The affect on leaf area index (LAI) and net ecosystem production (NEP) of the mountain pine beetle (Dendroctonus ponderosae) (MPB) outbreak in British Columbia affecting lodgepole pine (Pinus contorta var. latifolia) forests was examined from 1999 to 2008. The process-based carbon (C) cycle model – Boreal Ecosystem Productivity Simulator (BEPS) with remotely sensed LAI inputs was used to produce annual NEP maps, which were validated using field measurements. The annual NEP ranged from 2.43 to -8.03 MtC between 1999 and 2008, with sink to source conversion in 2000. The inter-annual variability for both LAI and NEP displayed initial decreases followed by a steadily increasing trend from 2006 to 2008 with NEP returning to near C neutrality in 2008 (-1.84 MtC). The resistance of LAI and NEP to MPB attack was attributed to ecosystem resilience in the form of secondary overstory growth and increased production of non-attacked host trees.

Le déclin de la biodiversité lié à l'augmentation des pressions sur les ressources naturelles, fait l'objet d'un large consensus. Cette situation souligne un besoin urgent de développer des outils de diagnostic et de suivi de l'état de la biodiversité qui soient spatialisés, rapides à mettre en œuvre, peu coûteux et qui permettent de réaliser des expertises à l'échelle des territoires. Une des hypothèses centrales en écologie est qu'il existe des relations positives entre l'hétérogénéité spatiale mesurée dans la mosaïque paysagère et la richesse en espèces qui peut y cohabiter à différentes échelles. Dans ce travail, nous nous appuyons sur cette hypothèse pour développer un Indice de Biodiversité Spécifique Potentielle afin de réaliser un diagnostic de l'état de la biodiversité dans la mosaïque paysagère intra-forestière à différentes échelles, en prenant l'exemple du massif du Vercors. Cet indice s'appuie sur des indicateurs et des critères capables de refléter le niveau de biodiversité potentiellement présente dans une zone géographique donnée, et permet d'approfondir les connaissances sur les relations entre la structure des peuplements, les caractéristiques de la mosaïque forestière et la richesse ou la répartition géographique des espèces. Les étapes clés de la méthodologie et de son évaluation sont valorisées sous forme d'articles. La représentation spatiale de la biodiversité potentielle à différentes échelles permet d'envisager de nombreuses applications dans les domaines de la conservation et de la gestion forestière multifonctionnelle. / There is a general consensus that as pressures on natural resources increase, biodiversity is being lost, and the rate of loss is not sustainable. Within the present situation is become a critical need to develop methods and tools for biodiversity monitoring and conservation. In particular, we need spatially-explicit tools and rapid assessment methods that are relatively easy to implement at different scales and at a relatively low cost. One of the basic assumptions in ecology is that there are positive relationships at different spatial scales between landscape heterogeneity and species richness in a given landscape mosaic. In this thesis, we focus on this assumption in order to build a Potential Species Biodiversity Index. Our aim was to assess potential biodiversity within a forest landscape mosaic, considering the Vercors' mountain range as a case study. The index encompasses indirect biodiversity indicators and criteria as a surrogate to biodiversity potential present for a given area. This approach allows a better understanding of the relationships between forests stand structure, forest landscape characteristics and species richness or geographical distribution. The main steps of the method and its evaluation are presented in scientific papers. The analysis of geographical distribution of the index at different spatial scales provides practical applications for conservation planning and multifunctional forest management related fields.

Over the 21st century, climate change and wetland habitat loss will pose major threats to the Eastern Massasauga (Sistrurus catenatus), a federally threatened and Great Lakes region endemic rattlesnake. I collected capture-recapture data from sites across the range and modeled the effect of climatic variables on growth rate and asymptotic size. I found that high snow residence time was associated with larger asymptotic sizes but slower growth, while high spring precipitation increased growth rate. I then projected future growth and size under different carbon emission scenarios. Given the threat posed by successional encroachment of woody vegetation, I used spatially explicit capture-recapture models to examine the effects of landscape characteristics and phenology on the spatial distribution of density for a population in Michigan. I found highest density in areas close to a stream and with low vegetation intensity, which can inform prescribed burn programs and give additional insights into life history.

No description available.

Tigers (Panthera tigris tigris) can be viewed as a proxy for intact and healthy ecosystems. Their wild populations have plummeted to fewer than 3,200 individuals in the last four decades and threats to these apex predators are mounting rather than diminishing. Global conservation bodies (Global Tiger Initiative, World Wildlife Fund, Wildlife Conservation Society, Panthera etc.) have recently called for solidarity and scaling up of conservation efforts to save tigers from extinction. In South Asia, tiger habitat ranges from tropical evergreen forests, dry arid regions and sub-tropical alluvial floodplains, to temperate mixed deciduous forest. The churia habitat is relatively unstudied and is considered a young and geologically fragile mountain range in Nepal. The contribution of the churia habitat to tiger conservation has not been considered, since modern conservation started in 1970's. This study focuses on the ecology of the tiger with respect to population density, habitat use, and prey occupancy and density, in the churia habitat of Chitwan National Park. This study also includes the first assessment of genetic diversity, genetic structure, and gene flow of tigers across the Terai Arc Landscape- Nepal. The Terai Arc Landscape harbors the only remaining tiger population found across the foothills of the Himalayas in Nepal and northwest India. I used a combination of camera-trapping techniques, which have been a popular and robust method for monitoring tiger populations across the landscape, combined with a noninvasive genetic approach to gain information on tigers, thus adding new information relevant to global tiger conservation. I investigated tiger, leopard (Panthera pardus fusca), and prey densities, and predicted the tiger density across the Churia habitat in Chitwan National Park. I used a camera-trap grid with 161 locations accumulating 2,097 trap-nights in a 60 day survey period during the winter season of 2010-2011. Additionally, I used distance sampling techniques for estimating prey density in the churia habitat by walking 136 km over 81 different line transects. The team photographed 31 individual tigers and 28 individual leopards along with 25 mammalian species from a sampling area of 536 km² comprising Churia and surrounding areas. Density estimates of tigers and leopards were 2.2 (SE 0.42) tigers and 4.0 (SE 1.00) leopards per 100 km². Prey density was estimated at 62.7 prey animals per 100 km² with contributions from forest ungulates to be 47% (sambar Rusa unicolor, chital Axis axis, barking deer Muntiacus muntjak, and wild pigs Sus scrofa). Churia habitat within Chitwan National Park is capable of supporting 5.86 tigers per 100 km² based on applying models developed to predict tiger density from prey density. My density estimates from camera-traps are lower than that predicted based on prey availability, which indicates that the tiger population may be below the carrying capacity. Nonetheless, the churia habitat supports 9 to 36 tigers, increasing estimates of current population size in Chitwan National Park. Based on my finding, the Churia habitat should no longer remain ignored because it has great potential to harbor tigers. Conservation efforts should focus on reducing human disturbance to boost prey populations to potentially support higher predator numbers in Churia. I used sign surveys within a rigorous occupancy framework to estimate probability of occupancy for 5 focal prey species of the tiger (gaur Bos gaurus, sambar, chital, wild pig, and barking deer); as well as probability of tiger habitat use within 537 km² of churia habitat in Chitwan National Park. Multi-season, auto-correlation models allowed me to make seasonal (winter versus summer) inferences regarding changes in occupancy or habitat use based on covariates influencing occupancy and detection. Sambar had the greatest spatial distribution across both seasons, occupying 431-437 km² of the churia habitat, while chital had the lowest distribution, occupying only 100-158 km². The gaur population showed the most seasonal variation from 318- 413 km² of area occupied, with changes in occupancy suggesting their migration out of the lowland areas in the summer and into the churia in the winter. Wild pigs showed the opposite, moving into the churia in the summer (444 km² area occupied) and having lower occupancy in the winter (383 km²). Barking deer were widespread in both seasons (329 - 349 km²). Tiger probability of habitat use Ψ SE(Ψ) was only slightly higher in winter 0.63 (SE 0.11) than in summer 0.54 (SE 0.21), but confidence intervals overlapped and area used was very similar across seasons, from 337 - 291 km². Fine-scale variation in tiger habitat use showed that tigers intensively use certain areas more often than others across the seasons. The proportion of available habitat positively influenced occupancy for the majority of prey species and tigers. Human disturbance had a strong negative influence on the distribution of the majority of prey species but was positively related to tiger habitat use. Tigers appear to live in areas with high disturbance, thus increasing the risk of human-tiger conflict in the churia habitat. Thus, efforts to reduce human disturbance would be beneficial to reducing human wildlife conflict, enriching prey populations, and would potentially support more tigers in churia habitat of Nepal. Overall, I found high prey occupancy and tiger habitat use, suggesting that the churia is highly valuable habitat for tigers and should no longer be neglected or forgotten in tiger conservation planning. Thirdly, I assessed genetic variation, genetic structure, and gene flow of the tigers in the Terai Arc Landscape, Nepal. I opportunistically collected 770 scat samples from 4 protected areas and 5 hypothesized corridors across the Terai Arc Landscape. Historical landuse change in the Terai Arc was extracted from Anthrome data sets to relate landuse change to potential barriers and subsequent hypothesized bottleneck events in the landscape. I used standard genetic metrics (allelic diversity and heterozygosity) to estimate genetic variation in the tiger population. Using program Structure (non-spatial) and TESS (spatial), I defined the putative genetic clusters present in the landscape. Migrant analysis was carried out in Geneclass and Bayesass for estimating contemporary gene flow. I tested for a recent population bottleneck with the heterozygosity test using program Bottleneck. Of the 700 samples, 396 were positive for tiger (57% success). Using an 8 multilocus microsatellite assay, I identified 78 individual tigers. I found large scale landuse changes across the Terai Arc Landscape due to conversion of forest into agriculture in last two centuries and I identified areas of suspected barriers. I found low levels of genetic variation (expected heterozygosity = 0.61) and moderate genetic differentiation (F_ST = 0.14) across the landscape, indicative of sub-population structure and potential isolation of sub-populations. I detected three genetic clusters across the landscape consistent with three demographic tiger sub-populations occurring in Chitwan-Parsa, Bardia, and Suklaphanta protected areas. I detected 10 migrants across all study sites confirming there is still some dispersal mediated gene flow across the landscape. I found evidence of a bottleneck signature, especially around the lowland forests in the Terai, likely caused by large scale landuse change in last two centuries, which could explain the low levels of genetic variation detected at the sub-population level. These findings are highly relevant to tiger conservation indicating that efforts to protect source sites and to improve connectivity are needed to augment gene flow and genetic diversity across the landscape. Finally, I compared the abundance and density of tigers obtained using two non-invasive sampling techniques: camera-trapping and fecal DNA sampling. For cameras: I pooled the 2009 camera-trap data from the core tiger population across the lowland areas of Chitwan National Park. I sampled 359 km² of the core area with 187 camera-trap locations spending 2,821 trap-nights of effort. I obtained 264 identifiable photographs and identified a total of 41 individual tigers. For genetics, I sampled 325 km² of the core area along three spatial routes, walking a total of 1,173 km, collecting a total of 420 tiger fecal samples in 2011. I identified 36 tigers using the assay of 8 multilocus genotypes and captured them 42 times. I analyzed both data types separately for estimating density and jointly in an integrated model using both traditional, and spatial, capture-recapture frameworks. Using Program MARK and the model averaged results, my abundance estimates were 46 (SE 1.86) and 44 (SE 9.83) individuals from camera and genetic data, respectively. Density estimates (tigers per 100 km²) via traditional buffer strip methods using half of the Mean Maximum Distance Moved (½ MMDM) as the buffer surrounding survey grids, were 4.01 (SE 0.64) for camera data and 3.49 (SE 1.04) for genetic data. Spatially explicit capture recapture models resulted in lower density estimates both in the likelihood based program DENSITY at 2.55 (SE 0.59) for camera-trap data and 2.57 (SE 0.88) for genetic data, while the Bayesian based program SPACECAP estimates were 2.44 (SE 0.30) for camera-trap data and 2.23 (SE 0.46) for genetic data. Using a spatially explicit, integrated model that combines data from both cameras and genetics, density estimates were 1.47 (SD 0.20) tigers per 100 km² for camera-trap data and 1.89 (SD 0.36) tigers per 100 km² for genetic data. I found that the addition of camera-trap data improved precision in genetic capture-recapture estimates, but not visa-versa, likely due to low numbers of recaptures in the genetic data. While a non-invasive genetic approach can be used as a stand-alone capture-recapture method, it may be necessary to increase sample size to obtain more recaptures. Camera-trap data may provide a more precise estimates, but genetic data returns more information on other aspect of genetic health and connectivity. Combining data sets in an integrated modeling framework, aiding in pinpointing strengths and weaknesses in data sets, thus ultimately improving modeling inference. / Ph. D.

Carnivore are undoubtedly among the most threatened of the mammal species in Africa because of the low density at which they occur and their large home range requirements that do not match with human propensity to develop and alter wildlife habitat. However, the degree of threat is unevenly distributed within the continent, with western and central African carnivores being the most threatened and the least studied. I estimated population size, density, and proportion of area occupied in relation to environmental factors of one medium-size (serval – Leptailurus serval) and two large carnivores (lion – Panthera leo and leopard – P. pardus) in the Niokolo Koba National Park, Senegal, West Africa, using remote camera surveys and both traditional (CR), spatially explicit capture-recapture (SECR) techniques for servals and leopards, and non-spatial (MR) and spatial mark resight (SMR) methods for lions. Lions selected optimal sites with both high tree density and prey activity; leopards occupied areas with high tree density but with less prey activity; and servals selected habitats with more dense canopy cover where leopards were absent. The presence of lions was favorable to serval presence, as we presume leopards avoid lions, although we did not have strong evidence to support it. Moreover, the half mean maximum distance moved (½ MMDM) method under CR methods appeared to overestimate leopard and serval density while full MMDM estimates were close to SECR methods density estimates. For lions, both ½ MMDM and full MMDM methods in MR framework overestimated density whereas the SMR method resulted in more reasonable estimates, especially in light of previous assessments of lion densities in West Africa.. These results are of high importance for conservation and management purposes of the imperiled Niokolo Koba carnivore community. / Master of Science

Estimates of animal abundance or density are fundamental quantities in ecology and conservation, but for many species such as rare, small mammals, obtaining robust estimates is problematic. In this thesis, I combine elements of two standard abundance estimation methods, capture-recapture and distance sampling, to develop a method called trapping point transects (TPT). In TPT, a "detection function", g(r) (i.e. the probability of capturing an animal, given it is r m from a trap when the trap is set) is estimated using a subset of animals whose locations are known prior to traps being set. Generalised linear models are used to estimate the detection function, and the model can be extended to include random effects to allow for heterogeneity in capture probabilities. Standard point transect methods are modified to estimate abundance. Two abundance estimators are available. The first estimator is based on the reciprocal of the expected probability of detecting an animal, ^P, where the expectation is over r; whereas the second estimator is the expectation of the reciprocal of ^P. Performance of the TPT method under various sampling efforts and underlying true detection probabilities of individuals in the population was investigated in a simulation study. When underlying probability of detection was high (g(0) = 0:88) and between-individual variation was small, survey effort could be surprisingly low (c. 510 trap nights) to yield low bias (c. 4%) in the two estimators; but under certain situations, the second estimator can be extremely biased. Uncertainty and relative bias in population estimates increased with decreasing detectability and increasing between-individual variation. Abundance of the Key Largo woodrat (Neotoma floridana smalli), an endangered rodent with a restricted geographic range, was estimated using TPT. The TPT method compared well to other viable methods (capture-recapture and spatially-explicit capture-recapture), in terms of both field practicality and cost. The TPT method may generally be useful in estimating animal abundance in trapping studies and variants of the TPT method are presented.

La fixation symbiotique d'azote par l'ajonc d'Europe (Ulex europaeus) représente une source importante d'azote dans la forêt cultivée de pins maritimes des 'Landes de Gascogne'. Cette thèse a pour objectif la création d'un modèle conceptuel de dynamique de population de l'ajonc dans la région en vue de la prédiction du flux d'azote associé. Pour cela plusieurs étapes du cycle de vie de l'espèce ont été étudiées: la production et la prédation des graines, puis le recrutement de nouveaux individus depuis le stock de graines du sol. Nos résultats suggèrent que le maintien de cette espèce héliophile à l'ombre de la canopée des pins est facilité par la diminution de l'allocation de ressources à la reproduction, lui permettant de maintenir sa croissance, et par la diminution de la prédation des graines. Par ailleurs, le recrutement de nouveaux ajoncs semble influencé par des facteurs écologiques identifiables (e.g. humidité du sol). Mais ces facteurs sont fortement variables dans l'espace et dans le temps, et aucun micro habitat n'apparait comme plus favorable à la régénération de l'espèce. Ces résultats sont intégrés à un modèle conceptuel, représentant les différentes étapes du cycle de vie de l'espèce, et l'impact des opérations sylvicoles sur ces étapes. Les connaissances issues de cette thèse pourraient aussi bénéficier à d'autres problématiques liées à l'espèce (e.g. c'est une espèce invasive dans de nombreuses régions du monde) et à la compréhension de l'écologie de la régénération des espèces ligneuses. En effet, l'allocation des ressources à la reproduction pourrait être plastique et permettre une réponse adaptative à un environnement changeant; et la variabilité spatiotemporelle de la régénération des ligneux pourrait reposer sur l'existence de niches écologiques de régénération définies dans l'espace écologique. / Symbiotic nitrogen fixation by European gorse (Ulex europaeus) is a major source of nitrogen in the 'Landes de Gascogne' cultivated forest of maritime pine. This thesis aims to build a conceptual model of the population dynamic of gorse in the region, with a view to predict the associated flux of nitrogen. To achieve this, several steps of the life cycle of the species were studied: production and predation of seeds, and the recruitment of new plants from the seedbank.The results suggest that the maintenance of this light demanding species in the shade of the canopy of pines is improved by the decrease of reproductive allocation, which enable to maintain its growth, and by the decrease of the predation of seeds. The recruitment of new gorse plants seems controlled by identifiable ecological factors (e.g. soil moisture), however these factors are highly variable in space and time, and no specific micro-habitat appears to be more favourable for the species regeneration.These results are integrated into a conceptual model based on the different steps of the life cycle of the species, and taking into consideration the influence of forestry practices on these steps. Furthermore, the production of knowledge could benefit other subjects related to the species (e.g gorse is a noxious weed in many region in the world) and the understanding of the ecology of woody plants' regeneration. Allocation of resources to reproduction may be plastic and enable an adaptative response to a changing environment; and spatiotemporal variability of the regeneration of woody plants may rely on the existence of ecological regeneration niches defined in the ecological space.

[Truncated abstract] Ecologists are increasingly interested in quantifying local interacting processes and their impacts on spatial vegetation patterns. In arid and semiarid ecosystems, theoretical models (often spatially explicit) of dynamical system behaviour have been used to provide insight into changes in vegetation patterning and productivity triggered by ecological events, such as fire and episodic rainfall. The incorporation of aerial imagery of vegetation patterning into current theoretical model remains a challenge, as few theoretical models may be inferred directly from ecological data, let alone imagery. However, if conclusions drawn from theoretical models were well supported by image data then these models could serve as a basis for improved prediction of complex ecosystem behaviour. The objective of this thesis is therefore to innovate methods for inferring theoretical models of vegetation dynamics from imagery. ... These results demonstrate how an ad hoc inference procedure returns biologically meaningful parameter estimates for a germ-grain model of T. triandra vegetation patterning, with VLSA photography as data. Various aspects of the modelling and inference procedures are discussed in the concluding chapter, including possible future extensions and alternative applications for germ-grain models. I conclude that the state-and-transition model provides an effective exploration of an ecosystem?s dynamics, and complements spatially explicit models designed to test specific ecological mechanisms. Significantly, both types of models may now be inferred from image data through the methodologies I have developed, and can provide an empirical basis to theoretical models of complex vegetation dynamics used in understanding and managing arid (and other) ecological systems.

Le Miscanthus x giganteus est une culture pérenne, nouvellement produite en Europe et présentant un intérêt fort pour son usage énergétique. Son implantation présage donc une réorganisation territoriale pérenne. Pour anticiper cette réorganisation, de nombreuses études modélisent les dynamiques spatialement explicites de son insertion. Notre thèse se positionne dans ce courant de recherche. Celle-ci vise à proposer un nouveau cadre de modélisation des processus de décision des agriculteurs, permettant la dissémination horizontale (scaling out) de ces processus issus d’études de cas, vers des territoires élargis. Pour cela, la thèse exploite le modèle du raisonnement à partir de cas. Elle articule (i) une démarche d’acquisition de connaissances sur les processus de décision des agriculteurs relatifs à l’insertion territoriale du miscanthus et (ii) la conception et évaluation d’un prototype ad hoc de raisonnement à partir de cas. La phase d’acquisition des connaissances montre que le processus d’insertion territoriale du miscanthus est complexe : celui-ci est étroitement lié aux contraintes parcellaires du territoire. Ces connaissances nous conduisent alors à discuter du choix des variables biophysiques et humaines intégrées à ce jour dans les modèles spatialement explicites. La phase de conception et d’évaluation du prototype de raisonnement à partir de cas montre que le modèle du raisonnement à partir de cas est particulièrement bien adapté pour modéliser un phénomène contextualisé. Evalués sur nos données d’enquêtes, ces résultats nous conduisent à discuter des modalités d’application du prototype sur d’autres bassins de production de miscanthus / Miscanthus x giganteus is the perennial crop, newly produced in Europe. Even if miscanthus is not so heavily produced nowadays, this crop would be of great interest for energy use. However, the allocation of miscanthus could produce a sustainable reorganization of the landscape. Therefore, many studies aim to model the land use change caused by miscanthus, in order to identify sustainable supply areas: our research belongs to this field. In our research, we propose a new framework for modeling decision-making process of farmers, relying on scaling out. More accurately, we propose to use the case-based reasoning model which solves problems based on an analogical reasoning. Then our research is structured: (i) by a knowledge acquisition step about decision-making process of farmers, based on farm surveys, conducted in the Côte d'Or department (Burgundy region) and (ii) by the design and evaluation of an ad hoc prototype of case-based reasoning. On the one hand, results of knowledge acquisition phase show that miscanthus allocation process is complex, more accurately, that miscanthus allocation process is closely related to land constraints, particularly in terms of logistic and environmental preservation of plots. These results lead us to discuss the selection of biophysical and human variables included to the current spatially explicit models. On the other hand, the design and evaluation phase of our prototype shows that case-based reasoning is particularly well suited to model a contextual phenomenon. These results lead us to discuss the modalities for implementing the prototype in other production areas of miscanthus