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Large carnivores are among the most challenging species to conserve in our modern and crowded world. Having large spatial requirements and living in low density, they generally require wide and relatively undisturbed areas. In Europe, one of the most anthropized areas of the planet, these needs must be fulfilled in a complex human-dominated landscape. The reintroduced brown bear population living in the Central Alps represents one of the most emblematic examples of a constrained carnivore: despite a steady population increase in the first few years after reintroduction, the population did not substantially expand its range, nor has the Alpine-Dinaric metapopulation been reestablished as envisioned. Although humans have lived in the Alps for centuries, little is known about their impact on the bear population. In other environments humans are known to function as a “super-predator” by changing habitats, competing for space, consuming resources, and harvesting, which alters the ecological niche of animals, especially large carnivores. This dissertation aims to evaluate this phenomenon by assessing the effects of human disturbance on brown bears in the Alps. Anthropogenic disturbance is generally assessed by structural proxies, such as infrastructure and land use, which overlook the impact of human presence. In the first Chapter, we developed the Cumulative Outdoor activity Index (COI) to derive anthropogenic disturbance using crowdsourced data by Strava and validated it with ground truth observations derived from a local camera trapping survey. The intensity of COI provided an effective measure of functional anthropogenic disturbance, and it outperformed all commonly-used proxies of structural disturbance in predicting bear habitat use. When displacement is not an option because of habitat limitations and social mechanisms, bear mobility may clash with human activity. During the moments of lowest mobility, such as resting periods, animals have decreased ability to cope with risky situations, and therefore the selection of suitable resting areas is crucial for the long-term survival of individuals. In the second Chapter, we measured multi-scale response to risk perception (i.e., COI) and resource proximity using bedding sites by GPS radio-collared adult brown bears in the Alps. To map resources across the study area, we developed a GIS-database combining spatial and non-spatial ecological information to map fruit availability. We observed that bears apply a security-food trade-off strategy, avoiding functional anthropogenic disturbance while in proximity to resources. In the third Chapter, we explicitly tested the effect of an abrupt interruption of human mobility during COVID-19 lockdown on bears’ use of ecological corridors. Using bear occurrences reported to local authorities during the recent COVID-19 outbreak, we observed that bears used human-dominated areas more frequently, approached more intensively hot spots for road crossing network, and used areas further from the population core areas more often than previous years, suggesting that connectivity increased with reduced human mobility. In a comparatively human-free system, for the fourth Chapter we used longitudinal morphometric data to analyze drivers of changes in body mass as part of an international collaboration with biologists studying the grizzly bear in the Greater Yellowstone Ecosystem. Specifically, we analyzed changes in lean body mass and fat percentage during years of major ecosystem perturbations. We observed that individual lean body mass during the last two decades was primarily associated with population density, but not body fat percentage, showing density-dependent factors. Our combined findings (Chapters 1-3) showed that brown bears have to adapt their space use, movement, and resource proximity as a result of functional anthropogenic disturbance. In Chapter 4 we explored one effect of unconstrained bear space use on individuals, as manifested through density-dependent effects on body size. In the Alps, however, we found multiple instances of the human-super predator outcompeting bears so as to make density-dependent effects likely less significant as compared to human-caused mortality. These effects could occur in a variety of socio-ecological contexts across Europe, jeopardizing the long-term establishment of both newly reintroduced bear populations, as well as spatially limiting those naturally present in the environment. In response to disturbance, bears have had to reduce their ecological niche in human-dominated landscapes. Allowing humans and bears to coexist in the same landscape is a challenging task, but it is essential for the long-term survival of this newly reintroduced population that are otherwise at risk of extinction.

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<p>  </p> <p>Bats serve important ecological and economic roles in their communities. However, due to anthropogenic land use and human-introduced disease, bat populations in North America are facing unprecedented declines. To better inform conservation efforts for bat species in northeastern Indiana, I studied two aspects of bat ecology: (1) the effects of urbanization and agriculture on bat community composition in northeastern Indiana and (2) the roosting behavior of a population of state endangered/federally threatened northern long-eared bats (<em>Myotis septentrionalis</em>; hereafter northern myotis) in a restored mesic forest adjacent to a moderately sized city (Fort Wayne, IN). To study the first aspect, I deployed acoustic detectors in green spaces throughout Fort Wayne and the surrounding rural areas of Allen County. For each detector site, I compared species occupancy rates with site-specific characteristics at the plot scale (e.g., % canopy cover, midstory density) and at multiple landscape scales (e.g., % impervious cover within 1 km). Across 429 survey nights, acoustic detectors recorded calls from eight unique bat species, of which six species were abundant enough to conduct occupancy modeling. In four of the six species, measures of the amount of forest and forest edge in the landscape were included in one or more of the top models. The top models for the two other bat species, tricolored bats (<em>Perimyotis subflavus</em>) and silver-haired bats (<em>Lasionycteris noctivagans</em>), included measures of urban land cover and revealed a negative relationship between probability of occupancy and the proportion of high-density urban land in the area. The effect of habitat scale also differed between species. For example, models in the confidence set for eastern red bats (<em>Lasiurus borealis</em>) included variables associated with the plots surrounding detectors and with landscape features within 100 m of detectors. In contrast, the top models for hoary bats (<em>Lasiurus cinereus</em>) included landscape features at larger scales, within 500m and 1 km of detector sites. These findings suggest that both generalist and forest-obligate bat species in this study area selected spaces with greater levels of forested habitat. Furthermore, heavily urbanized areas were less likely to support the same levels of bat diversity as areas with forests and other green space.</p> <p>To accomplish the second aspect of my project, I captured bats in Fox Island County Park (Fort Wayne, IN) using mist-nets and affixed temperature-sensitive radio transmitters to four northern myotis individuals. I tracked these individuals back to day roosts, where I recorded roost characteristics (e.g., tree height, # of roost trees within 0.1 ha) and monitored bat skin temperatures (Tsk). I compared the characteristics of selected roosts to those of randomly assigned available trees in the same landscape to determine trends in roost selection preferences. Northern myotis in this study strongly preferred standing dead trees within a 31-ha patch of flooded forest on the northern border of Fox Island. These trees were highly exposed to solar radiation and were consistently warmer than ambient weather conditions, which suggests they may provide important thermoregulatory benefits to reproductive females and other members of the population.</p> <p>My research offers valuable information regarding resource use by bat communities in a landscape dominated by anthropogenic development. Urban areas containing large stretches of forests with trees in various stages of decay will be more likely to meet the needs of bats that would otherwise struggle in developed landscapes. The results of this study can be used to inform conservation efforts aimed at protecting populations of bats throughout Indiana and the Midwestern United States.</p>

Management and conservation of populations of animals requires information on where they are, why they are there, and where else they could be. These objectives are typically approached by collecting data on the animals’ use of space, relating these to prevailing environmental conditions and employing these relations to predict usage at other geographical regions. Technical advances in wildlife telemetry have accomplished manifold increases in the amount and quality of available data, creating the need for a statistical framework that can use them to make population-level inferences for habitat preference and space-use. This has been slow-in-coming because wildlife telemetry data are, by definition, spatio-temporally autocorrelated, unbalanced, presence-only observations of behaviorally complex animals, responding to a multitude of cross-correlated environmental variables. I review the evolution of techniques for the analysis of space-use and habitat preference, from simple hypothesis tests to modern modeling techniques and outline the essential features of a framework that emerges naturally from these foundations. Within this framework, I discuss eight challenges, inherent in the spatial analysis of telemetry data and, for each, I propose solutions that can work in tandem. Specifically, I propose a logistic, mixed-effects approach that uses generalized additive transformations of the environmental covariates and is fitted to a response data-set comprising the telemetry and simulated observations, under a case-control design. I apply this framework to non-trivial case-studies using data from satellite-tagged grey seals (Halichoerus grypus) foraging off the east and west coast of Scotland, and northern gannets (Morus Bassanus) from Bass Rock. I find that sea bottom depth and sediment type explain little of the variation in gannet usage, but grey seals from different regions strongly prefer coarse sediment types, the ideal burrowing habitat of sandeels, their preferred prey. The results also suggest that prey aggregation within the water column might be as important as horizontal heterogeneity. More importantly, I conclude that, despite the complex behavior of the study species, flexible empirical models can capture the environmental relationships that shape population distributions.

Thesis (MTech (Nature Conservation))--Cape Peninsula University of Technology, 2015. / The klipspringer (Oreotragus oreotragus subsp. oreotragus) population became extinct on the Cape Peninsula in 1930. Being re-introduced into Table Mountain National Park (TMNP) in 1999 it became one of the species of special conservation concern to monitor in the Park. Most klipspringer territories are known by Park management but the distribution of all potentially suitable habitats for this species in the Park is not known. The main aim of this study is to produce a distribution range map that is representative of all potentially suitable habitats for the klipspringer within TMNP, through the use of a species distribution modelling tool. Since only presence data were available for this study, a popular presence-only modelling tool namely maximum entropy (MaxEnt) was used. The use of MaxEnt in species distribution modelling has become popular as it has proven to provide robust predictions of a species’ geographic distribution. Klipspringer occurrence data and five environmental variables namely altitude, slope, aspect, vegetation, and distance to urban edge were used as model input. Occurrence data were sourced through existing databases and employing a stratified random sampling technique of dividing the Park into different habitat subtypes to survey the Park for more klipspringer occurrences. These habitat subtypes consisted of a variety of vegetation communities or vegetation types and altitudinal and slope ranges available in the Park. Grid size for all the raster layers used was 10x10 m. Spatial filtering of one point per 100 m² grid was used to eliminate clumping of points. Six models were run at different regularisation multiplier (RM) values namely 0.25, 0.5, default (1), 2, 4 and 7. To assist in better understanding of the spatial extent of the occurrence data and the areas inhabited by the klipspringer, home range analyses were carried out. This was done through kernel density estimation in the Geospatial Modelling Environment (GME). All six bandwidth parameters in GME namely smoothed cross validation (SCV), biased cross-validation (BCV), a second BCV algorithm, plug-in estimator, least squares cross validation and the likelihood cross validation (CVh) were tested. The smoothed cross validation and likelihood cross validation bandwidth algorithms provided the best visual output of klipspringer home ranges and territories. Home range sizes from the SCV output ranged from about 3 – 11 ha across the study area, and home range size for the CVh output ranged from 0.6 – 2.5 ha. The output from the CVh algorithm was interpreted as territories rather than home ranges, as it is based on a univariate kernel unlike, the SCV algorithm that produces rotated bivariate kernels. iv The default regularisation multiplier of 1 provided the best probability distribution output, whilst values lower than the default tended to underestimate the prediction and those values higher than the default were tending towards overestimations. Response curves for the default RM also gave the most ecologically meaningful responses of the klipspringer to each environmental variable. Model evaluation in the form of area under the receiver operating characteristic curve (ROC AUC) showed that all models performed well. Therefore, the choice of the “best” model was based on the ability to provide ecological interpretation, on the shape of the response curve and the probability distribution maps. Consequently, the default RM model was considered the best, with an AUC score of 0.903. Altitude and vegetation contributed the most to suitable habitat and therefore indicates that klipspringer in the Park do prefer high altitudinal areas with the right vegetation to feed on. Suitable altitudinal ranges are from 400 m.a.s.l. and higher and ericaceous fynbos is the most preferred vegetation community. Slope, aspect and distance to urban edge played a less important role in suitable klipspringer habitat. The probability map and an additional binary map produced at the 10 percentile training logistic presence threshold showed that suitable habitat for the klipspringer occurs in all three sections of the Park in different proportions. These maps can be used by Park management to prioritise conservation efforts and future re-introductions. / National Research Foundation

Les Sicydiinae amphidromes constituent une part importante des peuplements piscicoles insulaires de la région Indo-Pacifique et sont vulnérables à de nombreuses pressions anthropiques (i.e. pêcherie, dégradation et fragmentation des habitats). La reproduction a lieu en eau douce, puis les jeunes dévalent en mer où ils débutent leur croissance pendant quelques mois avant de coloniser les rivières. L’objectif est d’acquérir des connaissances sur les traits de vie de S. lagocephalus (cosmopolite) et de C. acutipinnis (endémique). Les travaux de terrain démontrent que le choix de l’habitat quotidien est fortement lié aux interactions sociales, alors que l’habitat de fraie montre une forte sélection pour des conditions morphodynamiques favorisant l’oxygénation des oeufs. Les mâles sélectionnent des sites de ponte et gardent les oeufs. L’étude expérimentale de la survie en eau douce confirme que tous les embryons libres possèdent la capacité à rejoindre la mer. L’analyse des traits de vie marins à partir des otolithes des post-larves révèle des variations saisonnières d’âge et de taille au recrutement, en lien avec la croissance et la température marine. L’examen histologique des ovaires permet de décrire les variations spatiales et temporelles de l’activité de reproduction chez les femelles en rivière et de déterminer la fécondité et la taille de première reproduction. Les variations inter et intra-spécifiques des traits de vie sontcomparées en lien avec la répartition géographique des deux espèces. Ces travaux permettent d’identifier des perspectives concrètes dans le domaine de la gestion et de la conservation sur la base des caractéristiques de la stratégie amphidrome. / Amphidromous Sicydiinae are particularly widespread among fish freshwater assemblages of the Indo-Pacific region and are vulnerable to anthropogenic pressures (i.e. fishery, degradation and fragmentation of habitats). Spawning and hatching happen in freshwater, then offspring drift downstream to the sea where they begin their growth for a few months before recruiting in the rivers. This study aims at acquire knowledge about life traits of S. lagocephalus (cosmopolite) and C. acutipinnis (endemic). Field sampling shows that the usual habitat choice is related to social interactions, whereasspawning habitat shows a strong selection for morphodynamic conditions which favor eggs oxygenation. Males select spawning sites and care for the eggs. The experimental study of freshwater survival confirms that free embryos survival and swimming capacities are enough to drift to the ocean. Marine life history analysis, based on postlarvae otoliths examination, reveals a seasonal variation of both age and size-atrecruitment related to the larval growth rate and the sea temperature. Histological examination of ovaries is used to describe the spatial and temporal variation of reproductive activity of mature females in the rivers, and to determine fecundity and size at first reproduction. Inter and intra-specific variations of life history traits are compared in relation to the respective geographical distribution of both species. This study identifies concrete prospects for management and conservation based on the features of amphidromous life history strategy.

Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina), have overlapping ranges but contrasting population dynamics around the UK; whilst grey seals have generally increased, harbour seals have shown significant regional declines. A robust analytical methodology was developed to produce maps of grey and harbour seal usage estimates with corresponding uncertainty, and scales of spatial partitioning between the species were found. Throughout their range, both grey and harbour seals spend the majority of their time within 50 km of the coast. The scalability of the analytical approach was enhanced and environmental information to enable spatial predictions was included. The resultant maps have been applied to inform consent and licensing of marine renewable developments of wind farms and tidal turbines. For harbour seals around Orkney, northern Scotland, distance from haul out, proportion of sand in seabed sediment, and annual mean power were important predictors of space-use. Utilising seal usage maps, a framework was produced to allow shipping noise, an important marine anthropogenic stressor, to be explicitly incorporated into spatial planning. Potentially sensitive areas were identified through quantifying risk of exposure of shipping traffic to marine species. Individual noise exposure was predicted with associated uncertainty in an area with varying rates of co-occurrence. Across the UK, spatial overlap was highest within 50 km of the coast, close to seal haul outs. Areas identified with high risk of exposure included 11 Special Areas of Conservation (from a possible 25). Risk to harbour seal populations was highest, affecting half of all SACs associated with the species. For 20 of 28 animals in the acoustic exposure study, 95% CI for M-weighted cumulative Sound Exposure Levels had upper bounds above levels known to induce Temporary Threshold Shift. Predictions of broadband received sound pressure levels were underestimated on average by 0.7 dB re 1μPa (± 3.3). An analytical methodology was derived to allow ecological maps to be quantitatively compared. The Structural Similarity (SSIM) index was enhanced to incorporate uncertainty from underlying spatial models, and a software algorithm was developed to correct for internal edge effects so that loss of spatial information from the map comparison was limited. The application of the approach was demonstrated using a case study of sperm whales (Physeter macrocephalus, Linneaus 1758) in the Mediterranean Sea to identify areas where local-scale differences in space-use between groups and singleton whales occurred. SSIM is applicable to a broad range of spatial ecological data, providing a novel tool for map comparison.

In the late 1980s the endangered Chatham Island oystercatcher (Haematopus chathamensis) (CIO) was estimated at less than 110 individuals. Endemic to the Chatham Islands, New Zealand, it was feared to be declining and, based on existing productivity estimates, in danger of extinction within 50-70 years. These declines were thought to be caused by numerous changes since the arrival of humans, including the introduction of several terrestrial predators, the establishment of marram grass (Ammophila arenaria) which changes dune profiles, and increased disturbance along the coastline. The New Zealand Department of Conservation has undertaken recovery planning and conservation management to increase CIO numbers since the late 1980s. Recovery planning raised some key research questions concerning the population dynamics, habitat selection, and breeding biology of Chatham Island oystercatcher (CIO), and the critical factors currently limiting the population. The objectives of this study were to collect and interpret data on: 1) population size, trends, and distribution across the Chathams, 2) basic breeding parameters, 3) recruitment and mortality rates, 4) habitat selection at the general, territorial and nest-site levels, 5) habitat factors that are correlated with territory quality, and 6) cues that elicit territorial behaviour in CIO.