhere. Due to the high conservation value of the potentially impacted populations of brown trout, I strongly caution against further stocking of brook trout in European watersheds.

The earth’s climate is rapidly changing. With climate change currently altering the environment, water temperature is an important environmental factor that will have various effects on fishes since they are ectotherms. As the changes are expected to be greatest during winter, when salmonid fishes incubate their eggs, one might expect substantial effects on egg development. In this experiment pairs of fish, matched by length, were compared. For each pair, one fish had experienced ambient cold temperatures (cold treatment) during embryogenesis and the other elevated temperatures (warm treatment, ca. 4-5 oC). The fish were tested in stream. Aggressive interactions were recorded and dominance was determined by scoring each fish’s position relative to where food was delivered from and the amount of food taken. Salmon from the cold treatment had a strong tendency to have a higher dominance score than salmon from the warm treatment. The individual with the highest dominance score was not consistently larger or smaller than the individual with the lower dominance score. The results support the hypothesis that salmonids exposed to a cold environment during embryogenesis will be more dominant. Due to climate change, it is expected that water temperature will continue to rise in the future, which in turn will alter the fish’s behaviour. / Jordens klimat förändras snabbt. Med klimatförändringar som för närvarande förändrar miljön är vattentemperaturen en viktig miljöfaktor som kommer att ha olika effekter på fiskar eftersom de är ektoterma. Eftersom förändringarna förväntas vara störst under vintern, när laxfiskar inkuberar sina ägg, kan man förvänta sig betydande effekter på äggutvecklingen. I det här experimentet jämfördes fisk par, matchade med längd. För varje par hade en fisk upplevt kalla vattentemperaturer (kall behandling) under embryogenesen och de andra förhöjda temperaturerna (varm behandling, ca 4-5 oC). Fisken testades i strömakvarie. Aggressiva interaktioner registrerades och dominans bestämdes genom att poängsätta varje fisks position i förhållande till var mat levererades från och mängden mat som tagits. Lax från den kalla behandlingen hade en stark tendens att ha högre dominanspoäng än lax från den varma behandlingen. Individen med högsta dominanspoäng var inte konsekvent större eller mindre än individen med lägre dominanspoäng. Resultaten stöder hypotesen att salmonider utsätts för en kall miljö under embryogenes kommer att vara den mer dominerande. På grund av klimatförändringen är det förväntat att vattentemperaturen fortsätter att stiga i framtiden, vilket i sin tur kommer att förändra fiskens beteende.

The global mean temperature is predicted to increase by up to 5 °C during this century. For fish, being ectotherms, temperature is one of the most important environmental factors, influencing them in a number of different ways, including effects on physiological traits, timing of life history events and behavior. Atlantic salmon has been shown to grow faster after being incubated at warmer temperatures. One possible explanation for this could be that the increased incubation temperature causes decreased metabolic rates. The aim of this project was to examine whether this is true. Atlantic salmon eggs were incubated in three different temperature regimes: natural temperature conditions, heated water and a mixed temperature treatment, where eggs were incubated in increased temperature until the beginning of January and after that subjected to natural temperature conditions. Ventilation rate, a proxy for metabolism, was measured for fish from each treatment group, as well as fish length and weight. The results revealed significantly lower ventilation rates of the fish from the heated temperature treatment, but not of the fish from the mixed temperature treatment. This suggests that an increased incubation temperature causes lowered rates of metabolism in Atlantic salmon, and that the change occurs later than early January. Because of differences in size and life stage between fish from the different groups however, the results are uncertain and call for further investigations. A lowered metabolic rate will affect the fish’s behavior. A further development might therefore be to study fish survival in the wild in relation to a fish’s metabolic rate. / Jordens medeltemperatur beräknas öka med upp till 5 °C det här århundradet. För fiskar, som är ektotermer, är temperatur en av de viktigaste abiotiska faktorerna och påverkar dem på en mängd olika sätt, bland annat genom förändring av fysiologiska attribut, tidpunkter för steg i livscykeln och beteende. Lax har visats växa snabbare efter att ha blivit inkuberade i varmare vattentemperatur. En möjlig förklaring till det kan vara att en förhöjd inkuberingstemperatur orsakar en lägre metabolism. Det här projektet syftade till att undersöka om så är fallet. Ägg från lax inkuberades i tre olika temperaturförhållanden: naturliga temperaturförhållanden, förhöjd temperatur och en blandad temperaturbehandling, där ägg inkuberades i förhöjd temperatur till början av januari, varefter de utsattes för naturliga temperaturförhållanden. Gälslagsfrekvens, som fungerar som en indikator för metabolism, mättes på fisk från varje behandlingsgrupp, samt fiskarnas längd och vikt. Resultaten visade signifikant lägre gälslagsfrekvenser hos fiskarna från behandlingen med förhöjd temperatur, men inte hos fiskarna från behandlingen med blandad temperatur. Detta indikerar att en förhöjd inkuberingstemperatur orsakar en lägre metabolism hos lax, och att förändringen sker senare än tidiga januari. På grund av skillnader i storlek och livsstadier hos fiskarna från de olika grupperna är resultaten dock osäkra, vilket gör att ytterligare studier behövs. En lägre ämnesomsättning påverkar fiskars beteende. En uppföljning kan därför vara att studera fiskars överlevnad i det vilda i relation till deras metabolism.