Tests d'hypothèses en dynamique des populations fragmentées : développement et applications de modèles d'occupation des sites

Les approches classiques de modèles spatiaux pour les processus binaires de distribution d'espèces (i.e. occupation des sites) présentent trois importantes carences. i) Elles ne prennent pas explicitement en compte l'incertitude dans le processus d'échantillonnage. ii) Il y a un manque de modèles spatio-temporels, notamment hiérarchique. iii) La plupart des modèles existants sont de type phénoménologique et ne considèrent pas explicitement les mécanismes écologiques sous-jacents. Cette thèse répond à ces limitations en présentant des modèles spatio-temporels d'occupation des sites pour des processus écologiques dynamiques. Ces modèles sont appliqués à des sujets essentiels en écologie, tels que la sélection de l'habitat, les espèces invasives et les changements climatiques. Comprendre la dynamique d'occupation des sites permet de prédire les changements d'occupation qui accompagneront des modifications de l'habitat et de prendre des décisions adaptées en gestion des populations.Classical approaches to the development of spatial models for binary processes of species distribution (i.e. occupancy processes) present three important deficiencies. i) They do not explicitly accommodate sampling uncertainty. ii) There is a lack of spatio-temporal occupancy models, especially in the framework of hierarchical modeling. iii) Most of existing models are phenomenological and do not explicitly consider underlying ecological mechanisms. This thesis develops spatio-temporal occupancy models for dynamical ecological processes in order to respond to these limitations while incorporating scientific knowledge in every modeling step. Those models are applied to critical ecological topics ranging from the spread of invasive species to habitat selection via climate changes. Understanding range and occupancy dynamics will permit prediction of occupancy changes that are likely to accompany future changes and hopefully will permit informed attempts to mediate changes in occupancy

An inventory of avian species in Aldesa Valley, Saudi Arabia

Conducting species inventories is important to provide baseline information essential for management and conservation. Aldesa Valley lies in the Tabuk Province of northwest Saudi Arabia and because of the presence of permanent water, is thought to contain high avian richness. We conducted an inventory of avian species in Aldesa Valley, using timed area-searches during May 10–August 10 in 2014 and 2015 to detect species occurrence. We detected 6860 birds belonging to 19 species. We also noted high human use of this area including agriculture and recreational activities. Maintaining species diversity is important in areas receiving anthropogenic pressures, and we encourage additional surveys to further identify species occurrence in Aldesa Valley

Impact of climatic variations on bird species occupancy rate in a southern European forest

International audienceSpecies that are affected by climatic variations can undergo modification in range and/or abundance. Knowing how individuals or species occupy their habitat is essential to understand how species use their environment, and detecting variations that might affect this use can be determinant in species management. Hierarchical modeling is regularly used to assess for occupancy rate (i.e. proportion of patches occupied in a region), particularly when it is required to consider detectability-related issues. The present study is the first application of the conditional model presented in Dupuis et al. (Biometrics 2010), which is applied in the case of a heterogeneous area that might be divided into homogeneous sub-areas. Their approach is used to study the impact of three consecutive particularly cold winters on a selected set of bird species in a forest of southern France in the context of available prior information on birds detectability. We examined a limited range of factors that might influence the response of some bird species to climate. We considered the case of sedentary, partially migrating and migrating species. We also assessed if the biogeographical origins of the different species affect their occupancy rates. Globally, changes in occupancy rates between 1985 and 1987 indicates for the first time a continentalization of the regional forest fauna, reflected by the expansion of Palearctic and Turkestano-European faunistic type species, with depletion or extinction of European, Turkestano-Mediterranean and Mediterranean sedentary species. We have also shown the importance of prior information

Tests of hypotheses in fragmented population dynamics (development and applications of site occupancy models)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Estimating the occupancy rate of spatially rare or hard to detect species: a conditional approach

International audienceWe consider the problem of estimating the occupancy rate of a target species in a region divided in spatial units (called quadrats); this quantity being defined as the proportion of quadrats occupied by this species. We mainly focus on spatially rare or hard to detect species that are typically detected in very few quadrats, and for which estimating the occupancy rate (with an acceptable precision) is problematic. We develop a conditional approach for estimating the quantity of interest; we condition on the presence of the target species in the region of study. We show that conditioning makes identifiable the occurrence and detectability parameters, regardless of the number of visits made in the sampled quadrats. Compared with an unconditional approach, it proves to be complementary, in that this allows us to deal with biological questions that cannot be addressed by the former. Two Bayesian analyses of the data are performed: one is noninformative, and the other takes advantage of the fact that some prior information on detectability is available. It emerges that taking such a prior into account significantly improves the precision of the estimate when the target species has been detected in few quadrats and is known to be easily detectable

Marten and fisher detection data in the Upper Peninsula of Michigan

This file gives covariates, effort, marten detection data, fisher detection data and temporal data collected from the Upper Peninsula of Michigan during 2013-2015. See README file for full description