This study examined activity patterns and habitat use of pygmy rabbits (Brachylagus idahoensis) in mechanically treated and untreated areas in south-central Utah 2005-2008. We monitored fecal pellet plots in continuous sagebrush habitat as well as along treatment edges to record deposition and leporid presence over timed periods. Pygmy rabbit use of big sagebrush was higher than black-tailed jackrabbits (Lepus californicus) and mountain cottontail rabbits (Sylvilagus nuttallii ) (P< 0.01) relative to treated areas (P <0.01). We also compared pygmy rabbit use of areas with continuous sagebrush to residual sagebrush in a sample of mechanically treated areas. Our results suggest a treatment effect with higher (P <0.01) average counts of pygmy rabbit pellets in areas with continuous sagebrush compared to sagebrush strips and islands within treated areas. Before the big sagebrush biotype inhabited by pygmy rabbits is treated to reduce the occurrence and dominance of big sagebrush, we recommend managers consider two options. The first is no treatment, thus preserving, as is, the critical habitat of the pygmy rabbit and other sympatric big sagebrush obligate species of wildlife. The second option cautiously introduces the first prescription of habitat treatment ever recommended in relationship to the pygmy rabbit. This prescription includes recommended widths of the treated areas, seed mixes, widths of the preserved intact big sagebrush habitat for pygmy rabbits as well as suggested grazing systems for domestic livestock. Activity patterns of pygmy rabbits at their burrow were documented through the use of remote cameras. Photographs were analyzed for temporal and seasonal patterns of activity. Our results suggested that time of day was important in the activity level of pygmy rabbits while season was not. Pygmy rabbits were active during all time periods of the day but the greatest levels of activity occurred at night. Numerous other wildlife species were recorded by our remote cameras including other species of leporids, birds, rodents, reptiles and terrestrial predators.

No description available.

No description available.

No description available.

Marine protected areas (MPAs) are increasing in popularity as a tool to manage fish stocks through conservation of entire habitats and fish assemblages. Quantifying the habitat use, site fidelity, and movement patterns of marine species is vital to this method of marine spatial planning. The success of these protected areas requires that sufficient habitat is guarded against fishing pressure. For large animals, which often have correspondingly large home range areas, protecting an entire home range can be logistically challenging. For MPAs to successfully protect large top predator species, it is important to understand what areas of a home range are especially important, such as breeding and feeding grounds. New technologies, such as acoustic telemetry, have made it possible to track marine animal movements at finer spatial and temporal scales than previously possible, better illuminating these spatial use patterns. This study focused on the movement patterns of great barracuda (n=35), an ecologically important top predator, around Buck Island Reef National Monument, a no-take MPA in St. Croix, U.S.V.I. managed by the National Park Service. As developing standardized methods for acoustic telemetry is still a work in progress, the first half of this study focuses on determining appropriate tools for generating home range size estimates for great barracuda and analyzing ecological parameters driving these results. The second half of this study focused on the use of network analysis to look at spatial divisions within individual home ranges and to compare individual to population level spatial patterns, as well as to generate a relative estimate of population density within the park. Barracuda within the park demonstrated high site fidelity to individual territories, but at the population level they consistently used all habitats within the array. Core use areas within home ranges were evenly distributed throughout all habitats monitored by the acoustic array, although movement corridors were detected along high rugosity reef structures. Greater population densities within the park indicate that density dependent behaviors may be influencing habitat use within the park, and suggest that barracuda are contributing high levels of top down pressure through predation within the park boundaries.

This research tested the ability of fish morphology to predict membership of fishes in habitat guilds, their swimming performance, and habitat preference. Further, it considered methods for choosing a surrogate species to identify habitat of target species. Morphological discriminant functions were developed using morphological traits of fishes from one river to identify membership in two habitat guild systems (mesohabitat and microhabitat). Functions were then used to test factors influencing classification success of holdout tests and validated using fishes of a second river. Morphology was only partly successful (50%) at predicting membership in habitat guilds. Morphology identified species by shape, i.e., classifying test species into guilds with members of their genus, but not habitat use, because morphology and habitat were not strongly linked through function. By improving guild definition, relationships between morphology and habitat (Froude number) were identified for all fish groups examined (darters, benthic minnows, pelagic minnows, and suckers). Relationships were not transferable among groups. Further, morphology of eight minnows was linked to swimming performance, a key task for using habitat, in lab measurements of critical swimming speeds. In turn, swimming performance was related to habitat (Froude number). Morphology will be most successful at predicting habitat use of fishes when (1) more, discrete guilds are used, (2) guilds are identified within families, (3) variation in lifestyles (benthic vs. pelagic) is considered, and (4) key tasks related to using habitat are strongly associated with morphology. Finally, I examined a phylogenetic approach to identifying useable habitat. Closely related surrogate species were not more accurate in identifying habitat of target species than surrogates chosen by other methods. When a target species used only one mesohabitat, the highest overlap in habitat use occurred with other fishes of the same family using that mesohabitat (within a physiographic province). For target species using several mesohabitat types, surrogates from the next highest taxonomic unit, e.g., genus or subgenus, provided the most accurate information. Ecomorphology offers a mechanistic and defensible method for identifying habitat preferences of fishes and should be more widely considered as a tool for establishing habitat relationships of stream fishes. / Ph. D.

The diversity of fish species found in warmwater stream systems provides a perplexing challenge when selecting species for Instream Flow Incremental Methodology (IFIM) studies. An often-suggested approach has been to use habitat guilds to incorporate the diversity found in these systems. My goal is to determine the feasibility of developing habitat suitability criteria (HSC) for the entire fish assemblage in the North and South Fork Shenandoah River, Virginia, using habitat guilds. I examined the strengths and weaknesses of direct underwater observation via snorkeling and throwable anode electrofishing to sample fish habitat use (e.g., depth, velocity, distance to cover, dominant and subdominant substrate, cover, and embeddedness) indicates that using the data collected from both techniques may produce better criteria than using just one of the two sampling techniques. To develop habitat suitability criteria using habitat guilds I placed each species a priori into a guild based on a hypothesized guild structure. Transitional life stages with significantly different habitat use were placed separately into the guild structure. The four guilds (riffle, fast generalist, pool-run, and pool-cover) were found to be significantly different from each other using the data collected for the species assigned to the guilds. Criteria were then developed for representative species from each guild and the entire guilds. Criteria developed for depth, velocity, Froude number, cover, distance to cover, substrate, and embeddedness were used to estimate a habitat response function (i.e., the relations between usable habitat and stream flow) for a representative species from each guild, the guild itself, and for a second species from each guild for comparisons. Both the representative species and guild criteria showed similar habitat response functions for the riffle guild, fast generalist guild, and pool-run guild. However, neither set of criteria performed well for the pool-cover guild. For guilds, other than pool-cover, either the guild or the representative species approach may be a viable option to developing habitat suitability criteria. The transferability tests were performed to determine if criteria developed in the North Fork Shenandoah River, Virginia would transfer to the South Fork Shenandoah River, Virginia. Only criteria for the margined madtom (Noturus insignis) and the juvenile smallmouth bass (Micropterus dolomieu) transferred for both suitable and optimal habitat. Criteria for mottled sculpin (Cottus bairdi), Cyprinella sp. (spotfin and satinfin shiners), river chub (Nocomis micropogon), adult and juvenile redbreast sunfish (Lepomis auritus), and adult smallmouth bass did not transfer. Only the pool-cover guild criteria transferred for both suitable and optimal habitat, while riffle guild, fast generalist guild, and pool-run guild criteria did not transfer. I recommend the use of site-specific criteria for the South Fork Shenandoah or different variable combinations. / Master of Science

Population structure and vital rates of Gulf of Maine (GOM) humpback whales, Megaptera novaeangliae, were studied by a combination of longitudinal data, region-wide surveys and modern mark-recapture statistical methods. Demography and rates of exchange were examined among six GOM areas. Juveniles and females were preferentially encountered in southern GOM habitats, including at the Studds Stellwagen Bank National Marine Sanctuary (SBNMS). Multi-state modelling also revealed unequal probabilities of movement between areas that was not explained by inter-area distance, adjacency, whale density or dominant prey type. Aerial surveys and photo-identification data indicated that the population was likely closed to migration between June and September. Otherwise, seasonal trends in population composition were consistent the demographically staggered migration reported in other oceans. Over-wintering occurred,but there was little evidence that a significant number of humpback whales failed to undertake or complete migration each year. Vital rates varied with sex, age and time. Juveniles exhibited lower and more variable survival than adults and so were a potential source of downward bias in “non-calf” survival estimates. Males exhibited higher survival than females and achieved maximal survival at age five, the estimated age at male puberty. By contrast, females did not reach peak survival until the current average age at first birth (8.78 years, s = 2.33). The latter was significantly higher than previous estimates and females that recruited by age seven had a lower likelihood of subsequent survival than those that recruited late. Costs of reproduction persisted into adulthood, with breeders exhibiting lower survival than nonbreeders. Calves born during years of low fecundity exhibited lower survival than those born when fecundity was high, possibly due to lower maternal investment. Costs of reproduction have not previously been described in cetaceans, but are consistent with the risks potentially associated with capital breeding.

La variabilité spatiale et temporelle de l’écoulement en rivière contribue à créer une mosaïque d’habitat dynamique qui soutient la diversité écologique. Une des questions fondamentales en écohydraulique est de déterminer quelles sont les échelles spatiales et temporelles de variation de l’habitat les plus importantes pour les organismes à divers stades de vie. L’objectif général de la thèse consiste à examiner les liens entre la variabilité de l’habitat et le comportement du saumon Atlantique juvénile. Plus spécifiquement, trois thèmes sont abordés : la turbulence en tant que variable d’habitat du poisson, les échelles spatiales et temporelles de sélection de l’habitat et la variabilité individuelle du comportement du poisson. À l’aide de données empiriques détaillées et d’analyses statistiques variées, nos objectifs étaient de 1) quantifier les liens causaux entre les variables d’habitat du poisson « usuelles » et les propriétés turbulentes à échelles multiples; 2) tester l’utilisation d’un chenal portatif pour analyser l’effet des propriétés turbulentes sur les probabilités de capture de proie et du comportement alimentaire des saumons juvéniles; 3) analyser les échelles spatiales et temporelles de sélection de l’habitat dans un tronçon l’été et l’automne; 4) examiner la variation individuelle saisonnière et journalière des patrons d’activité, d’utilisation de l’habitat et de leur interaction; 5) investiguer la variation individuelle du comportement spatial en relation aux fluctuations environnementales. La thèse procure une caractérisation détaillée de la turbulence dans les mouilles et les seuils et montre que la capacité des variables d’habitat du poisson usuelles à expliquer les propriétés turbulentes est relativement basse, surtout dans les petites échelles, mais varie de façon importante entre les unités morphologiques. D’un point de vue pratique, ce niveau de complexité suggère que la turbulence devrait être considérée comme une variable écologique distincte. Dans une deuxième expérience, en utilisant un chenal portatif in situ, nous n’avons pas confirmé de façon concluante, ni écarté l’effet de la turbulence sur la probabilité de capture des proies, mais avons observé une sélection préférentielle de localisations où la turbulence était relativement faible. La sélection d’habitats de faible turbulence a aussi été observée en conditions naturelles dans une étude basée sur des observations pour laquelle 66 poissons ont été marqués à l’aide de transpondeurs passifs et suivis pendant trois mois dans un tronçon de rivière à l’aide d’un réseau d’antennes enfouies dans le lit. La sélection de l’habitat était dépendante de l’échelle d’observation. Les poissons étaient associés aux profondeurs modérées à micro-échelle, mais aussi à des profondeurs plus élevées à l’échelle des patchs. De plus, l’étendue d’habitats utilisés a augmenté de façon asymptotique avec l’échelle temporelle. L’échelle d’une heure a été considérée comme optimale pour décrire l’habitat utilisé dans une journée et l’échelle de trois jours pour décrire l’habitat utilisé dans un mois. Le suivi individuel a révélé une forte variabilité inter-individuelle des patrons d’activité, certains individus étant principalement nocturnes alors que d’autres ont fréquemment changé de patrons d’activité. Les changements de patrons d’activité étaient liés aux variables environnementales, mais aussi à l’utilisation de l’habitat des individus, ce qui pourrait signifier que l’utilisation d’habitats suboptimaux engendre la nécessité d’augmenter l’activité diurne, quand l’apport alimentaire et le risque de prédation sont plus élevés. La variabilité inter-individuelle élevée a aussi été observée dans le comportement spatial. La plupart des poissons ont présenté une faible mobilité la plupart des jours, mais ont occasionnellement effectué des mouvements de forte amplitude. En fait, la variabilité inter-individuelle a compté pour seulement 12-17% de la variabilité totale de la mobilité des poissons. Ces résultats questionnent la prémisse que la population soit composée de fractions d’individus sédentaires et mobiles. La variation individuelle journalière suggère que la mobilité est une réponse à des changements des conditions plutôt qu’à un trait de comportement individuel. / Spatiotemporal flow variability contributes to create a dynamic habitat mosaic sustaining ecological diversity. One of the most important topics in ecohydraulic research is to identify the relevant scales of flow variability affecting organisms at different life stages. The general objective of the thesis is to examine the links between habitat variability and the behaviour of juvenile Atlantic salmon. More specifically, three themes are addressed: turbulence as a fish habitat variable, the spatial and temporal scales of habitat selection and individual variability in fish behaviour. Through detailed field measurements incorporating a variety of sampling techniques and statistical analyses our objectives were to: 1) Quantify the causal links between standard habitat variables and flow turbulence at multiple scales; 2) Test a new in situ portable flume to analyse the effect of turbulent flow properties on the prey capture probability and foraging behaviour of juvenile Atlantic salmon; 3) Analyse the spatial and temporal scale dependence of fish-habitat associations within a reach during the summer and autumn; 4) Examine individual variation of seasonal and daily activity patterns and habitat use and their interaction; 5) Investigate the individual variation in seasonal daily movement behaviour in relation to environmental fluctuations. The thesis provides a detailed characterization of turbulence in pools and riffles and showed that the capacity of ‘standard’ fish habitat variables to explain turbulent properties was relatively low, especially at smaller spatial scales, but varied greatly between the units. From a practical point of view, this level of complexity suggested that turbulence should be considered as a ‘distinct’ ecological variable within this range of spatial scales. In a second experiment, using an in situ portable flume and underwater videotaping of fish, we did not conclusively confirm or rule out the effect of turbulence on prey capture probability, but observed a preferential selection of locations where flow velocity was downward and turbulence intensity was lower. The selection of lower turbulence habitat was also observed in natural habitat conditions in an observational field study, in which 66 PIT-tagged fish were tracked for three months in a river reach using a high resolution network of antennas buried in the bed. Juvenile salmon habitat selection was dependant on the scale of observations. Fish were associated with moderate depth micro-scale habitats, but also with higher depth patch-scale habitats. Furthermore, the range of habitat used by individuals increased asymptotically with the temporal scale. The scale of one hour was considered as optimal to describe the range of habitats used in a day and three days optimal to describe the range of habitat used in a month. Individual tracking revealed high inter-individual variability in activity patterns, as some individuals were predominantly nocturnal whereas others frequently changed their daily activity pattern. Changes in activity patterns were linked to environmental fluctuations, but also to individual habitat use patterns, which might signify that lower quality habitats require fish to increase daytime activity when food intake and the risk of predation are both high. High inter-individual variability was also observed in the fish movement behaviour. It appeared that most fish exhibited low mobility on most days, but also showed occasional bouts of high mobility. Between-individual variability accounted for only 12-17% of the variability in the mobility data. These results challenge the assumption of a population composed of a sedentary and mobile fraction. Individual variation on a daily basis suggested that movement behaviour is a response to changing environmental conditions rather than an individual behavioural trait.

A construção de reservatórios modifica drasticamente a paisagem transformando um ambiente lótico em lêntico e criando uma nova linha de margem com características muitas vezes diferentes. Estes novos habitats são passíveis a utilização e colonização por diversas espécies. Com relação aos crocodilianos existem registros de ocorrência para três espécies nesta região Caiman crocodilus, Paleosuchus palpebrosus e Melanosuchus niger. O presente estudo verificou abundância, densidade, taxa entre os sexos e o uso de habitat para as espécies C. crocodilus e P. palpebrosus, encontradas no reservatório em um período de dez meses de monitoramento pós-represamento. Para efetuar as observações e capturas de indivíduos, focagens noturnas em barco a motor foram realizadas ao longo de cinco campanhas bimestrais. Foram visualizados 659 jacarés sendo 259 C. crocodilus, 102 P. palpebrosus e 298 indeterminados. Nenhum exemplar da espécie M. niger foi observado. O número de crocodilianos por campanha não variou de forma significativa, sendo C. crocodilus mais freqüente. Foram efetuadas 75 capturas, sendo 43 C. crocodilus (21 &#9792; e 22 &#9794; ) e 32 P. palpebrosus (10 &#9792; e 22 &#9794;). A eficiência de captura foi de 16,60% para C. crocodilus, 31,37% para P. palpebrosus e 11,38% para ambas as espécies considerando também os indeterminados. A captura de exemplares de P. palpebrosus foi mais eficiente se comparada a de C. crocodilus. Foram capturados 29 filhotes entre o final da estação chuvosa e o pico da estação seca, nas três últimas campanhas, evidenciando reprodução pós-represamento, sendo 26 C. crocodilus e 3 P. palpebrosus. Os filhotes de C. crocodilus foram observados agrupados em três regiões diferentes sendo que um destes agrupamentos se manteve no mesmo local pelas três últimas campanhas apresentando redução paulatina do número de filhotes. Os três filhotes agrupados de P. palpebrosus só foram observados na quinta campanha. A classificação não-supervisionada de imagens LANDSAT – TM, resultou em oito classes (manchas de habitats) representando 93% da área. Tais manchas foram caracterizadas a partir de anotações de campo e interpretação da imagem. A macha 1, caracterizada como um buritizal alagado próximo ao aeroporto, foi a que apresentou as maiores densidades 60 e 110 ind/km2 para C. crocodilus e P. palpebrosus respectivamente, explicada pela reduzida área ocupada por este habitat. A mancha 2 foi caracterizada como água com sedimento apresentando os maiores valores para área total e amostrada e conseqüentemente baixas densidades. A mancha 3 caracterizada como margem rasa apresentou a maior abundância para C. crocodilus. A mancha 5 caracterizada como solo arenoso não se destacou por elevadas densidades sendo porém a mais abundante para P. palpebrosus. As manchas 6, 7 e 8 se agrupadas mediante a caracterização como habitats de vegetação seca apresentam a segunda maior densidade com 27,55 ind/km2. A mancha 9 foi caracterizada como um habitat onde ocorria a presença de gramíneas (pasto e cerrado campo limpo) sendo C. crocodilus a espécie predominante neste habitat. Conclui-se com este trabalho que C. crocodilus e P. palpebrosus são as espécies de crocodilianos encontradas na região do reservatório e não se mostram relativamente vulneráveis, em um primeiro momento, devido ao represamento do rio. C. crocodilus é mais abundante do que P. palpebrosus no reservatório. C. crocodilus é mais seletivo quanto ao uso das manchas de habitats definidos A observação de grupos de filhotes corrobora para o fato destas espécies se adequarem ao novo ambiente. / The construction of river dams modifies drastically the local landscape, changing a lotic environment into a lentic one and, therefore, originating a new river edge, generally with quite different features. These new habitats could be used and occupied by a plenty of species. There are many projects, constructions and dams in most of its main rivers. Regarding the crocodilians, there are three species recorded in this region: Caiman crocodilus, Paleosuchus palpebrosus, and Melanosuchus niger. The present study verified the abundance, density, sex ratio, and habitat use of Caiman crocodilus and Paleosuchus palpebrosus. These species were found in the dam during a monitoring period of ten months carried out after flooding. Observations and captures were performed during nocturnal surveys using a motorboat. The surveys occurred in five campaigns with intervals of two months. 659 crocodilians, 259 C. crocodilus, 102 P. palpebrosus and 298 undetermined were visualized considering all campaigns. None specimens of M. niger were observed. The number of crocodilians by campaign did not show significant variation and C. crocodilus was the most frequent species. We captured 75 specimens, 43 C. crocodilus (21 &#9792; and 22 &#9794;), and 32 P. palpebrosus (10 &#9792; and 22 &#9794;). Capture effectiveness was 16.60% for C. crocodilus, 31.37% for P. palpebrosus, and 11.38% for both species considering the undetermined specimens. Capture of specimens of P. palpebrosus was more effective compared to C. crocodilus. Twenty nine hatchlings (26 C. crocodilus and 3 P. palpebrosus) were captured between the end of rainy season and the peak of dry season (during the last three campaigns), suggesting reproductive activity after flooding. Hatchlings of C. crocodilus were observed in groups in three different areas. One of these groupings was in the same place during the last three campaigns, showing a slight decrease in number of hatchlings. The three hatchlings of P. palpebrosus were observed only in the last campaign. The unsupervised classification of the LANDSAT – TM images, resulted in eight classes (habitat patches) which represented 93% of the dam. The patches were characterized based on field notes and image interpretation. Patch 1, characterized as a flooded “buritizal" near the airport, showed the highest density (60 and 110 individuals/km2 of the C. crocodilus and P. palpebrosus, respectively). Patch 2 was characterized by water with sediments, representing a great percentage of the sampled and total area and, consequently, showed the lowest density of crocodiles. Patch 3 represents shallow edges and showed the largest abundance of C. crocodilus. Patch 5 represents sandy grounds and, even though this habitat showed no high densities, P. palpebrosus was more abundant in this habitat. Patches 6, 7 and 8 were considered as dry vegetation, showing the second major density (27.55 individuals/km2). Patch 9 was characterized by the presence of grass (pasture and “cerrado campo limpo") and C. crocodilus was the predominant species in this habitat. It can be concluded that C. crocodilus e P. palpebrosus are the species that occur in the dam and, apparently, they are not vulnerable due to the river modifications. C. crocodilus is more abundant than P. palpebrosus in the study area. C. crocodilus is more selective than P. palpebrosus in function of habitat patches. The presence of hatchlings corroborate to the species adaptation to the new habitats.