Thesis (M.S.)--Mississippi State University. Department of Wildlife and Fisheries. / Title from title screen. Includes bibliographical references.

In 2000 the European Union introduced the Water Framework Directive, new legislation that regulates the use of surface waters within the European Community. The goal of this legislation is to protect, enhance and restore all surface waters within the Community to Good Surface Water Status. Good-Status is described as having low levels of anthropogenic distortion in its hydro-morphological and physiochemical components as well as possessing biota that would normally be associated with the type-specific aquatic ecosystem. The assessment of ecosystem status is to be defined by comparisons with intact representative reference sites, by using modelling techniques that define reference conditions, a combination of the two, or expert judgement. As undisturbed aquatic ecosystems are rare or non-existent in Europe the base-line data will have to be defined using the latter methodologies. The aim of this project is to help define reference conditions for lotic systems in Europe based on the physical instream habitat parameters of a resident species. Brown trout (Salmo trutta), a ubiquitous and well studies species endemic to Europe, was used as the target organism to develop the assessment protocol. The project focused on the requirements this species has of aspects of its physical habitat; specifically, its usage of depth, velocity, and substrate. An extensive survey of the scientific literature was used to define the requirements trout has for the three physical parameters at four life stages. These are the spawning, nursery, juvenile and adult-resident life stages. These requirements were expressed as tolerance profiles, which defined suitable, usable and not-suitable habitat. The methodology was demonstrated by evaluating the physical habitat available at six reaches in three small streams, March, Burnhouse and Bin Burns, which drain into the Carron Valley Reservoir in central Scotland. From the perspective of water depth, these streams seem best suited as nursery areas, are less well suited as juvenile habitat, and do not appear to be well matched for adult residents. The assessment of both velocity and substrate indicated that the portion of the study reaches available for use by resident brown trout increased with trout size. The assessment of all three physical habitat parameters at all study reaches found variable portions of the streams suitable for use by spawning trout. When the habitat variables are integrated all stream segments streams seem best suited as nursery and spawning areas. To a lesser extent juvenile trout can use these burns and very little habitat is available for use by adult resident trout. The tolerance profiles that were created in this study are standardized assessment criteria that when compared with stream survey data can produce an appraisal of habitat availability in any fluvial freshwater system that supports populations of brown trout (Salmo trutta). The assessment method can be combined to produce an integrated habitat assessment, using both an index and by the calculation of Froude number, which is a more realistic approach than the assessment of individual habitat parameters as salmonids choose their microhabitat based on multiple factors. This approach allows an investigator to determine the amount and relative portion of useable habitat and to determine the quality of that habitat. Finally, by examining the physical habitat variable that most strongly correlates with the final integrated habitat distribution the individual habitat parameter that is most important to the distribution of physical habitat at a site can be determined. While this technique would certainly benefit from further development it does show potential to aid in physical habitat assessment of trout streams.

Thesis (Ph.D.)--Mississippi State University. Department of Wildlife and Fisheries. / Title from title screen. Includes bibliographical references.

This study examined the effects of the January 2010 cold spell on mangrove utilizing coral reef fishes off the southeast coast of Florida, USA, in the vicinity of Biscayne National Park (BNP). An ongoing, fishery-independent mangrove visual survey documenting fish assemblages in BNP provided data from the years 1998 to 2014 for examination. Of particular interest were the presence, abundance, and size structure for five mangrove utilizing coral reef fishes: sergeant major (Abudefduf saxatilis), yellowfin mojarra (Gerres cinereus), schoolmaster snapper (Lutjanus apodus), gray snapper (Lutjanus griseus), and great barracuda (Sphyraena barracuda). These species were selected for analysis due to their economic and ecologic importance, their potential as environmental indicators, their connectedness to multiple habitats, and their abundance within the available data set. Data were collected using a modified visual ‘belt transect’ method, consisting of 60 m2 transects running parallel to the mangrove shorelines. Data for average length of fish were reconstructed to form standard normal distributions and the resulting lengths were assigned to various age-classes to create species-specific length-frequency distributions. Variations in presence and abundance were examined across three time periods (1998-2009; 2010-2011; 2012-2014), as well as comparisons of length-frequency distributions. Following the January 2010 cold spell, the presence and abundance values for the two years immediately following the event were significantly decreased compared to the years prior to the cold spell for most of the five species at either mainland (ML) or leeward key (LK) locations. Additionally, the presence and abundance estimates typically remained statistically decreased when compared against the remaining years in the available data set. The size structures for the majority of the five species at either location, however, were not consistently significantly different between the three time periods, as was hypothesized. Instead, the analyses showed mixed results, with the size structure typically shifting towards smaller individuals immediately following the event. These findings suggest that drops in water temperature resulting from cold spells are capable of directly impacting mangrove utilizing reef fish species, albeit to varying degrees depending on various factors, such as physiological tolerances, ecological life history strategies, and habitat requirements.

Predators are key components of aquatic ecosystems and innovative approaches to understanding their spatial distribution are imperative for research, effective management, and conservation. Discontinuities, created by abrupt changes between two unlike entities, are irregularly-distributed, intermediate-scale features that can have a disproportionate effect on organismal distribution within the seascape. Here I use the discontinuity concept to relate the distribution of a predator, striped bass (Morone saxatilis), to physical features within Plum Island Estuary (PIE), MA. I mapped the distribution of 50 acoustically-tagged striped bass during four monthly surveys at 40 sites to evaluate if heterogeneity in physical features concentrated predators. All striped bass survived tagging, were coastal migrants, displayed seasonal residency within PIE, and moved freely throughout the estuary. However, these highly mobile predators were not evenly distributed. Specifically, striped bass were clustered in the middle region of PIE in response to sandbar area, intermediate bottom unevenness, channel networks, and, to a lesser extent, confluences and drop-offs. The highest predator counts occurred at sites with the greatest additive habitat complexity. I measured 23 geomorphic metrics at 40 sites within the seascape to characterize the spatial patterns of confluences, drop-offs, bathymetry and land features. Then, I mapped integrated measurements of multimetric physical features to reveal distinct spatial trends in physical complexity of the estuary. By expanding the discontinuity concept and combining irregularly-distributed, intermediate-scale physical features with smaller-scale, traditional fish habitat methodologies, I revealed consistent and ecologically-meaningful patterns within a north temperate estuarine seascape.

Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices. / Many large scale studies have identified habitat modification or habitat losses as primary threats for the conservation of freshwater fish communities. In Canada, No Net Loss (NNL) of the productive capacity of habitats is the guiding principle of the Department of Fisheries and Oceans’ policy for the management of fish habitat. To respect NNL, a better understanding of fish-habitat relationships is required, as well as tools to quantify the impact of habitat modifications on fish. Fish habitat use models (FHUM) are tools that can improve our understanding of fish-habitat relationships, predict species occurrences, densities or biomass on the basis of habitat descriptors and quantify habitat requirements. They consist in relationships between biological descriptors of fish and habitat descriptors. The general objective of my thesis is to improve the performance of FHUM for the lower Laurentian streams by suggesting refinements on 2 crucial aspects in the development of these models: a precise description of the fish community and the use of efficient statistical models. In the first chapter, I evaluate the relative performance of electrofishing and visual surveys (snorkeling) for estimating the abundance of combinations of fish species and size classes in rivers. I also assessed the effect of environmental conditions on potential differences between the results obtained using these two sampling methods. Sampling sites consisted in 10 river sections of 20 m in length distributed in the Laurentian region of Québec. Both methods were used while sections were blocked. Three snorkelers that swam the river sections upstream while identifying and counting fish of each species and size-classes performed visual surveys. Three-pass electrofishing was performed and abundances were estimated with a maximum likelihood depletion model. Greater abundances of fish were observed by snorkeling than by electrofishing at all sites. Snorkeling species richness was higher (6/10) or equal (4/10) to electrofishing richness. Differences in the fish communities observed by both sampling methods were not related to environmental conditions. The results of our work are therefore contrary to that of most published studies that suggested the superiority of electrofishing on visual surveys. Compared to the conditions found in previous studies, our sampling sites had different environmental characteristics (no fallen trees, insignificant cover of large cobble and boulder) but the most striking dissimilarity was in terms of fish communities (dominance of cyprinids and centrarchids instead of salmonids). Behavioural characteristics favouring capture avoidance (schooling) and facilitating underwater observation (curiosity) may be responsible for the superiority of visual surveys in our study rivers. Survey methods should be selected based on fish community composition. In the second chapter, I develop FHUM for complex stream fish communities. In order to simplify the modelling of such communities, as well as improve our understanding of fish – habitat relationships, I used the ecological guild concept and the niche filtering hypothesis to explore the relationships between guilds based on different types of traits (eco-morphological, reproductive, alimentary and taxonomic) and local environmental descriptors, at the coarse meso-habitat scale. Reproductive guilds led to FHUM that clearly outperformed the other 3 approaches, because of the close relationship between preferred spawning grounds and non spawning habitat preferences, and also because reproductive traits are linked to habitat characteristics at the reach or coarse mesohabitat scale. We also defined guilds based on habitat-use and related them to species traits. Traits related to the feeding biology of fishes seemed to be the best at explaining the habitat-use guilds, but our model did not correctly represent the among-guild relationships. Validation of our reproductive trait model on an independent dataset would confirm our finding, which represents a promising way of modelling fish - habitat relationships in complex fish communities. In conclusion, my thesis suggests important improvements to FHUM models in the Laurentian streams by giving new insights on the choice of a sampling method that take into account the biological characteristics of the streams targeted, and by using a promising way of simplifying FHUM for species rich communities: reproductive guilds.

Puisque l’altération des habitats d’eau douce augmente, il devient critique d’identifier les composantes de l’habitat qui influencent les métriques de la productivité des pêcheries. Nous avons comparé la contribution relative de trois types de variables d’habitat à l’explication de la variance de métriques d’abondance, de biomasse et de richesse à l’aide de modèles d’habitat de poissons, et avons identifié les variables d’habitat les plus efficaces à expliquer ces variations. Au cours des étés 2012 et 2013, les communautés de poissons de 43 sites littoraux ont été échantillonnées dans le Lac du Bonnet, un réservoir dans le Sud-est du Manitoba (Canada). Sept scénarios d’échantillonnage, différant par l’engin de pêche, l’année et le moment de la journée, ont été utilisés pour estimer l’abondance, la biomasse et la richesse à chaque site, toutes espèces confondues. Trois types de variables d’habitat ont été évalués: des variables locales (à l’intérieur du site), des variables latérales (caractérisation de la berge) et des variables contextuelles (position relative à des attributs du paysage). Les variables d’habitat locales et contextuelles expliquaient en moyenne un total de 44 % (R2 ajusté) de la variation des métriques de la productivité des pêcheries, alors que les variables d’habitat latérales expliquaient seulement 2 % de la variation. Les variables les plus souvent significatives sont la couverture de macrophytes, la distance aux tributaires d’une largeur ≥ 50 m et la distance aux marais d’une superficie ≥ 100 000 m2, ce qui suggère que ces variables sont les plus efficaces à expliquer la variation des métriques de la productivité des pêcheries dans la zone littorale des réservoirs. / As freshwater fisheries become increasingly prone to habitat alteration, it is critical we identify the components of habitat that greatly influence fisheries productivity metrics. Using fish habitat modeling, we compared relative contributions of three types of habitat variables to explain variation in abundance, biomass and richness metrics, and identified habitat variables most effective at explaining these variations. During the summers of 2012 and 2013, fish communities in 43 littoral sites were sampled from Lac du Bonnet, a reservoir in southeastern Manitoba (Canada). Seven different sampling scenarios, consisting of different sampling methods, years and time periods, were used to measure relative abundance, biomass and richness metrics for all species combined per site. Three types of habitat variables were measured: local (i.e. within site), lateral (i.e. shore characterization) and contextual (i.e. position relative to landscape attributes) variables. Together local and contextual habitat variables explained on average 44% R2adj of the variation across fisheries productivity metrics, while only 2% R2adj of the variation was explained by lateral habitat variables. Specifically, macrophyte coverage, distance to tributaries ≥ 50 m wide, and distance to marshes ≥ 100,000 m2 ranked most significant across metrics, suggesting these habitat variables may be most effective at explaining variation in fisheries productivity metrics in the littoral zone of reservoirs.

The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. Underlying the dynamic development of streams is potential capacity. Streams express this capacity as an array of habitats over time and across the landscape. Human land uses in the western United States have rapidly altered aquatic habitats as well as the processes that shape habitat. As a result, the diversity of native fishes and their habitats has been suppressed. Restoration is fundamentally about allowing stream systems to re-express their capacities. Four steps are provided to guide stream restoration activities. Key tasks include: identification of the historic patterns of habitat development; protection of the developmental diversity that remains; local application of specific knowledge about suppressive factors; classification of sensitive, critical or refugium habitats; release of anthropogenic suppression; and monitoring of biotic response to habitat change. Applying these concepts, I describe potential habitat refugia for aquatic organisms in the Joseph Creek basin in the Blue Mountains of northeast Oregon. Five valley segment classes, differing in valley corridor landforms, are described. Of these, low-gradient wide alluvial valleys have been most altered by human land use. Riparian vegetation has been extensively removed or altered in alluvial valleys. Currently, stream habitats are structurally depauperate, and warm to temperatures well above thermal tolerances of native salmonids. Potential refugia for native coldwater fishes in these valleys include patches of complex habitat within stream reaches. Reaches fenced to exclude domestic livestock exhibit narrower channels, more pools, and higher frequencies of stable vegetated banks than nearby unfenced reaches. During summer low flow periods, cold groundwater seeping into and accumulating in stream channels forms "cold pools". Cold pools provide potential seasonal refuge for coldwater fish at microhabitat scales. Cold pools are associated with channel complexity, and are more frequent in reaches with vigorous riparian vegetation. Seven classes of cold pools are described. Cold pool classes differ in minimum temperature, maximum depth and volume. Distributions of cold pool classes between valley segment classes suggest that valley geomorphology in addition to local channel form may influence development of certain cold pool types. Although refugia at the microhabitat to reach scales are important, the context within which remnant or refugium habitats and associated relict populations are maintained may ultimately determine the persistence of those species and habitats. In managed landscapes, protection and restoration of habitats at many scales may be necessary if we are to best insure the persistence of native species. / Graduation date: 1995

The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. / Graduation date: 2013

Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices. / Many large scale studies have identified habitat modification or habitat losses as primary threats for the conservation of freshwater fish communities. In Canada, No Net Loss (NNL) of the productive capacity of habitats is the guiding principle of the Department of Fisheries and Oceans’ policy for the management of fish habitat. To respect NNL, a better understanding of fish-habitat relationships is required, as well as tools to quantify the impact of habitat modifications on fish. Fish habitat use models (FHUM) are tools that can improve our understanding of fish-habitat relationships, predict species occurrences, densities or biomass on the basis of habitat descriptors and quantify habitat requirements. They consist in relationships between biological descriptors of fish and habitat descriptors. The general objective of my thesis is to improve the performance of FHUM for the lower Laurentian streams by suggesting refinements on 2 crucial aspects in the development of these models: a precise description of the fish community and the use of efficient statistical models. In the first chapter, I evaluate the relative performance of electrofishing and visual surveys (snorkeling) for estimating the abundance of combinations of fish species and size classes in rivers. I also assessed the effect of environmental conditions on potential differences between the results obtained using these two sampling methods. Sampling sites consisted in 10 river sections of 20 m in length distributed in the Laurentian region of Québec. Both methods were used while sections were blocked. Three snorkelers that swam the river sections upstream while identifying and counting fish of each species and size-classes performed visual surveys. Three-pass electrofishing was performed and abundances were estimated with a maximum likelihood depletion model. Greater abundances of fish were observed by snorkeling than by electrofishing at all sites. Snorkeling species richness was higher (6/10) or equal (4/10) to electrofishing richness. Differences in the fish communities observed by both sampling methods were not related to environmental conditions. The results of our work are therefore contrary to that of most published studies that suggested the superiority of electrofishing on visual surveys. Compared to the conditions found in previous studies, our sampling sites had different environmental characteristics (no fallen trees, insignificant cover of large cobble and boulder) but the most striking dissimilarity was in terms of fish communities (dominance of cyprinids and centrarchids instead of salmonids). Behavioural characteristics favouring capture avoidance (schooling) and facilitating underwater observation (curiosity) may be responsible for the superiority of visual surveys in our study rivers. Survey methods should be selected based on fish community composition. In the second chapter, I develop FHUM for complex stream fish communities. In order to simplify the modelling of such communities, as well as improve our understanding of fish – habitat relationships, I used the ecological guild concept and the niche filtering hypothesis to explore the relationships between guilds based on different types of traits (eco-morphological, reproductive, alimentary and taxonomic) and local environmental descriptors, at the coarse meso-habitat scale. Reproductive guilds led to FHUM that clearly outperformed the other 3 approaches, because of the close relationship between preferred spawning grounds and non spawning habitat preferences, and also because reproductive traits are linked to habitat characteristics at the reach or coarse mesohabitat scale. We also defined guilds based on habitat-use and related them to species traits. Traits related to the feeding biology of fishes seemed to be the best at explaining the habitat-use guilds, but our model did not correctly represent the among-guild relationships. Validation of our reproductive trait model on an independent dataset would confirm our finding, which represents a promising way of modelling fish - habitat relationships in complex fish communities. In conclusion, my thesis suggests important improvements to FHUM models in the Laurentian streams by giving new insights on the choice of a sampling method that take into account the biological characteristics of the streams targeted, and by using a promising way of simplifying FHUM for species rich communities: reproductive guilds.