The kit fox (Vulpes macrotis) is a species of conservation concern in western North America. Recent methods for monitoring populations of kit fox include using lures and remote cameras in an occupancy-modeling framework and habitat modeling to predict areas of occupancy. In chapter one, we tested the optimal lure and movement procedure for scent stations to maximize visits and detection of foxes, thereby improving estimates of occupancy. Between May 2015 and October 2016, we placed remote cameras at 522 random locations throughout nine study areas in the Colorado Plateau, Great Basin Desert, and Mojave Desert. Each location was randomly assigned one of three methods (Scented Predator Survey Disks, cotton swabs, or hollowed golf ball) to broadcast one of three lure types (Red and Gray Fox liquid lure, Willey liquid lure, and fatty acid lure). After seven nights, half of all stations were moved 100 meters within the same sample grid cell, while the others remained in the same location. Stations were then monitored for an additional week. We used Program MARK and AIC model selection to identify optimal lure types and broadcast methods and to estimate rates of occupancy. Detection of kit foxes differed by method of scent deployment; cotton swabs were associated with the highest rates of visitation. Detection of kit foxes did not differ by lure type. Relocating the scent station after one week did not influence detection probability. We suggest that the use of cotton swabs maximizes detection, and therefore, the precision of estimates of occupancy. For chapter two, we used resource selection functions to identify variables that best discriminated between locations where kit fox were detected and random locations. We then produced a habitat map that predicted the relative probability of kit foxes occurring across seven study areas throughout the state of Utah. We placed remote cameras at 458 randomly selected locations throughout the study areas in the Colorado Plateau, Great Basin Desert, and Mojave Desert. We detected kit foxes at 157 "use" points from these cameras between May 2015 and October 2016. We then compared the attributes of these "use" points to 14,742 available, randomly selected points located within the study areas using variables derived from a Geographic Information System (GIS). We used model selection and minimization of AIC values to determine key habitat characteristics that differentiated use and random locations. We identified slope, elevation, and soil type as significant variables (P < 0.05) in habitat selection of kit foxes. Kit foxes selected areas that were 1) less steep, 2) lower in elevation, and 3) classified as having silty soils. The identification of these specific variables from our modeling effort was generally consistent with kit fox ecology. Our study produced a habitat model that can serve as a foundation for future monitoring efforts of kit foxes in potential habitat across Utah.

Climate change threatens to disrupt biological systems around the globe, sparking debate over natural capacity for adaptation in a fragmented landscape. Marine turtles are evolutionarily ancient and have survived millions of years of prehistoric climate change, but are threatened by the rapidity of modern warming and a history of severe overexploitation that has left most populations depleted. This thesis explores a nesting aggregation of the green turtle (Chelonia mydas) in northern Cyprus, where a longitudinal programme of both intensive and extensive monitoring enables insight into individual and population level parameters and processes. Nesting on the two coastlines covered by this project is in the early stages of recovery, possibly in response to exhaustive nest protection efforts over the last twenty years. Saturation tagging at one key site allows us to confirm that recruitment of new breeders is an important driver of this trend, and that average clutch frequency has remained stable around three nests per female per year, validating nest-count derived abundance estimates at a regional scale. Concern has been raised, however, regarding recent changes in fishing practices which are impacting the local juvenile neritic phase, which may have a lagged effect on the recovery of this nesting population. A collaborative tracking effort including all other countries with major nesting in the Mediterranean allows us to identify major foraging grounds for this species, with two hotspots accounting for >50% of tracked individuals, as well as coastal and pelagic seasonal corridors of high use. Bycatch levels and mortality rates for turtles in these key areas are largely unknown and should be prioritised for investigation. Hatchling sex ratios from the main study beach are extremely female-biased (estimated 97% female for the twenty year period 1993-2012). A 1oC rise in average incubation temperatures threatens near complete hatchling feminisation on this beach, whilst a 2oC rise could reduce hatch success to less than 50%. Thermal effects on hatchling morphometrics are evident, with a 1oC rise in temperature reducing average length, width and weight by 1%, 2% and 3% respectively. More favourable incubation conditions were found early in the season, in deeper nests laid by larger females, and on beaches of lighter sand. In contrast, adult sex ratios at the main site are male-biased, posing questions regarding sex-specific survival rates and optimal hatchling sex ratios. A phenological shift towards earlier nesting is demonstrated for the first time in this species, and could potentially ameliorate warming effects. Carry-over climate forcing effects from the foraging ground influence the breeding frequency of individuals, driving population level responses in annual magnitude of nesting. This work emphasises the utility and necessity of long-term individual-based monitoring programmes in elucidating population trends and climate responses in iteroparous species with non-annual breeding.

Dans le contexte général de l’érosion de la biodiversité, deux espèces d’oiseaux forestiers, le Grand Tétras (Tetrao urogallus) et la Gélinotte des bois (Bonasa bonasia), présentes dans le massif Jurassien sont menacées par la perte et la fragmentation de leur habitat à l’échelle régionale. En particulier, dans le massif Jurassien l’extension progressive des tâches de régénération du hêtre induit la transformation du couvert végétal constitué de myrtilles et d’herbacées favorable en un habitat fermé défavorable. Le destin de ces deux espèces emblématiques dépend pour la première d’actions de gestions et pour la seconde d’une meilleure connaissance de la distribution et de la dynamique des populations. La coupe des zones de régénération fait partie des principales actions envisagées pour restaurer l’habitat forestier. Cependant ces actions de gestion ou de suivi des populations sont couteuses en temps et en argent. Ainsi, l’opportunité d’utiliser deux jeux de données LiDAR (Light Detection and Ranging) couvrant la majorité de l’aire de distribution des deux espèces dans le massif Jurassien a initié le projet de cartographie des habitats de chaque espèce et de la présence des tâches de régénération du hêtre en utilisant des modèles de distribution d’espèces (SDMs). L’objectif est de soutenir les gestionnaires dans leurs décisions et actions grâce à la production de prédictions spatiales adaptées. La réalisation de cet objectif dépend de la fiabilité des modèles produits, mais aussi de la bonne transmission des résultats par le chercheur aux gestionnaires qui ne sont pas familiers avec les méthodes utilisées. Dans un premier temps, le choix d’une méthode de modélisation appropriée (correction du biais d’échantillonnage, échelles, algorithmes) par rapport aux caractéristiques des jeux de données et aux objectifs a été évalué. Dans un second temps, l’utilisation de variables environnementales LiDAR orienté-objet (arbres et trouées) pour faciliter l’appropriation des résultats par les gestionnaires a été testée. Enfin, les résultats obtenus ont permis la création de modèles multi-échelles et de carte de prédictions pour chacune des espèces démontrant la capacité du LIDAR de représenter la structure de la végétation qui influence la présence des espèces d’oiseaux forestières étudiées. Des modèles de distribution de la régénération du hêtre ont pu aussi être créés à une échelle fine. / In the general context of biodiversity erosion, two forest bird species occurring in the French Jura massif, the Capercaillie (Tetrao urogallus) and the Hazel Grouse (Bonasa bonasia), are threatened by habitat loss and fragmentation at the regional scale. In particular, intensive beech regeneration patches extension in the Jura massif is leading to the transformation of the understory cover, once suitable with bilberry and herbaceous vegetation, to closed unfavorable habitat. The fate of those two emblematic species is depending for the first on future management actions and for the second on a better knowledge of the species population’s dynamics and occurrences. In particular, the cutting of the beech regeneration patches is one of the efficient management actions undertaken to restore the habitat. However, management actions and surveys are money and time consuming due to the large area that need to be covered. The opportunity to use two Light Detection and Ranging (LiDAR) datasets covering a major part of the distribution of the two species in the Jura massif initiated the phD project, with the objective to support managers in their decisions and actions by the creation of adapted distribution predicted maps using Species Distribution Models (SDMs) (Hazel Grouse, Capercaillie and beech regeneration). The realization of this objective is depending on the reliability of the models produced and on the capacity of the researcher to transfer the results to managers who are not familiar with modeling methods. In a first step, the choice of the appropriate modeling method regarding the datasets characteristics and the objectives was investigated (sampling bias correction, scales, and algorithms). In addition, the use of object-oriented LiDAR predictors (trees and gaps) pertinent from both species and managers point of view to facilitate the results transfer was tested. The results obtained were used to create appropriate multi-scale SDMs and to predict distribution maps for both target species, demonstrating the capacity of LiDAR to represent vegetation structures that influence the targeted forest bird species occurrences. Models at a fine scale were also created to map the beech regeneration distribution in the Jura massif.

La biodiversité est actuellement fortement menacée par les activités humaines. Dépendant des milieux marins et terrestres, les oiseaux marins sont particulièrement exposés aux pressions anthropiques. À La Réunion, les conséquences des impacts des aménagements sur les populations restent méconnues. Dans une optique de conservation et de réalisation d'études environnementales pertinentes, des informations fiables sur la répartition des espèces, sur leur comportement de vol et une évaluation de leur vulnérabilité vis-à-vis des aménagements sont nécessaires. Les objectifs de cette thèse sont de préciser des données biologiques et d'évaluer la vulnérabilité des oiseaux marins nocturnes de La Réunion face aux aménagements. Nous avons étudié l'évolution de la taille et de la répartition des colonies de puffin tropical Puffinus bailloni à l'échelle de l'île sur une période de 19 ans. Les patterns de vol du puffin tropical et du pétrel de Barau Pterodroma baraui ont été caractérisés par imagerie radar à différentes échelles temporelles et spatiales. Nos résultats montrent une stabilité apparente de la population de puffin tropical malgré la forte pollution lumineuse. Le puffin tropical et le pétrel de Barau présentent des patterns de vol spécifiques. Les effectifs estimés de pétrel de Barau suggèrent une population plus importante que celle connue actuellement. Les effectifs estimés de puffin tropical sont cohérents avec les estimations actuelles. Les jeunes pétrels de Barau s'envolent principalement durant les premières heures de la nuit. Des outils d'aide à la décision ont été produits. Nos travaux soulèvent la nécessité de poursuivre des recherches fondamentales et appliquées. / The biodiversity is currently threatened by human activities. As they depend both of marine and terrestrial habitats, seabirds are particularly exposed to human pressures. In Reunion Island, the consequences of the urbanization on populations are unknown. For conservation and environmental assessment purposes, accurate information on the species repartition, flight patterns and vulnerability to infrastructure is required. The goals of this thesis are to update biological information on species and to assess the vulnerability of nocturnal seabirds of Reunion Island exposed to infrastructure. We studied the evolution of the size and the repartition of the colonies of tropical shearwater Puffinus bailloni at the scale of the entire island over a 19-years period. The flight patterns of tropical shearwater and Barau's petrel Pterodroma baraui were described with radar technology at different spatial and temporal scales. Our results show an apparent stability of the tropical shearwater population despite an important light pollution. Tropical shearwater and Barau’s petrel present specific flight patterns. The estimated census of Barau's petrel suggests a population size higher than current estimation whereas the estimated census of tropical shearwater is reliable to current estimations. Barau's petrels' juveniles mostly take off during the first hours of the night. Decision making tools have been produced. Our study also highlights the need to conduct further fundamental and applied researches.

During the past century the Swedish otter (Lutra lutra) population showed a rapid decline in abundance and genetic diversity. Among the most affected areas was the southern province of Skåne. After prohibiting hunting of otters and banning harmful pollutants like PCB, Swedish populations slowly recovered. To some areas the otter returned late, like Kristianstad in north-eastern Skåne. Here, the River Helge å enters Kristianstad’s Vattenrike, Biosphere Reserve and forms a biodiverse wetland. By 2011, otters had established once more along the river. In recent years, a female otter with cubs have appeared outside Vattenriket visitor’s centre “naturum”, to the joy of inhabitants and visitors. In Kristianstad, otters have become a recurring winter attraction. However, not much is known about this new population. For assessment of abundance and genetic diversity, microsatellite variation was investigated among now-living individuals from eleven sites in the Biosphere reserve, and stored museum samples from ten otters with origins in North-eastern Skåne. Using a non-invasive methodology, investigated DNA was extracted from faeces and muscle tissue from dead individuals. Multiple replicate screening was performed to detect errors in genotyping procedures. Results show the presence of three now-living individuals (two males and one female). Now-living otters and museum specimens from north-eastern Skåne were not closely related. Sampled individuals show Hardy-Weinberg Equilibrium, but their heterozygosity is very low. Results suggest that, even though some individuals may remain undetected, low admixture of new genes may be a cause for concern. For long-term protection and management in Kristianstad’s Vattenrike, Biosphere Reserve, further knowledge is needed about our new and precious otter population. / Den svenska utterstammen (Lutra lutra) genomgick drastiska populationsminskningar under mitten av 1900-talet. Minskningen ledde till en förlust av genetisk diversitet i många områden, och bland de värst drabbade var Skåne. Uttern blev fredad från jakt och ett förbud mot det skadliga miljögiftet PCB infördes, vilket skapade förutsättningar för utterpopulationen i Sverige att långsamt återhämta sig i antal. Men uttern återvände sent till vissa områden, som Kristianstad i Nordöstra Skåne. Genom staden Kristianstad rinner Helge å, som formar vidsträckta, artrika våtmarker i Biosfärområde Kristianstads Vattenrike. Uttern visade inga tecken på återkomst till området förrän 2011. De senaste åren har en utterhona med ungar regelbundet visat sig vid besökscentret ”naturum”, till glädje för stadens invånare och besökare. Uttrarna har blivit en återkommande vinterattraktion i Kristianstad. Men kunskapen om den nya populationen är begränsad. För uppskattning av antal och genetisk diversitet, undersöktes mikrosatellitvariationer hos nu levande individer från elva lokaler i Vattenriket. För jämförelse inkluderades arkiverade prover från Naturhistoriska Riksmuseets ”Miljöprovbank”, från tio döda uttrar med ursprung i Nordöstra Skåne. Med icke-invasiva metoder undersöktes DNA som extraherats från avföring- och muskelvävnad. Multipel replikatanalys gjordes för detektering av eventuella fel i genotypningsproceduren. Resultaten visar förekomsten av tre nu levande individer i Vattenriket (två hanar och en hona). Det är dock troligt att en- eller flera nu levande individer kan ha undkommit identifiering. Individerna var inte nära släkt med museiexemplaren från Nordöstra Skåne. Studerade individer är i Hardy-Weinberg jämvikt, men heterozygositeten är låg. Låg heterozygositet kan bero på en låg genomblandning i populationen, vilket kan vara en anledning till oro och bör undersökas närmre. Det behövs ytterligare kunskap och studier för att långsiktigt skydda och förvalta den nya, värdefulla utterpopulationen i Kristianstads Vattenrike.

The population of northern pike in the Baltic sea has seen a drasticdecrease in numbers in the last couple of decades. The reasons for this are believed to be many, but the majority of them are most likely anthropogenic. Today, many measures are being taken to prevent further decline of pike populations, ranging from nutrient runoff control to habitat restoration. This inevitably gives rise to the problem addressed in this project, namely: how can we best monitor pike populations so that it is possible to accurately assess and verify the effects of these measures over the coming decades? Pike is currently monitored in Sweden by employing expensive and ineffective manual methods of individual marking of pike by a handful of experts. This project provides evidence that such methods could be replaced by a Convolutional Neural Network (CNN), an automatic artificial intelligence system, which can be taught how to identify pike individuals based on their unique patterns. A neural net simulates the functions of neurons in the human brain, which allows it to perform a range of tasks, while a CNN is a neural net specialized for this type of visual recognition task. The results show that the CNN trained in this project can identify pike individuals in the provided data set with upwards of 90% accuracy, with much potential for improvement.

Like many species, Florida's population of Northern Crested Caracaras (Caracara cheriway, hereafter "caracara") is likely declining due to loss of breeding habitat. Consequently, management-oriented restrictions on landscape modification are applied where breeding occurs, but management rarely is extended beyond breeding areas. Focusing management on breeding areas can be effective if all caracaras occupy breeding areas, all breeding areas are detected, and no intermittent breeding occurs. Management may not operate as intended if any of these criteria are unmet. To explore this possibility, I investigated the movement, habitat, survival, and social biology of non-breeding caracaras. I also investigated long-term occupancy of breeding habitat, and factors contributing to detection of breeding. Non-breeding caracaras occupy areas much larger than individual breeding territories, particularly during breeding seasons. Pastures occupied by cattle were the most used habitat, but non-breeding caracaras also occupied habitats atypical of breeding areas. Specifically, citrus groves were occupied extensively, and row crops were used particularly during breeding seasons. Non-breeding caracaras also shared communal roosts, sometimes with hundreds of conspecifics, and roosts were occupied year-round. Survival of non-breeding caracaras was lowest during breeding seasons. Adult non-breeding caracaras persisted in groups for multiple years without establishing breeding territories. This implies that breeding habitat is limited and saturated. Given the proportion of adults in groups, adults also were the first to find carrion more often than expected. Apparently, young caracaras benefit from grouping by following adults. I found caracaras at all sampled breeding areas where nests were originally documented during the 1990s, and found nests at 83% of territories where nests likely existed. I also found that observer experience, visit start time, and weather affected the probability that a nest would be detected. Thus, not all caracaras occupy breeding areas, and not all breeding attempts are likely to be detected. Long-term occupancy of breeding areas should render annual verification of nesting unnecessary as a trigger for maintaining management actions. Rather management should persist even without confirmation of annual breeding. Caracara management also may be optimized through supporting the non-breeding population by maintaining a matrix of cattle pasture and citrus groves, particularly around roosts. / Ph. D.