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Fire suppression, combined with lack of forest thinning and short-rotation, monodominant management, has drastically altered the landscape in the southeastern U.S., leading to the loss of open pine ecosystems and associated avian species. Management of open pine ecosystems is a common practice; yet, there remains uncertainty regarding how vegetation structure impacts priority species. Using empirical data, I assessed changes in species abundance and associated vegetation characteristics before and after management. I also sought to identify vegetation characteristics that influence home range establishment and microhabitat selection of Bachman’s Sparrows. Priority species were negatively associated with hardwood midstory and abundance per site increased following management. Home range establishment of Bachman’s Sparrows was influenced by disturbance, canopy cover, and slope, while microhabitat selection was influenced by pine basal area, available perching options, vegetation density, and herbaceous groundcover. Understanding how vegetation structure impacts priority species may be helpful in guiding conservation and management efforts.

Coyote (Canis latrans) range expansion in the Central Appalachian Mountains has stimulated interest in ecology of this predator and potential impacts to prey populations. This is particularly true in the Ridge and Valley Region in western Virginia where white-tailed deer (Odocoileus virginianus) populations are restricted by low nutritional carrying capacity and are subject to two other predators, bobcats (Lynx rufus) and American black bears (Ursus americanus), in addition to an active hunter community. I address two primary objectives of the Virginia Appalachian Coyote Study: to investigate 1) spatial ecology and 2) population dynamics of coyote populations in Bath and Rockingham counties. I deployed 21 GPS satellite collars on 19 coyotes over 32 months. I estimated home range size (mean = 13.46 km², range = 1.23 km² - 38.24 km²) across months using biased-random bridges and second-order habitat selection at four scales using eigenanalysis of selection ratios. I developed a metric to classify social status of individuals as either resident or transient based on stability of home range centers over time. I found evidence for class substructure for selection of territories where adult residents had a higher probability of mortality in high productivity/high risk habitats, compared to subadults and transients that were restricted to less productive habitats. I collected scat samples over five scat surveys across 2.5 years and extracted fecal DNA to identify individual coyotes in a mark-recapture framework. I estimated coyote densities in Bath (5.53 – 9.04 coyotes/100 km²) and Rockingham Counties (2.41 – 8.53 coyotes/100 km²) using a spatial capture-recapture model. Six-month apparent survival was lower in Bath County (Φ_Bath = 0.442, 0.259 – 0.643; Φ_Rockingham = 0.863, 0.269 – 0.991). The Bath County population demonstrated persistence despite high mortality and the Rockingham population demonstrated boundedness with recruitment inverse of changes in density. Findings at both sites suggest density-dependence, and tests of territoriality, presence of transients, and territory turnover demonstrate a capacity for immediate local immigration in response to high mortality in Bath County. I suggest that landscape-level habitat management may be a viable strategy to reduce potential conflicts with coyotes in the region. / Ph. D.

Le débit joue un rôle de première importance dans la modulation des caractéristiques physico-chimiques des rivières. Les poissons, à travers leur habitat, dépendent directement de cet ensemble de caractéristiques riveraines. De nombreuses études ont démontré qu’une altération du débit naturel des rivières, telle que par des installations hydro-électriques, a un effet négatif à l’échelle des populations et communautés de poissons. Par contre, les mécanismes qui sous-tendent ces relations sont toujours méconnus. Les processus physiologiques des poissons déterminent la façon dont ils sélectionnent leur habitat. La réponse au stress a été proposée comme étant un mécanisme qui les guide à travers les changements qui surviennent dans leur environnement. Le comportement, le cortisol plasmatique, le glucose et le lactate sanguin sont des indicateurs de la réponse au stress chez les poissons. Dans un premier temps, le mouvement de grands brochets Esox lucius L. a été observé dans deux rivières: l’une est régulée par éclusées, l’autre est non régulée et donc libre de barrage. Les résultats démontrent que le taux de mouvement chez des poissons qui habitent la rivière régulée est plus élevé que celui des poissons qui habitent dans la rivière non régulée. De plus, la direction de relation entre la distance parcourue par les poissons et le débit diffère entre rivières, et ce pour une même espèce. Dans un deuxième temps, l’effet d’une élévation de vitesse d’eau sur le cortisol, glucose et lactate de brochets qui proviennent de deux rivières qui présentent des types de gestion de débit contrastés est évalué. Ce chapitre conclut que les poissons de la rivière régulée 1) relâchent moins de glucose dans leur sang, et 2) ont des mécanismes qui permettent une accumulation moindre de lactate dans leur sang, que les poissons de la rivière non régulée lorsqu’ils sont soumis à une augmentation de vitesse d’eau. Dans un troisième temps, une approche analytique a été développée permettant de quantifier l’effet du débit sur la façon dont les brochets sélectionnent les conditions physiques de leur habitat, telle que la vitesse de l’eau. Les résultats des chapitres précédents suggèrent que les poissons de la rivière régulée sont soumis à des vitesses d’eau plus grandes que les poissons de la rivière non régulée. Ce nouvel outil permet de valider cette hypothèse. En dernier lieu, les taux de base et maximaux de cortisol plasmatique, ainsi que de glucose et lactate sanguin ont été mesurés chez des brochets qui vivent dans les deux types de rivière. Ces indicateurs témoignent de la qualité de l’habitat dans lequel les poissons vivent. Nos résultats suggèrent que les poissons qui vivent dans la rivière régulée peuvent moduler leurs niveaux de base et maximaux en cortisol plasmatique dans le but d’éviter le stress chronique. Cette thèse évalue les effets des changements de débit sur les poissons par des approches innovantes, situées à la frontière entre les domaines physiologiques et écologiques. Elle contribue à approfondir nos connaissances en ce qui a trait aux mécanismes par lesquels les poissons se distribuent à travers les différents habitats de rivière. / Flow is an important determinant of physicochemical characteristics of rivers. Fish communities in rivers are strongly dependant of their habitat, which is directly dictated by this set of characteristics. The loss of the natural flow regime, through regulation by hydroelectric facilities, for example, has the potential to directly affect the fish communities. Numerous studies have shown that the loss of natural flow regimes negatively impact fish populations and communities, but not much is known about the mechanisms that underlie such a relationship. Physiological processes determine the way that fish select their habitat. The stress response has been proposed as a mechanism that guides fish throughout the environmental changes happening in their habitat. Indicators of the fish stress response comprise behaviour, plasma cortisol, and blood glucose and lactate. First, northern pike Esox lucius L. movements were assessed in two rivers with contrasting flow regimes: a hydropeaking regulated river and an unregulated free-flowing river. Using manual tracking by radio-telemetry, we found that pike moved at a higher rate in the regulated river than in the unregulated river. Results also show that the direction of the relationship between movement of pike and flow can vary between rivers. Second, the effect of a water velocity increase on plasma cortisol, blood glucose and blood lactate levels in wild pike originating from the two rivers with contrasting flow regimes were assessed. Our results show that blood glucose and lactate concentrations are significantly diminished for fish originating from the regulated river, in comparison to fish originating from the unregulated river, following an increase in water velocity. Third, a novel analytical framework was developed that allow one to quantify the effect of the flow on fish selection of the physical conditions of their habitat (e.g. water velocity). Results obtained in the previous chapters suggest that pike living in the regulated river might be subjected to higher water velocities than fish living in the unregulated river. This novel tool will allow us to validate this hypothesis. Lastly, basal and maximum acute stress-induced concentrations in plasma cortisol, and blood glucose and lactate were quantified in pike living in both the regulated and the unregulated rivers. These physiological parameters can give an indication of the fish habitat quality. Our results suggest that fish from the regulated river are able to modulate their plasma cortisol to dampen their HPI-axis responsiveness and avoid chronic stress. This thesis assesses the effects of flow fluctuations on fish using novel approaches, situated at the intersection between the fields of physiology and ecology. It significantly contributes to broaden our knowledge of the mechanisms underlying fish habitat selection in rivers.

A percepção e interpretação da interação de indivíduos e populações com o ambiente e a forma como tal relação condiciona sua distribuição espacial é questão-chave e recorrente em estudos ecológicos. Padrões de uso de área observados para populações emergem em ultima análise da variabilidade entre seus indivíduos em selecionar habitats e interagir com os mesmos. Este estudo teve como foco o uso de área pela população do boto-cinza, Sotalia guianensis, e sua variabilidade individual no estuário de Cananeia, localizado na costa sudeste do Brasil (25°03\' S; 47°55\' W), durante o verão e o inverno de 2015 e o verão de 2016. Parâmetros ambientais e geográficos (distâncias da desembocadura de rios, da entrada do estuário e de áreas urbanas, profundidade, maré e autocorrelação espacial) foram testados para explicar a distribuição da população e de seus indivíduos a partir de funções de probabilidade de seleção de recursos (RSPF) em modelos aditivos generalizados (GAM). Onze indivíduos fotoidentificados com 18 ou mais recapturas foram avaliados com o uso de modelos individuais de ocupação e sua interpretação foi subsidiada por estimativas de áreas domiciliares obtidas a partir de kerneis fixos de densidade. Nas três temporadas a população apresentou densidades de grupos desiguais ao longo do estuário e todas as variáveis, com exceção da distância de áreas urbanas, explicaram as probabilidades de presença observadas. Análises individuais revelaram discrepâncias nos tamanhos e disposição geográfica de áreas domiciliares e diferenças na composição e estimativa dos parâmetros selecionados para cada indivíduo. A variabilidade individual na população deve ter papel fundamental em termos de utilização do espaço e seleção de habitat pelo boto-cinza no estuário local. / Understanding and interpreting the interaction of individuals and populations with the environment and how this relationship outlines their spatial distribution is a key question common in ecological studies. Area use patterns observed for populations are ultimately an outcome from individual variability in habitat selection and their interaction with such environments. Are use and habitat selection by the population of Guiana dolphins, Sotalia guianensis, and its individual variability were accessed in the Cananeia estuary (25°03\' S; 47°55\' W), southeastern Brazil, during the summer and winter of 2015 and the summer of 2016. Environmental and geographic parameters were estimated aiming to explain population distribution and differences within individuals. For this purpose, resource selection probability functions (RSPF) were applied in generalized additive models (GAM). Covariates tested included: distance to river mouths, distance to the estuary entrance, distance to urban areas, depth and tide. Geographic coordinates were used to model spatial autocorrelation. Eleven photo-identified individuals had their occupancy modelled and accessed in relation to their home range obtained from fixed kernel densities estimates. The population exhibited patchy group densities throughout the estuary in all seasons. Except from distance to urban areas all variables were selected in our final model for the population\'s RSPF. Individual analysis revealed discrepancies in size and location of home ranges which lead to remarkable differences in the composition and estimates of parameters selected in the models for each individual.

O mutum-do-sudeste é endêmico da Mata Atlântica de baixada e foi extinto de quase toda sua distribuição original devido ao desmatamento e a caça. Hoje é listado como ameaçado e a falta de conhecimento sobre sua ecologia dificulta o manejo da espécie. Este trabalho teve como objetivo estimar a densidade populacional do mutum-do-sudeste na Reserva Natural Vale (RNV) através do método de transecção linear. Os registros feitos durante as amostragens também foram utilizados para verificar a existência de seleção de habitat por meio da comparação de áreas onde a espécie foi registrada com áreas aleatórias onde nunca obtivemos registros. A estimativa populacional obtida mostrou a existência de uma razão sexual desviada em relação aos machos que parecia estar relacionada a diferenças de comportamento entre os sexos, devido aos poucos registros de fêmeas. Para confirmar nossos resultados, utilizamos dados de armadilhas fotográficas que foram utilizadas para estudar onças na reserva. Estes dados confirmaram um número maior de machos na população, porém menos acentuado do que o encontrado nos transectos, comprovando que o comportamento discreto das fêmeas afetou nossa amostragem. Combinando os dados dos dois métodos obtivemos a estimativa de 1.6 indivíduos/Km2. As análises de seleção de habitat confirmaram a relação positiva do mutum-do-sudeste com matas altas e sub-bosque denso, e mostraram que o mutum-do-sudeste tem menor probabilidade de ocorrência em áreas com abundância de árvores mortas em pé, troncos em decomposição e serapilheira profunda. Tal influencia negativa provavelmente se deve a aspectos relacionados à sua dieta e a baixa tolerância a habitats que sofreram distúrbio. As informações contidas neste trabalho servirão de base para guiar o manejo de populações selvagens e futuros projetos de reintrodução. Além disso, estudos futuros devem considerar as diferenças de comportamento entre os sexos para que os dados sejam analisados de forma correta, evitando assim, erros que podem afetar diretamente o manejo da espécie. / The Red-billed Curassow was formerly found throughout the lowland Brazilian Atlantic Forest but is now extinct across most of its former range due to habitat loss and hunting pressure. Althought classified as globally threatened, there is still a chronic lack of information on Red-billed Curassows\' biology hindering efforts to mitigate the impacts of anthropogenic threats. We investigated population size and habitat relations of Red-billed Curassows at Vale Nature Reserve (VNR) using line transect and presence/absence method. Line transects results showed a male skewed sex ratio that appeared to be related to different behavivour between sexes as we recorded a low number of females. To evaluate any bias in the estimates of sex ratio from line transect we used data from a camera trap survey designed to monitor jaguars at the reserve. Camera trap data confirmed the existence of a male skewed sex ratio in the population but less pronounced than the one found on line transects, showing that different behavior between sexes affected our estimates. Using the sex ratio calculated with camera trap data we were able to estimate 1.6 individuals/Km2. The habitat assessment showed a positive relation of the Red-billed Curassow with taller forests and dense undergrowth. The abundance of snags, decaying log and leaf litter depth, negatively influenced Red-billed Curassows\' occurrence and appear to be related to its mainly frugivorous diet and low tolerance to habitat disturbances. Our study provides critical baseline information about an important population of Red-billed Curassows and will serve to guide management strategies and future reintroduction attempts. It also reveals that survey efforts must take into account sexual differences in behaviour to increase the reliability of modeled estimates. Failing to take these considerations into account may lead to misleading inferences from data, and impact management strategies for a seriously threatened species.