Climate change is considered a major threat to freshwater ecosystems through altering biodiversity, structure, and function. Having a thorough understanding of how diverse ecosystems respond to temperature change is vital to ecosystem management and conservation. During summer 2012, I quantified fish biomass, somatic growth, secondary production, and habitat data for fish communities in 25 Appalachian streams from Vermont to North Carolina. Multiple statistical tests were conducted to determine the relationship between community fish production and air and water temperature, species thermal guild production and air and water temperature, and the relationship between community fish production and diversity. Community fish production estimates ranged from 0.15 to 6.79 g m-2 yr-1 and community P/B ratios ranged from 0.21 to 1.07. No significant differences existed between mean community production estimates at the cold-water, cool-water, warm-water, and extreme northern sites (P=0.19), but P/B ratios in the extreme northern streams were statistically higher than mean community P/B in cold- and cool-water streams in the southern Appalachians (P=0.002). Water temperatures had a positive effect on community fish production (P=0.01) while air temperatures did not (P=0.10). Both air and water temperatures were significant in predicting whether community production would be dominated by cold-water or cool-water fish (P=0.001, P<0.0001, respectively). Community fish production was significantly, positively related to species richness (R2=0.38, P=0.001) and was one of the highest correlates of community production (R2=0.52). As climate change alters freshwater ecosystems, fish communities may transform by means of shifting fish abundance, biomass, and production among species ultimately affecting ecosystem structure, function, and biodiversity. / Master of Science

The creation of the Mississippi River Gulf Outlet (MRGO) in 1963 by the U.S. Army Corps of Engineers (USACE) represents one of the most catastrophic, anthropogenic stressors ever to impact the Lake Pontchartrain estuary in southeastern Louisiana, USA. The artificial tidal pass provided a direct route from the Gulf of Mexico to New Orleans. It allowed for high saline waters to enter Lake Pontchartrain, resulting in detrimental changes to the biotic community of the Lake and surrounding wetland areas. In July 2009, the USACE closed the MRGO in hopes of restoring natural ecosystems. This study assesses changes in the adult, juvenile, and larval fish assemblages in the Lake from data taken before and after the closure. Water quality data were also examined for shifts related to the MRGO closure. Significant decreases in salinity were found following the closure, however no significant differences were found in adult or larval fish assemblages.

Dissertação(mestrado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2011. / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-12-16T03:31:29Z No. of bitstreams: 1 Priscila Martins de Moura.pdf: 499869 bytes, checksum: 89e9bd15d4cf51cf14c19da5f5c8c309 (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-12-18T17:58:11Z (GMT) No. of bitstreams: 1 Priscila Martins de Moura.pdf: 499869 bytes, checksum: 89e9bd15d4cf51cf14c19da5f5c8c309 (MD5) / Made available in DSpace on 2013-12-18T17:58:11Z (GMT). No. of bitstreams: 1 Priscila Martins de Moura.pdf: 499869 bytes, checksum: 89e9bd15d4cf51cf14c19da5f5c8c309 (MD5) Previous issue date: 2011 / A presente dissertação é composta de um capítulo (em Português) sintetizando os principais resultados obtidos, os quais são apresentados na forma de um manuscrito (em inglês) no apêndice. O principal objetivo foi analisar o padrão de distribuição das assembléias de peixes e a influência de algumas variáveis ambientais na abundância relativa das espécies dominantes ao longo de um amplo eixo espacial (~300 km), englobando o estuário da Lagoa dos Patos, canal São Gonçalo e Lagoa Mirim. No total, sete locais foram amostrados mensalmente entre 03/2004 e 02/2005 com uma rede de arrasto em zonas rasas (< 2 m). Foram capturadas 63 espécies e 45.929 indivíduos. As análises de escalonamento multidimensional (MDS) evidenciaram a presença de dois grupos principais espacialmente distintos: um formado pelas amostras do estuário e outro formado pelo Canal São Gonçalo e Lagoa Mirim. Os peixes foram agrupados em guildas ecológicas e, através da análise de composição e abundância relativa, verificou-se uma marcada substituição dessas guildas entre a zona estuarina (estuário e norte do canal) e zona límnica (sul do canal e Lagoa Mirim). Essa substituição foi mais pronunciada em termos de abundância do que em termos de frequência de ocorrência, sendo que a segregação entre as guildas foi intensificada pela presença de uma barragem-eclusa, posicionada na porção mediana do gradiente. Variáveis físico-químicas (e.g., salinidade e transparência da água) e outras relacionadas às características estruturais dos habitats (e.g., declividade e percentual de silte e argila no sedimento) foram os principais fatores, dentre os investigados, que melhor explicaram a variabilidade na abundância e distribuição da ictiofauna ao longo do gradiente. / This dissertation is comprised of a chapter (in Portuguese) summarizing our main findings, which are shown in a manuscript (in English) in the annex. Our main goal was to analyze the distribution pattern of fish assemblages and the influence of some environmental variables on the relative abundance of dominant species along a broad spatial axes (~300 km), including the Patos Lagoon estuary, São Gonçalo channel and Mirim Lake. A total of seven sites were sampled monthly between 03/2004 and 02/2005 with a beach seine in shallow areas (<2 m). A total of 63 fish species and 45.929 individuals were caught. The multidimensional scaling (MDS) analyses revealed two main groups spatially distinct: one formed by the estuarine samples and other by freshwater samples from the channel and the Mirim. Fish species were grouped into ecological guilds and the analyses of their composition and relative abundance revealed a marked substitution of ecological guilds between the estuarine zone (estuary and northern portion of the channel) and the limnetic zone (southern portion of the channel and Mirim). This substitution was more pronounced in terms of abundance than in terms of frequency of occurrence. Guilds segregation was intensified by the presence of a dam lock positioned in the middle portion of the gradient. Physico-chemical variables (e.g., salinity and water transparency) and others related to the structural characteristics of habitats (e.g., slope and percentage of silt and clay in the sediment) were the main factors, among those investigated, that better explained the variability in the distribution and abundance of fish fauna along the gradient.

Cette thèse cherche à déterminer l’influence de l’environnement abiotique sur la structure des assemblages de poissons dans les estuaires européens tidaux à partir d’une approche macroécologique. L’environnement abiotique de 135 estuaires, du Portugal à l’Ecosse, est caractérisé par une quinzaine de descripteurs en utilisant une approche écohydrologique. Les assemblages de poissons d’une centaine d’estuaires sont caractérisés par les données de pêche acquises au cours de campagnes scientifiques conduites dans le cadre de la Directive-Cadre européenne sur l’Eau (DCE). Néanmoins, ces données sont souvent hétérogènes du fait des différences entre les protocoles d’échantillonnage utilisés. Afin de limiter cette hétérogénéité, une sélection rigoureuse et une procédure de standardisation des données ont été effectuées. Les assemblages de poissons sont décrits à l’aide d’indices globaux ou fonctionnels relatifs à la richesse spécifique et à l’abondance. A l’aide de modèles linéaires généralisés, des relations sont établies entre des attributs de l’ichtyofaune et des gradients abiotiques à large échelle et au sein de l’estuaire. La richesse spécifique totale, et en particulier celle des espèces marines et migratrices amphihalines, augmente avec la taille de l’estuaire. De plus, elle apparaît plus élevée dans les estuaires associés à un large plateau continental. Les plus fortes densités totales et, en particulier, celles des espèces résidentes et marines, sont associées aux estuaires présentant une grande proportion en zones intertidales. Les assemblages de poissons estuariens apparaissent fortement structurés par le gradient de salinité à la fois en termes de richesse spécifique et de densité. En parallèle, cette thèse apporte des éléments témoignant d’un décalage vers le Nord de plusieurs espèces de poissons estuariens dans le contexte du réchauffement climatique global. Les résultats de cette thèse contribueront à l’amélioration des indicateurs biotiques basés sur l’ichtyofaune qui sont actuellement développés dans le contexte de la DCE. / Based on a macroecological approach, this thesis aims at determining the influence of the abiotic environment on the structure of fish assemblages among European tidal estuaries. The abiotic environment of 135 North-Eastern Atlantic estuaries from Portugal to Scotland was characterised by fifteen descriptors using an ecohydrological approach. The fish assemblages of about a hundred estuaries were characterised by fish data collected during scientific surveys conducted in the context of the European Water Framework Directive (WFD). Nonetheless, differences among sampling protocols resulted in highly heterogeneous datasets. To limit this heterogeneity, a rigorous selections and standardisation processes were carried out. Fish assemblages were described by total or functional indices related to species richness or abundance. Relationships were identified between large-scale and intra-estuarine abiotic gradients and fish attributes by fitting generalised linear models. Results showed that the total number of species, and more especially of marine and diadromous species, increased with the estuary size. Moreover, the total species richness appeared higher in estuaries associated to a wide continental shelf. The greatest total densities, and more particularly total densities of resident and marine species, were associated to estuaries with a great proportion of intertidal areas. Fish assemblages appeared also strongly structured by the salinity gradient in terms of both species richness and density. Furthermore, this thesis brought some evidence of northward migration of estuarine fish species in the context of the global warming. The results of this thesis will contribute to improve the fish indicators that are currently developed in the context of the European WFD.

The cross-sectional form of semi-alluvial bedrock channels was investigated. Channel geometry data were collected from a variety of streams in Ontario and Québec, Canada to develop empirical downstream scaling relationships. The relationships revealed that bedrock, mixed, and alluvial channels scale at similar rates with respect to discharge. The widest channels were formed in low-relief sedimentary bedrock with minimal alluvial cover. Channels influenced by resistant igneous/metamorphic bedrock produced a strong scaling relationship, whereas channels influenced by weak sedimentary bedrock produced a weak scaling relationship. Alluvial cover appeared to exhibit more control on channel width in low-relief settings in comparison to high-relief settings, with increased alluvial cover promoting channel narrowing. Channels influenced by igneous/metamorphic bedrock produced identifiable thalwegs, presumably due to well-defined bedload transport pathways. Channels influenced by sedimentary bedrock tended to have planar beds. Additionally, fish habitat was investigated at one semi-alluvial bedrock stream in Ontario, Canada. Fish sampling was conducted at proximate bedrock and alluvial sections followed by a survey of physical habitat parameters to evaluate habitat preferences. Adult logperch (Percina caprodes), juvenile white sucker (Catostomus commersonii), adult round goby (Neogobius melanostomus), and adult longnose dace (Rhinichthys cataractae) demonstrated preference toward alluvial substrate, whereas juvenile logperch and adult banded killifish (Fundulus diaphanus) demonstrated preference toward bedrock. Juvenile silver shiner (Notropis photogenis) and juvenile yellow perch (Perca flavescens) were indifferent to substrate type. Empirical depth and flow velocity habitat suitability indices (HSIs) were developed for each fish species. This study presents the first fish habitat suitability criteria developed from a small semi-alluvial bedrock stream and may provide valuable information for fisheries management endeavours in such environments.

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Les sites d'agrégation de ponte (AP) sont des zones où des poissons d'une même espèce se rassemblent pour frayer. En dépit de leur importance dans la reproduction de nombreuses espèces de poissons des récifs coralliens, bien peu de sites d'AP sont gérés. Le but de cette étude est d'améliorer la compréhension générale sur l'écologie des sites d'AP en vue de faciliter la gestion. L'étude, réalisée aux Seychelles, se concentre sur les individus regroupant sur les sites d'AP pour frayer et aussi sur ceux résidant sur ces sites. La télémétrie acoustique et le recensement visuel sous-marin ont, ici, été employé comme principaux outils d'observation des espèces formant des agrégations de reproduction (cordonnier (Siganus sutor), mérou camouflage (Epinephelus polyphekadion) et mérou marbré (E. fuscoguttatus)) et des espèces résidant sur les sites d'AP. Les détections acoustiques ont montré que les individus de S. sutor présentent une grande fidélité à leur site de ponte et une périodicité liée à la période de pleine lune. Par ailleurs, les agrégations de ponte d'E. fuscoguttatus et E. polyphekadion se chevauchent spatialement et temporellement avec une forte périodicité liée à la nouvelle lune. La formation d'AP de E. fuscoguttatus et E. polyphekadion provoque des changements complexes dans l'assemblage de poissons résidents sur le site. L'effet de la phase lunaire sur les assemblages de poissons résidant sur les sites d'AP de S. Sutor apparait être dépendant de l'échelle considérée. Les informations sur la dynamique spatiale et temporelle des espèces étudiée sont utilisées pour proposer des mesures de gestion susceptibles d'améliorer la protection des sites d'AP. / Fish spawning aggregation (FSA) sites are areas where repeated concentration of conspecific fish gathers for the purpose of spawning. Despite of their importance in the reproduction of many coral reef fishes, few FSA sites are actively managed. The aim of this study, conducted in the Seychelles, was to improve general understanding on the ecology of FSA sites to facilitate their management. It focuses on both the individuals that aggregate at FSA sites to spawn and those that are resident at FSA sites. Acoustic telemetry and underwater visual census were used to study three species that form spawning aggregations (spinefoot shoemaker (Siganus sutor), Camouflage grouper (Epinephelus polyphekadion) and Brown-marbled grouper (E. fuscoguttatus)) and the resident fish assemblages at FSA sites. Acoustic detections found individual S. sutor to have high fidelity to individual FSA sites and to show significant periodicity with the full moon period in the timing of their arrival and departure from FSA sites. Conversely, spawning aggregations of E. fuscoguttatus and E. polyphekadion overlapped spatially and temporally, with strong periodicity for spawning aggregation to form with the new moon period. The formation of E. fuscoguttatus and E. polyphekadion FSAs caused complex changes in the fish assemblage that is resident at the FSA site. The effect of lunar phase on the resident fish assemblages at S. sutor FSA sites appeared to be scale-dependent, having greater impact at the larger than the smaller FSA site. Information on the spatial and temporal dynamics of aggregating and resident fish species is used to propose management actions to improve the protection of FSA sites.

Latitudinal patterns in reef fish assemblages reflect the influence of long-term environmental conditions, evolutionary processes and the recent, short-term influence of fishing. Long-term processes generate the typically common latitudinal patterns in reef fish assemblages, such as decreases in diversity and herbivory towards higher latitudes. These patterns reflect the global gradient in water temperature and the isolation of temperate regions from the tropics. Fishing also influences reef fish assemblages in that it decreases the abundance of large-bodied carnivore species on reefs, often leading to over-exploitation, depletion and in some cases the extirpation of populations. Indirectly, the removal of these large-bodied carnivores can influence the abundance of their prey, leading to an increase in non-target species. This study examines the latitudinal patterns in reef fish assemblages across a unique biogeographic region, the temperate Western Australian coast, and incorporates an investigation of the influence of fishing on the structure of these assemblages. Seven regions across seven degrees of latitude and seven degrees of longitude covering approximately 1500 km of coastline were sampled. Fish assemblages were characterised at each region using diver operated stereo-video transects. At each region, four locations, and within each location, four reefs were surveyed totalling 1344 transects. A significant gradient in water temperature exists with latitude and longitude. Along the Western Australian coast, and in contrast to other regions species diversity of reef fish increased towards higher latitudes and there was no evidence for a decrease in the biomass and abundance of herbivorous reef fish. The presence of the poleward flowing warm water Leeuwin current combined with the absence of major extinction events means the temperate Western Australian coast contrasts with global latitudinal trends in reef fish assemblage structure. The unique biogeographic history of temperate Western Australia has also generated a high degree of endemism among reef fish. Nearly 30 % of the species found along the west coast in this study are endemic to Western Australia, with the narrow range of these species playing an important role in the large scale patterns and spatial vi heterogeneity in reef fish assemblage structure. Furthermore, many of these endemic species are large-bodied carnivores and targeted by fishers. The impact of fishing on the abundance of large-bodied carnivores throughout the Western Australian temperate region is clear both spatially and temporally. The distribution of fishing effort is greatest along the west coast and decreases towards the south following the gradient in SST. Along the west coast, high levels of fishing effort have reduced the biomass and abundance of target carnivores to well below the standing biomass of the south coast where a low level of fishing effort occurs. This reduction in biomass is related to the historical declines in catch per unit effort (CPUE) of many key target species. These target species include endemic species such as Choerodon rubescens, Glaucosoma herbraicum, Epinephilides armatus Nemadactylus valenciennesi and Achoerodus gouldii.

Le concept d’habitat, qui définit le lieu de vie des organismes par des conditions abiotiques et biotiques, est déterminant pour étudier les relations entre les organismes et leur environnement. La sélection d’habitat est le processus à travers lequel l’organisme va choisir l’habitat où il se trouve en fonction des différents habitats disponibles autour de lui. Cette sélection va dépendre d’un choix individuel, qui est propre à l’organisme (ex. son comportement), et d’un choix commun, qui est observable chez des organismes qui partagent des traits communs (ex. les individus d’une même espèce). Les modèles spécifiques de sélection d’habitat cherchent à expliquer et prédire ce choix commun, et sont notamment utilisés pour les cours d’eau dans les outils d'aide à la définition de débits écologiques. Pour les poissons de rivière, la plupart des modèles spécifiques à l’échelle du microhabitat sont peu transférables à d’autres rivières. En effet, ils sont construits à partir de données d’abondance échantillonnées dans le même site pendant quelques campagnes. Afin d’améliorer la qualité prédictive de ces modèles, j’ai développé une approche prometteuse de modélisation multi-sites et multi-campagnes permettant à la fois de considérer la réponse non linéaire de la sélection et la surdispersion des données d’abondance. A partir de suivis individuels par télémétrie, j’ai montré la pertinence des modèles de sélection spécifiques malgré la forte variabilité individuelle observée. Finalement, la sélection d’habitat étant dépendante de processus structurant les communautés et agissant à l’échelle du paysage, telle que la dispersion des individus, j’ai mis en évidence l’intérêt d’utiliser des techniques légères d’échantillonnage comme les observations par plongée pour caractériser les structures des communautés et leurs répartitions spatiales. Ces techniques permettront alors d’étudier l’influence des processus du paysage sur les modèles de sélection d’habitat / The habitat concept, which defines the place where organisms live, is composed by abiotic and biotic conditions and differs for examples between species or activities. The habitat selection is the process where organisms choose the habitat to live in function of all habitats available around them. This habitat selection depends on an individual choice related to the organism, for example its behavior and a common choice related to organisms sharing common traits as individuals from the same species. Specific habitat selection models are developed to understand and represent this common choice and used to build ecological flow tools. For freshwater fish, most of specific habitat selection models have low transferability between reaches and rivers. Indeed, they are built from abundance data and sampled in the same study reach during few numbers of surveys. In order to improve predictive quality of models, I developed an attractive modelling approach, both multi-reach and multi-survey, involving the non-linear response of habitat selection and abundance data overdispersion. Then, despite the high individual variability of habitat selection, I showed, from telemetry data, the relevance of developing specific habitat selection models. Finally, as the habitat selection is also depending on processes which influence community structures at the landscape scale (e.g. dispersal), I demonstrate the benefits of sampling methods such as snorkeling to characterize community structures and their longitudinal distributions at a large spatial scale. These techniques will allow studying the influence of landscape processes on habitat selection models.