The streams of the southeastern United States are both hotspots for biodiversity and centers of imperilment. The specific spatiotemporal scales at which stressors impact biota are often unknown, partly due to inadequate knowledge about many species' life-histories. I conducted two complementary studies to investigate the habitat associations of an imperiled highland stream fish, the Candy Darter Etheostoma osburni. In Chapter 2, I asked (1) does micro-habitat suitability correlate with the "robustness" (i.e., viability) of four distinct populations? In Chapter 3, I expanded the extent of investigation, and asked (2) which environmental factors, expressed at what spatial scales, best explain in-stream conditions, and (3) do stream segments where Candy Darters persist have cooler temperatures and less fine-sediment than segments where the species is extirpated or historically went undetected? Chapter 2 revealed Candy Darters demonstrate ontogenetic habitat shifts, with age-0 individuals selecting slower water velocities than adults. Despite, clear habitat selection for multiple habitat variables, suitability attributed to fine-sediment avoidance most strongly correlated with population robustness across streams. Chapter 3 indicated Candy Darters are extirpated from most areas in Virginia and southern West Virginia. Land use and natural catchment features, including geology, elevation, and stream geomorphology, predominantly explained instream conditions. Populations persist in segments with cool stream temperatures and low embeddedness year-round. To recover Candy Darters, managers will need to remedy pervasive land-use threats and restore stream habitat, while operating within the impending context of warming air and water temperatures and the existential threat of the introduced Variegate Darter E. variatum. / M. S.

This dissertation examines the relationship between abundances of Roanoke darter, Roanoke logperch, and black jump rock and availability of stream habitat features at three spatial scales in two reaches of the Roanoke River, Virginia. The utility of underwater observation as a method of estimating benthic fish densities is also assessed. Distributions of perpendicular sighting distances indicate models assuming equal sighting probability are not appropriate for benthic species but distance sampling models assuming decreased sighting probability with increased distance from observers provide reasonable alternatives. Abundances estimated using two distance sampling models, a strip transect model, and a backpack electroshocker were strongly correlated. At the microhabitat scale (45 m² cells), differential use of depth, velocity, substrate, and siltation level by all three species during summer low flows was evident. Habitat use characteristics were not transferable, as depths and velocities associated with high fish densities varied between reaches. Univariate and multivariate habitat suitability indices gave similar rankings for combinations of the four habitat variables, but site suitabilities based on these indices were poor predictors of fish abundance. Habitat cells were not selected independently of surrounding habitat characteristics, as fish densities were highest in target cells adjacent to cells with preferred microhabitat characteristics. Roanoke darter and black jumprock abundances were highest at sites where preferred microhabitat patches were non-contiguous while contiguity had no effect on logperch abundance. Multiple regressions showed area of suitable habitat and patch contiguity accounted for 42 %, 34 %, and 33 % of variation in darter, logperch, and jumprock abundances, respectively. Estimates of area of target riffles, area of pools and riffles upstream and downstream of target riffles, and depth, velocity, and substrate characteristics of pools and riffles immediately upstream and downstream of target riffles were obtained. Fish densities were correlated with at least one measure of proximal habitat for all three species. Significant multiple regression models relating fish density to adjacent habitat unit characteristics were also obtained, but the explanatory power of adjacent unit variables varied among small, medium and large riffles and among species. In summary, fish abundance was related to habitat at all spatial scales but explanatory power was limited. / Ph. D.

This dissertation investigates the spatio-temporal dynamics of intermittent stream fish metacommunities in response drought-induced fragmentation and re-connectivity using both field and experimental approaches. A detailed field study was conducted in two streams and included pre-drought, drought, and post-drought hydrological periods. Fish assemblages and metacommunity structure responded strongly to changes in hydrological conditions with dramatic declines in species richness and abundance during prolonged drought. Return of stream flows resulted in a trend toward recovery but ultimately assemblages failed to fully recover. Differential mortality, dispersal, recruitment among species indicates species specific responses to hydrologic fragmentation, connectivity, and habitat refugia. Two manipulative experiments tested the effects of drought conditions on realistic fish assemblages. Fishes responded strongly to drought conditions in which deeper pools acted as refugia, harboring greater numbers of fish. Variability in assemblage structure and movement patterns among stream pools indicated species specific habitat preferences in response predation, resource competition, and desiccation. Connecting stream flows mediated the impacts of drought conditions and metacommunity dynamics in both experiments. Results from field and experimental studies indicate that stream fish metacommunities are influenced by changes in hydrological conditions and that the timing, duration, and magnitude of drought-induced fragmentation and reconnecting stream flows have important consequences metacommunity dynamics.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Neste trabalho tivemos como objetivo caracterizar a dieta, uso do habitat e padrões comportamentais de Astyanax taeniatus da bacia do Rio Mato Grosso, que encontra-se na porção leste do Estado do Rio de Janeiro (22 52 S; 42 40 W e 22 53 S; 42 34 W). Para a análise da dieta, os exemplares foram coletados bimestralmente entre março de 2006 e janeiro de 2007 em três localidades que diferiram pelas variáveis físicas. As observações de uso dos recursos do habitat foram realizadas por observação subaquática, na posição focal dos exemplares avistados, enquanto a quantificação da disponibilidade foi realizada em 50 quadrats de 20x20cm (400cm2) ao longo dos mesmos 50m onde foi realizada a observação sub-aquática. A análise do conteúdo estomacal de 651 exemplares foi realizada sob microscópio estereoscópico de acordo com métodos qualitativos e quantitativos (Freqüência de Ocorrência e Volumétrica). A participação relativa de cada item registrado nos estômagos em relação à totalidade da dieta foi analisada através do Índice Alimentar (IAi). Para verificar possíveis diferenças entre as proporções dos itens de origem animal e vegetal, autóctone e alóctone, os valores proporcionais foram testados pelo 2 de contingência. A partir dos dados de comprimento padrão e comprimento do intestino, foi calculado o valor do quociente intestinal. Os itens de origem vegetal tiveram maior contribuição na dieta da espécie para as localidades com maior altitude, enquanto os itens animais tiveram maior contribuição na localidade baixa. A diferença na contribuição dos itens de origem autóctone e alóctone também foi significativa. Na dieta de jovens e adultos, houve diferença significativa na contribuição de itens de origem vegetal e animal somente na localidade mais alta, onde os adultos consumiram maior quantidade de matéria vegetal. Os valores médios de quociente intestinal em jovens e adultos foram significativamente diferentes nas localidades de maior altitude, com valores maiores para indivíduos adultos. Observamos 52% dos indivíduos em profundidades entre 30 e 45 cm, 72% em áreas de rápido, 72% em velocidades entre 0 e 0,5km/h, 66% encontravam-se distantes da margem entre 40 e 120 cm, 37,6% em substrato do tipo areia e 34,4% em substrato do tipo pedra. De todos os padrões comportamentais observados, aquele que mais se destacou foi o forrageamento, onde 70,91% dos indivíduos estavam forrageando no meio da coluna dágua. Os resultados da dieta reforçam a idéia de as espécies de Astyanax têm hábito alimentar onívoro e oportunista, onde a espécie alimentou-se dos recursos disponíveis no ambiente evidenciando sua alta plasticidade alimentar ao longo do riacho. Espécies do gênero Astyanax são consideradas generalistas em relação ao uso do habitat e altamente ativas, corroborando com os resultados do presente estudo. / In this work we aimed to characterize the diet, habitat use and behavior patterns of Astyanax taeniatus at Mato Grosso River Basin. This basin is located in the eastern portion of the State of Rio de Janeiro (22 52 'S; 42 40' W and 22 53 'S; 42 34' W). For the diet analysis, the specimens were collected bimonthly between March 2006 and January 2007 in three locations that differed by physical variables. Observations of resource "use" on the habitat were made by underwater observations, on the focal position of the specimens, while the quantification of resource "availability" was performed in 50 quadrats 20x20cm (400cm2) over the same 50m where the underwater observation was made. The analysis of stomach contents of 651 specimens was performed under a stereomicroscope according to qualitative and quantitative methods (Frequency of Occurrence and Volumetric). The proportional contribution of each item recorded in the stomachs for the whole diet was assessed through the Alimentary Index (IAi). To verify possible differences between the proportions of items of animal and vegetable, autochthonous and allochthonous, we used 2 contingency test. From the data of standard length and length of the intestine, we calculated the value of intestinal quotient. Items of plant origin were the major contributors in the diet of the species for locations with higher altitude, while the animal items were the major contributors in the low altitude locality. The difference in the contribution of autochthonous items and allochthonous was also significant. In the diet of youngers and adults, there was a difference in the contribution of items of plant and animal origin only in the highest location, where adults consumed greater amount of vegetable detritus. Mean values of intestinal quotient in youngers and adults were significantly different in places of higher altitude, with higher values for adults. We observed 52% of the individuals at depths between 30 and 45 cm, 72% in areas of rapid, 72% at water velocities between 0 and 0.5 km / h, 66% were distant from the margin between 40 and 120 cm, 37.6 % in the sand substrate and 34.4% in substrate with stones. Of all the behavioral patterns, the one that stood out was the foraging, where 70.91% of individuals were foraging in the middle of the water column. Diet results reinforce the idea of the Astyanax species are omnivorous and opportunistic, where the specie fed the resources available in their environment showing high feeding plasticity along the stream. Species of the genus Astyanax are considered generalists in relation to habitat use and highly active, corroborating the results of this study.

The distribution and abundance of stream fishes are influenced by many factors operating at multiple scales. Understanding how environmental variables influence the structure of stream fish assemblages is important for habitat assessment, stream restoration, and for predicting responses to environmental change. An emerging view in community ecology is that a focus on the functional structure of species assemblages in relation to environmental gradients may reveal more general patterns applicable across geographic regions. In this study, I used functional traits related to the trophic ecology, habitat use, and life-history strategies of fishes to examine the influences of environmental factors on stream fish assemblages. The research was carried out in two large regions: the Río Grijalva basin in southern Mexico and the Brazos and Trinity basins in Central Texas. In both regions, relationships between functional structure of stream fish assemblages and environmental factors at local, landscape, and regional scales were examined. Environmental characteristics at all three scales influenced the functional attributes of assemblages studied here. At the local reach scale, stream size, substrate characteristics, the availability of riffle and pool habitats, and abundance of in-stream cover structures were related to the functional trait composition of fish assemblages in the Río Grijalva Basin and in Central Texas streams. Landscape features most strongly related to functional structure in both regions were the extent of forested area in the watershed and the amount of land developed for urban and agricultural uses. At the regional scale, broad physiographic differences between ecoregions had a large influence on the taxonomic and functional composition of stream fish assemblages in Central Texas. Along the broad-scale longitudinal fluvial gradient of the Grijalva region, pronounced changes in the species composition, functional trait diversity, and trophic structure of fish assemblages were observed.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Neste trabalho tivemos como objetivo caracterizar a dieta, uso do habitat e padrões comportamentais de Astyanax taeniatus da bacia do Rio Mato Grosso, que encontra-se na porção leste do Estado do Rio de Janeiro (22 52 S; 42 40 W e 22 53 S; 42 34 W). Para a análise da dieta, os exemplares foram coletados bimestralmente entre março de 2006 e janeiro de 2007 em três localidades que diferiram pelas variáveis físicas. As observações de uso dos recursos do habitat foram realizadas por observação subaquática, na posição focal dos exemplares avistados, enquanto a quantificação da disponibilidade foi realizada em 50 quadrats de 20x20cm (400cm2) ao longo dos mesmos 50m onde foi realizada a observação sub-aquática. A análise do conteúdo estomacal de 651 exemplares foi realizada sob microscópio estereoscópico de acordo com métodos qualitativos e quantitativos (Freqüência de Ocorrência e Volumétrica). A participação relativa de cada item registrado nos estômagos em relação à totalidade da dieta foi analisada através do Índice Alimentar (IAi). Para verificar possíveis diferenças entre as proporções dos itens de origem animal e vegetal, autóctone e alóctone, os valores proporcionais foram testados pelo 2 de contingência. A partir dos dados de comprimento padrão e comprimento do intestino, foi calculado o valor do quociente intestinal. Os itens de origem vegetal tiveram maior contribuição na dieta da espécie para as localidades com maior altitude, enquanto os itens animais tiveram maior contribuição na localidade baixa. A diferença na contribuição dos itens de origem autóctone e alóctone também foi significativa. Na dieta de jovens e adultos, houve diferença significativa na contribuição de itens de origem vegetal e animal somente na localidade mais alta, onde os adultos consumiram maior quantidade de matéria vegetal. Os valores médios de quociente intestinal em jovens e adultos foram significativamente diferentes nas localidades de maior altitude, com valores maiores para indivíduos adultos. Observamos 52% dos indivíduos em profundidades entre 30 e 45 cm, 72% em áreas de rápido, 72% em velocidades entre 0 e 0,5km/h, 66% encontravam-se distantes da margem entre 40 e 120 cm, 37,6% em substrato do tipo areia e 34,4% em substrato do tipo pedra. De todos os padrões comportamentais observados, aquele que mais se destacou foi o forrageamento, onde 70,91% dos indivíduos estavam forrageando no meio da coluna dágua. Os resultados da dieta reforçam a idéia de as espécies de Astyanax têm hábito alimentar onívoro e oportunista, onde a espécie alimentou-se dos recursos disponíveis no ambiente evidenciando sua alta plasticidade alimentar ao longo do riacho. Espécies do gênero Astyanax são consideradas generalistas em relação ao uso do habitat e altamente ativas, corroborando com os resultados do presente estudo. / In this work we aimed to characterize the diet, habitat use and behavior patterns of Astyanax taeniatus at Mato Grosso River Basin. This basin is located in the eastern portion of the State of Rio de Janeiro (22 52 'S; 42 40' W and 22 53 'S; 42 34' W). For the diet analysis, the specimens were collected bimonthly between March 2006 and January 2007 in three locations that differed by physical variables. Observations of resource "use" on the habitat were made by underwater observations, on the focal position of the specimens, while the quantification of resource "availability" was performed in 50 quadrats 20x20cm (400cm2) over the same 50m where the underwater observation was made. The analysis of stomach contents of 651 specimens was performed under a stereomicroscope according to qualitative and quantitative methods (Frequency of Occurrence and Volumetric). The proportional contribution of each item recorded in the stomachs for the whole diet was assessed through the Alimentary Index (IAi). To verify possible differences between the proportions of items of animal and vegetable, autochthonous and allochthonous, we used 2 contingency test. From the data of standard length and length of the intestine, we calculated the value of intestinal quotient. Items of plant origin were the major contributors in the diet of the species for locations with higher altitude, while the animal items were the major contributors in the low altitude locality. The difference in the contribution of autochthonous items and allochthonous was also significant. In the diet of youngers and adults, there was a difference in the contribution of items of plant and animal origin only in the highest location, where adults consumed greater amount of vegetable detritus. Mean values of intestinal quotient in youngers and adults were significantly different in places of higher altitude, with higher values for adults. We observed 52% of the individuals at depths between 30 and 45 cm, 72% in areas of rapid, 72% at water velocities between 0 and 0.5 km / h, 66% were distant from the margin between 40 and 120 cm, 37.6 % in the sand substrate and 34.4% in substrate with stones. Of all the behavioral patterns, the one that stood out was the foraging, where 70.91% of individuals were foraging in the middle of the water column. Diet results reinforce the idea of the Astyanax species are omnivorous and opportunistic, where the specie fed the resources available in their environment showing high feeding plasticity along the stream. Species of the genus Astyanax are considered generalists in relation to habitat use and highly active, corroborating the results of this study.

Stream ecosystems and their riparian zones have previously been regarded as two different ecosystems, linked through numerous reciprocal subsidies. Today, ecologists agree that the stream and the riparian zone should be regarded as one system, the stream-riparian ecosystem, which is characterised largely by the subsidies between land and water. The terrestrial subsidies to the stream affect stream-living biota in several ways, some of which are well-known while others less so. The input of wood to the stream from the riparian zone is believed to play an important role in the population dynamics of stream-living fish. In this doctoral thesis, I explore effects of fine stream wood (FW, &lt;10 cm diameter) on wild stream-living young-of-the-year brown trout (Salmo trutta) by reporting and discussing results from laboratory, semi-natural and field experiments. My results show that the local density of drifting prey is higher in the presence of FW than in its absence, and also that young-of-the-year brown trout decrease their diurnal foraging time and prey capture success when FW is added to their habitat. I show that trout decrease their swimming activity in the presence of FW, aggregate in FW bundles, and have lower growth rates than trout without FW access. Also, the degree of sheltering in FW bundles was higher during day than at night in a study performed at low water temperatures; moreover, the presence of an ectothermic nocturnal predator (burbot, Lota lota) did not affect the degree of sheltering in FW bundles by trout. Taken together, my results indicate that young-of-the-year brown trout with access to FW bundles spend considerable amounts of time sheltering in the FW, and by doing so they miss the opportunity for higher growth and foraging rates outside of the shelter. The most probable explanation for this behaviour is that growth is traded off against survival, i.e., the predation risk is higher outside of the shelter. / Stream ecosystems and their riparian zones have previously been regarded as two different ecosystems, linked through numerous reciprocal subsidies. Today, ecologists agree that the stream and the riparian zone should be regarded as one system, the stream-riparian ecosystem, which is characterised largely by the subsidies between land and water. In this doctoral thesis, I explore one such subsidy – the input of fine stream wood (FW) to streams. Wild stream-living young-of-the-year brown trout (Salmo trutta) was chosen as study species. My results show that the local density of drifting prey is higher in the presence of FW than in its absence, and that young-of-the-year brown trout decrease their diurnal foraging time and prey capture success when FW is added to their habitat. I show that trout decrease their activity in the presence of FW, aggregate in FW bundles, and have lower growth rates than trout without FW access. Taken together, my results indicate that young-of-the-year brown trout spend considerable amounts of time in FW bundles, and by doing so they miss the opportunity for higher growth and foraging rates outside of the shelter. The most probable explanation for this behaviour is that growth is traded off against survival. / <p>Artikel 3 publicerades i avhandlingen som manuskript med samma titel.</p>

Human alteration of the landscape for agricultural and urban land use has been linked to the degradation of streams and stream biota. Natural physical and climatic characteristics, or physiographic template, are important for determining natural land cover and constraining human land use, and are strongly related to stream habitat and stream biotic assemblages. Since the physiographic template differs among watersheds and is an important determinant of the processes being studied, it is important to account for these natural differences among watersheds so that the relationship between land cover and streams can be properly understood. The purpose of this thesis is to develop and assess the utility of a regional framework that classifies watersheds based on physical and climatic predictors of land cover. In Chapter 1, I identified physical and climatic predictors of land cover and classified watersheds into Land cover Distinguished Physiographic Regions (LDPRs) based on these predictors. I was able to identify and create classes based off eight climatic and landform characteristics that determined natural land cover and human land use patterns for both the Eastern and Western U.S. In Chapter 2, I utilized LDPRs to stratify a study region and investigated whether the relationships between land cover and stream fish assemblages varied between these regions. Five commonly used metrics covering trophic, reproductive and taxonomic groupings showed significant variation in their response to agricultural land use across LDPRs. The results suggest that the physiographic differences among LDPRs can result in different pathways by which land cover alterations impact stream fish communities. Unlike other commonly used regional frameworks, the rationale and methods used to develop LDPRs properly accounts for the causal relationship between physiography and land cover. Therefore, I recommend the use of LDPRs as a tool for stratifying watersheds based on physiography in future investigations so that the processes by which human land use results in stream degradation can be understood. / Master of Science

The index of biotic integrity (IBI) comprises several fish-assemblage attributes, called metrics, that reflect how a site differs from least-disturbed (by anthropogenic influences) conditions. Understanding how metrics at least-disturbed sites vary across landscape classes (e.g., physiographies, ecoregions) and stream sizes helps one determine appropriate regions and stream-size ranges in which to develop and use the IBI. The IBI’s utility depends on how accurately and reliably each metric reflects disturbance. I make recommendations for developing the IBI for use in Virginia. I examined metric variation across landscape classes: physiographies, ecoregions, and drainage groups; and across stream sizes. I examined intra-region relations between metrics and disturbance measures and whether relations met conventional IBI assumptions. Taxonomic metrics (e.g., number of native minnow species) and reproductive metrics (e.g., proportion of individuals as lithophils) varied more across physiographies than across ecoregions or drainages. Trophic metrics (e.g., proportion as invertivores) varied least across landscape classes and most with stream size. For Virginia, I recommend three regions: Coastal Plain, Piedmont, and Mountain, in which to develop and use distinct versions of the IBI. In Coastal Plain, disturbance-vs-metric relations were mostly contrary to IBI assumptions. In Piedmont, trophic and tolerance metrics best reflected disturbance and met IBI assumptions; in Mountain, reproductive metrics did so. Disturbance measures accounted for about 20% of the variance in metrics, suggesting that my data incompletely represented disturbance effects on fish. Until further validation, I recommend that each regional IBI retain at least two taxonomic, two trophic, two reproductive, and one tolerance metric. / Master of Science

Rigorous modeling of the spatial species distributions is critical in biogeography, conservation, resource management, and assessment of climate change. The goal of chapter 2 of this dissertation was to evaluate the potential of using historical samples to develop high-resolution species distribution models (SDMs) of stream fishes of the United States. I explored the spatial transferability and temporal transferability of stream–fish distribution models in chapter 3 and chapter 4 respectively. Chapter 2 showed that the discrimination power of SDMs for 76 non-game fish species depended on data quality, species' rarity, statistical modeling technique, and incorporation of spatial autocorrelation. The area under the Receiver-Operating-Characteristic curve (AUC) in the cross validation tended to be higher in the logistic regression and boosted regression trees (BRT) than the presence-only MaxEnt models. AUC in the cross validation was also higher for species with large geographic ranges and small local populations. Species prevalence affected discrimination power in the model training but not in the validation. In chapter 3, spatial transferability of SDMs was low for over 70% of the 21 species examined. Only 24% of logistic regression, 12% of BRT, and 16% of MaxEnt had AUC > 0.6 in the spatial transfers. Friedman's rank sum test showed that there was no significant difference in the performance of the three modeling techniques. Spatial transferability could be improved by using spatial logistic regression under Lasso regularization in the training of SDMs and by matching the range and location of predictor variables between training and transfer regions. In chapter 4, testing of temporal SDM transfer on independent samples resulted in discrimination power of the moderate to good range, with AUC > 0.6 for 80% of species in all three types of models. Most cool water species had good temporal transferability. However, biases and misspecified spread occurred frequently in the temporal model transfers. To reduce under- or over-estimation bias, I suggest rescaling the predicted probability of species presence to ordinal ranks. To mitigate inappropriate spread of predictions in the climate change scenarios, I recommended to use large training datasets with good coverage of environmental gradients, and fine-tune predictor variables with regularization and cross validation. / Ph. D.