The development of effective management plans for animal populations relies on an understanding of how the population is utilizing the habitat as well as the identification of any critical habitat areas. The St. Johns River (SJR), an urban estuary with a high level of anthropogenic disturbance, is home to a resident population of bottlenose dolphins (Tursiops truncatus). In chapter one, SJR dolphin habitat use patterns, the factors that influenced these patterns, and the critical habitat areas were identified. Significant associations were found in most pair-wise comparisons between season, behavioral state, group size, water depth, and location, indicating that the overall habitat use patterns of SJR dolphins were influenced by complex interactions among these variables. Additionally, two critical habitat areas were identified. Both critical habitats had high levels of anthropogenic activity and the SJR will undergo further development during the Jacksonville Port expansion project. In conjunction with increasing levels of activity, anthropogenic sound can have numerous effects on cetaceans including the masking of signals, alterations in behavior, abandonment of critical habitats, and physiological stress. In chapter two, the soundscape of the SJR was characterized to evaluate the potential impacts of anthropogenic sound on SJR dolphins. Sound levels in the SJR were consistently high and anthropogenic sound was pervasive throughout the river. Therefore, the dolphins in the SJR are at risk of experiencing long-term behavioral and physiological stress due to anthropogenic sound. Together, this work provides valuable knowledge about dolphin habitat use and the soundscape ecology of an urbanized estuary that will enable more informed management decisions and hopefully lead to more effective conservation practices.

Abstract My main objectives in this thesis were to explore general patterns and mechanisms driving salmonid invasions globally and, more specifically, to examine the invasion dynamics and impacts of the North American brook trout in North European stream systems. Non-native salmonids have often spread extensively and caused many harmful impacts on their native counterparts. Among the three globally introduced salmonids, the European brown trout appeared as the 'worst' alien species (strongest impact on native fish), followed by the North American rainbow trout and brook trout. Brook trout, which is widely established in European streams, was found to be a non-aggressive species. Moreover, the growth of brown trout was unaffected by brook trout, indicating negligible interspecific interactions between the two species. Habitat niche segregation between brook trout and brown trout was evident, with brook trout occupying mainly low-velocity pool habitats, whereas brown trout resided in fast-flowing riffles. At the river-wide scale, brook trout occurred mainly in small, slightly acid headwater streams, whereas brown trout was found primarily in larger downstream river sections. Evidently, North European streams with a very low number of native fish species offer underutilized niche space for tolerant headwater specialists such as brook trout. However, the habitat niche filled by brook trout was not completely vacant, as brown trout co-occurred with brook trout in numerous small and mid-sized (3–16 m wide) streams. In these streams, brown trout reproduction was negligible presumably related to the presence of brook trout. Brook trout had also increased in density relative to brown trout during the 10-yr study period (1994 vs. 2004). Moreover, the growth rate and population densities of brook trout were high and the species had spread extensively towards the upmost headwater streams during the 10-yr study period. Thus, harmful effects on the native brown trout by brook trout are likely to occur in the core habitat of the invader, i.e. headwater streams, leaving populations of the native species unaffected elsewhere. Due to the high conservation value of the potentially impacted populations of brown trout, I strongly caution against further stocking of brook trout in European watersheds.

Le déclin du thon rouge de l'Atlantique nord-est et de Méditerranée (ABFT, Thunnus thynnus) qui faisait suite à une forte surexploitation a été largement médiatisé au cours de la dernière décennie. Pour contrer cette tendance et reconstituer ce stock, d’importantes mesures de gestion ont été mises en place à partir de 2007. En dehors des difficultés liées à leur mise en œuvre et à leur contrôle, la gestion des pêcheries thonières est aussi limitée dans les capacités à suivre précisément les variations d’abondance de ces espèces dont les observations reposent principalement sur les données de pêche. Le manque d’indice d’abondance fiable fait que l’évaluation du thon rouge, comme celle des autres espèces de poissons grands pélagiques, est entachée d’importantes incertitudes. Cependant, les suivis aériens pourraient permettre de fournir un indice d’abondance du thon rouge. Ils sont en effet fréquemment utilisés pour l'évaluation de l'abondance des mammifères marins et aussi par les pêcheurs pour détecter les poissons épipélagiques, comme les thons. Dans ce contexte général, cette thèse a pour objectifs : (i) d'évaluer des facteurs qui affectent potentiellement la détectabilité des thons pendant les suivis aériens, (ii) d’analyser leur comportement horizontal et vertical et les facteurs environnementaux qui l’influencent, et (iii) d’intégrer les connaissances acquises pour développer un indice abondance robuste du thon rouge en Méditerranée Nord Occidentale. Les analyses reposent sur des suivis aériens conduits depuis 2000 dans le golfe du Lion, une zone de nourricerie importante pour le thon rouge. Une modélisation des données basée sur le « distance sampling » montre des effets significatifs des observateurs, de la taille des bancs de thons et de l'état de la mer sur l’estimation d’abondance. Cette étude confirme par ailleurs une augmentation importance des abondances entre 2003 et 2009, probablement en réponse aux mesures de gestion mises en œuvre depuis 2007 (notamment la taille minimale de débarquement de 30 kg). Pour évaluer les effets du comportement sur les estimations d'abondance, une étude a porté sur les trajectoires de thons issues du marquage électronique. Ces analyses montrent une disponibilité des thons rouge ainsi qu’une présence en surface dans la zone et la période (Août-Octobre) des suivis aériens ; résultat confortant la fiabilité de l’indice d’abondance. On note également des changements saisonniers du comportement, avec un approfondissement des thons à partir de mi-Novembre correspondant à la dé-stratification de la colonne d’eau. Le comportement de plongée profonde était particulièrement fréquent pendant les mois de forte productivité biologique (février-Mai), mais des plongées profondes ont également été observées à la fin de l'été en relation avec des fronts thermiques. La variabilité des schémas migratoires sur l’horizontale et du comportement sur la verticale indique une forte composante opportuniste, probablement liée à la disponibilité des ressources alimentaires. Les résultats obtenus durant cette thèse démontrent la faisabilité d’obtenir un indice d’abondance de thon rouge robuste à partir des suivis aériens (donc indépendants des données de pêche) et fournissent un cadre théorique et méthodologique pour une extension de ce type de suivi afin de diminuer les incertitudes autour de l’évaluation de ce stock. Outre le thon rouge, les suivis aériens ont également permis un suivi du rorqual commun (Balaenoptera physalus) et des dauphins rayés (Stenella coeruleoalba). La présence des mammifères marins semble également être liée à la productivité élevée et l'activité méso-échelle de la zone d'étude. Si les dauphins présentent une distribution spatiale en partie corrélée à celle du thon rouge, les rorquals ne présentent pas de forte co-occurrence avec le thon rouge, résultat qui confirmerait une certaine proximité des régimes alimentaires des thons et des dauphins. / Declines in Atlantic bluefin tuna stocks (ABFT, Thunnus thynnus), due to extensive over-fishing, have been widely publicized in recent decades. To counteract this trend, regulatory measures have been introduced by the fisheries managers, aiming at the rebuilding of ABFT stocks. However, apart from difficulties in controlling the implementation of these measures, fisheries management is limited in its capabilities to track their efficiency due to major uncertainties in the stock assessment. Indeed, there is a general need of reliable indicators of ABFT abundance. Aerial surveys may provide a helpful tool for the abundance monitoring of this highly exploited fish species. They are frequently used for the abundance assessment of marine mammals and also by fishermen to detect epipelagic fish, such as tunas. The aim of this thesis was to address these issues and to create a robust fishery-independent abundance index for ABFT through aerial surveys. To achieve this goal, the focus was set on (i) the assessment of factors that potentially affect the detectability of ABFT during the aerial surveys, (ii) the habitat use of ABFT, i.e. their horizontal and vertical behaviour as well as the factors driving it, and (iii) the integration of the knowledge gained through these analyses in the development of a robust index of ABFT abundance. Surveys were conducted from 2000 onwards in the Gulf of Lions, an important nursery ground for ABFT in the Northwestern Mediterranean Sea. Line transect modelling of the sighting data revealed significant effects of detectability changes on abundance estimates, related to the observer teams employed, the size of detected ABFT schools and the sea state during the aerial surveys. Derived estimates of ABFT abundance confirmed a significant increase from 2003 to 2009, likely reflecting the success of recently implemented management measures (e.g. minimum landing size of 30 kg since 2007). To assess behavioural effects on abundance estimates, auxiliary archival tagging experiments, conducted since 2007, focused on the presence and surface availability of ABFT during the aerial surveys, and aimed to identify factors influencing these variables. The data gained from these experiments demonstrated seasonal changes in the migratory behaviour of ABFT, but also a high area and surface presence of ABFT in the study zone during the survey period (August–October), supporting the reliability of the abundance index. Surface presence of ABFT decreased with the breakdown of the thermal stratification of the water column (mid-November), when the fish left the survey zone and moved South. By contrast, deep diving behaviour was particularly frequent during months of high biological productivity (February--May), although deep and unusual long spike dives were also observed during late summer in relation to thermal fronts. However, the variability in the migration patterns indicates a strong opportunistic component in both, the horizontal and vertical behaviour of ABFT, probably related to the availability of food resources. Apart from ABFT, the aerial surveys also allowed an abundance monitoring of fin whales (Balaenoptera physalus) and striped dolphins (Stenella coeruleoalba) as well as an analysis of their co-occurrence with ABFT. In fact, similar to ABFT, the presence of these species appeared to be related to the high productivity and mesoscale activity of the study zone, improving our understanding of their habitat use, essential for the conservation of these much less abundant and endangered species. Regarding the stock assessment of ABFT, the results gained through this thesis prove the feasibility to derive robust fishery independent abundance indicators for ABFT through aerial surveys, providing the theoretical and methodological background for an extension of these efforts for a more sustainable management of the stocks of this species.

In the tradition of previous studies of threatened species, this thesis was undertaken with the aim of improving our understanding of the ecology of the White-winged Nightjar Caprimulgus candicans, and providing the information necessary to facilitate conservation efforts on its behalf. In 1998-2001, I studied a population of White-winged Nightjars at Aguará Ñu, an area of cerrado habitats within the Reserva Natural del Bosque Mbaracayù, eastern Paraguay. Over the course of three fieldwork seasons, I captured and ringed a total of 49 nightjars (34 adults and 15 young birds). Young females first bred at approximately one year old, while still in pre-definitive plumage. Young males exhibited a form of delayed plumage maturation, whereby they only attained definitive plumage following a prolonged moult spanning much of their first potential breeding season. No evidence was obtained to suggest that they succeeded in breeding while in this conspicuously intermediate state of moult. Considerable variation was noted in the plumage whiteness of definitive males, but no clear evidence was found for consistent age-related increases in white. During the breeding season, males defended small aggregated display territories, at which they conducted nuptial display flights between late August and early January. Female nightjars were responsible for all the parental care, and apparently visited male display arenas solely to obtain copulations. Chick paternity data confirmed that the study population was polygynous, with patterns of male aggregation suggestive of an exploded lek or 'landmark' mating system. Radio-telemetry studies showed that nightjars utilised home ranges of at least 20 to 40 hectares during the eight to ten months for which they were monitored. Home ranges contained a disproportionately large amount of young campo cerrado vegetation, but no forest or old campo cerrado habitats. When selecting foraging sites within their ranges, nightjars preferred younger and avoided older campo cerrado vegetation; wet grassland was utilised roughly in proportion to its availability. Observed patterns of habitat selection were potentially explained by the greater abundance of insect prey in younger habitats. When selecting daytime roost sites, nightjars preferred vegetation of intermediate age, reflecting their need for a balance between cover and ease of access. A more general analysis of patterns of sexual dimorphism within the Caprimulgidae showed that, although almost 80% of nightjar species exhibit some dimorphism of plumage whiteness, the study species was by far the most extreme case. The striking plumage of the male was partly explained by a strong positive relationship between wing white and openness of breeding habitats within the family. However, this failed to explain the complete absence of white in the female plumage, or the extent of white dimorphism shown by the species. The most likely explanation would appear to be that extreme plumage dimorphism occurred in conjunction with the evolution of polygyny and female-only care in this open-country species. The implications of these findings for the conservation of the White-winged Nightjar are highlighted, and recommendations are proposed for future work and conservation action.

A Ilha de São Sebastião está localizada em um dos remanescentes de Mata Atlântica e, apesar de sua importância, o conhecimento sobre as taxocenoses da herpetofauna ainda é fragmentado. Assim, considerando a inexistência de dados, este trabalho teve como objetivo o estudo da ecologia da herpetofauna, enfocando os seguintes aspectos: composição, riqueza, dominância, abundância relativa, uso do ambiente e uso do substrato. Para a amostragem de campo, foram utilizados os métodos armadilha de interceptação e queda, armadilha de funil, procura visual limitada por tempo, procura de carro e encontro casual. Os dados de campo foram complementados por dados de coleções científicas e literatura. Foram registradas 34 espécies de anfíbios anuros, um anfíbio gimnofiono, um anfisbenídeo, dez lagartos, 26 serpentes e um quelônio. Serapilheira, arbusto e solo foram os substratos mais utilizados pela herpetofauna. A maioria das espécies é especialista. A distribuição das espécies indica que ocorre estruturação das taxocenoses, com maior diversidade na altitude intermediária. / The ilha de São Sebastião is located in one of the most representative remnants of the Atlantic forest, and although its great importance, the knowledge of herpetofaunal assemblages remain poorly known, mainly in ecology. Thus, considering the data or quantitative studies absence, this work goal the herpetofaunal ecology, focusing: composition, richness, dominance, relative abundance, habitat use and macrobabitat use. Fieldwork included pitfall traps with drift fences, funnel traps, time constrained search, sampling by car and incidental encounters. The fieldwork data was complemented by herpetological collections and literature records. We recorded 34 species of anuran amphibians, one gymnophiona, one amphisbenid, ten lizards, 26 species of snakes and one turtle. There were many differences on macrohabitat use, and the main were litter, shrub and ground. The most of species is specialist in the macrohabitat use. In the habitat use, the species distribution shows that the assemblage structure is complex, with superior diversity in the intermediate altitude.

No description available.

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

During the summer of 2008 and 2009, we studied the ecology of the Kittlitz’s Murrelet (Brachyramphus brevirostris), a small diving seabird and candidate for the U.S. Endangered Species List, in Prince William Sound (PWS), Alaska. At-sea survey data suggests that the population significantly increased from 2001 to 2009, however there is limited evidence of reproductive success. Habitat use models showed individuals were observed in shallower waters, closer to glaciers, the shoreline, and further from moraines than the available habitat during the daytime. Finer extent sampling from 2008 suggests temperature-depth profiles also influence Kittlitz’s Murrelet daytime habitat use. The associations between Kittlitz’s Murrelets and water column characteristics are likely an effect of prey availability. Stable isotope work in 2009 suggests birds were generalist foragers prior to the breeding season, becoming more specialized following the breeding season. This specialization may have been a response to strict foraging constraints during the flightless fall molt. Time budgets of radio-tagged individuals suggest birds may have been responding to ephemeral prey concentrations, and working near their maximum energetic limits. Remote monitoring of radio-tagged individuals showed birds left the glacial fjord system during the nighttime, possibly spending these hours near gillnet fishing areas, suggesting a new possible area of concern in evaluating potential threats to Kittlitz’s Murrelet populations.

No description available.

State and Federal agencies have created sanctuaries and speed zones to help reduce manatee mortality while incorporating the recreational and commercial resource needs of these same habitats for humans. Specific habitat resources are considered necessary to increase manatee survivorship. We have only recently begun to address how manatees use some of these resources based on physiological or reproductive strategies. In this study, I quantified patterns of habitat use during seasonal and diel periods for different sex and reproductive manatee classes using data from a radio-telemetry study conducted by the Florida Fish and Wildlife Conservation Commission during 1991-1996. I used five environmental geographic data layers: bathymetry, distance to seagrass, distance to shoreline, distance to warm water refuge sites, and distance to fresh water sources, to discriminate seasonal and diel habitat use patterns for different manatee classes: males (M), females with calves (FWC), and females without calves (FNC). Mean occupancy values were calculated for environmental variable locations and seasonal, diel, and manatee class differences were tested using a Multi-Response Permutation Procedure (MRPP). Nonmetric Multidimensional Scaling (NMS) was used to visualize the ordination patterns of the manatee classes and to assess importance of correlated environmental variables. Significant differences in habitat use were noted between summer and winter based on distances to warm water, seagrass, and fresh water sources but similar habitat use patterns were exhibited within summer diel periods among manatee classes. All manatee classes appeared to have used a higher proportion of locations closer in proximity to seagrass at night than day in winter indicating a disproportionate difference in feeding bouts between diel periods. These differences may be attributed to adjusting feeding strategies to reduce thermoregulatory costs or to decrease human interactions. Differences in patterns were exhibited for the winter diel periods specifically for the FWC manatee classes during winter days. FWC had a higher proportion of locations within the warm water refuges during the day indicating a possible trade off situation between food consumption and thermal exposure. This study demonstrates coarse and fine scale patterns of variation in habitat use for manatees both seasonally and daily within winter. It also suggests that during winter months, manatees were not just utilizing their habitat but they appeared to have preferences and selection for certain habitat types. Recovery of a species is greatly enhanced when patterns of habitat use within the species' environment has been clearly defined. Understanding more specifically what types of habitats manatees choose might allow management to adjust strategies for protection of key habitats while encouraging further recovery of this species.