Mettre en place des mesures de protection efficaces contre la dégradation et la fragmentation de l'habitat d'une espèce nécessite d'être capable de comprendre l'impact de l'environnement sur sa dynamique de population ainsi que sa sensibilité à la perte de connectivité entre les populations. Obtenir ces informations est déjà un défi en soi, qui se complique encore pour les espèces trop sensibles au dérangement pour être suivies de manière classique. Lors de ce travail, nous avons étudié la dynamique et la génétique des populations d'une chauve-souris forestière qui a subi un très fort déclin dans le nord de l'Europe, le Petit rhinolophe (Rhinolophus hipposideros), à l'aide de méthodes non-invasives (comptages, génétique non-invasive).Nos résultats ont montré que le climat et le paysage autour des colonies de maternités influence la taille et la dynamique des populations du Petit rhinolophe. Nous avons également confirmé un impact direct du paysage sur la survie des juvéniles. Enfin, nous avons observé que la diversité génétique des populations pouvait être fortement diminuée par leurs histoires démographiques et par un manque de connectivité entre les populations. Ces résultats ont des implications directes pour la conservation du Petit rhinolophe mais aussi pour le développement des analyses intégrant des données de génétique non-invasive pour la biologie de la conservation. / Efficient conservation management against habitat degradation and fragmentation of a species requires understanding how the environment impacts its population dynamics and the species’ sensitivity to connectivity loss. Acquiring sufficient knowledge about these processes is challenging for any species, and is even more complicated for species too sensitive to be studied with classical methods. During this work, we studied the population dynamics and genetics of a woodland specialized bat who has undergone a serious decline in the north of Europe, the lesser horseshoe bat (Rhinolophus hipposideros), with non-invasive methods (counts, non-invasive genetics).Our results shown that climate and landscape around maternity colonies explain population size variations and dynamics of the lesser horseshoe bat. We also confirmed a direct impact of landscape on juvenile survival. We finally observed that genetic diversity could be strongly decreased by population history and a lack of connectivity between populations. Our results have direct implications for the lesser horseshoe bat conservation but also for the development of analyses integrating non-invasive genetic data in conservation biology.

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