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The global effort to rehabilitate and restore destroyed mangrove forests is unable to keep up with the high mangrove deforestation rates which exceed the average pace of global deforestation by three to five times. Our knowledge of the underlying processes of mangrove forest regeneration is too limited in order to find suitable techniques for the restoration of degraded mangrove areas. The general objective of my dissertation was to improve mangrove restoration by understanding regeneration processes and local plant-plant interaction in a regenerating Avicennia germinans forest. The study was conducted in a high-shore mangrove forest area on the Ajuruteua peninsula, State of Para, Northern Brazil. The dwarf forest consisting of shrub-like trees is recovering from a stand-replacing event caused by a road construction in 1974 which interrupted the tidal inundation of the study area. Consequently, infrequent inundation and high porewater salinity limit tree growth and canopy closure. All trees and seedlings were stem-mapped in six 20 m x 20 m plots which were located along a tree density gradient. Moreover, height, crown extent, basal stem diameter of trees were measured. The area of herbaceous ground vegetation and wood debris were mapped as well. The mapped spatial distribution of trees, seedlings and covariates was studied using point pattern analysis and point process models, such as Gibbs and Thomas point process, in order to infer underlying ecological processes, such as seed dispersal, seedling establishment, tree recruitment and tree interaction. In the first study (chapter 2), I analyzed the influence of abiotic and biotic factors on the seedling establishment and tree recruitment of A. germinans during the recolonization of severely degraded mangrove sites using point process modeling. Most seedlings established adjacent to adult trees especially under their crown cover. Moreover, seedling density was higher within patches of the herbaceous salt-marsh plants Blutaparon portulacoides and Sesuvium portulacastrum than in uncovered areas. The higher density of recruited A. germinans trees in herb patches indicated that ground vegetation did not negatively influence tree development of A. germinans. In addition, tree recruitment occurred in clusters. Coarse wood debris had no apparent effect on either life stage. These results confirm that salt-marsh vegetation acts as the starting point for mangrove recolonization and indicate that the positive interaction among trees accelerates forest regeneration. In the second study (chapter 3), I analyzed how intraspecific interaction among A. germinans trees determines their growth and size under harsh environmental conditions. Interaction among a higher number of neighboring trees was positively related to the development of a focal tree. However, tree height, internode length and basal stem diameter were only positively associated in low-density forest stands (1.2 trees m-2) and not in forest stands of higher tree density (2.7 trees m-2). These results indicated a shift from facilitation, i.e. a positive effect of tree interaction, towards a balance between facilitation and competition. In the third study (chapter 4), I used point process modeling and the individual-based model mesoFON to disentangle the impact of regeneration and interaction processes on the spatial distribution of seedlings and trees. In this infrequently inundated area, propagules of A. germinans are only dispersed at a maximum distance of 3 m from their parent tree. Furthermore, there is no evidence that the following seedling establishment is influenced by trees. I was able to differentiate positive and negative tree interactions simulated by the mangrove model mesoFON regardless of dispersal processes based on static tree size information using the mark-correlation function. The results of this dissertation suggest that mangrove forest regeneration in degraded areas is a result of facilitative and not competitive interactions among mangrove trees, seedling and herbaceous vegetation. This has important implications for the restoration of degraded mangrove forest. Degraded mangrove areas are usually restored by planting a high number of evenly spaced seedlings. However, high costs constrain this approach to small areas. Assisting natural regeneration could be a less costly alternative. Herbaceous vegetation plays a crucial role in forest recolonization by entrapping propagules and possibly ameliorating harsh environmental conditions. So far only competition among mangrove trees has been considered during restoration. However, facilitative tree interactions could be utilized by planting seedling clusters in order to assist natural regeneration instead of planting seedlings evenly-spaced over large areas. This dissertation also showed that point pattern analysis and point process modeling can enable forest ecologists to describe the spatial distribution of trees as well as to infer underlying ecological processes.

This dissertation analyses the effects of current fisheries practices and management regulations of the green spiny lobster (Panulirus gracilis) in the Eastern Tropical Pacific Region (ETP). P. gracilis has reached a critical state in the ETP. Country-based studies report that between 60 and 98% of lobsters caught in the wild are under the minimum landing size (MLS). This means that spiny lobsters are being extracted before reproducing and contributing to the replenishment of interconnected populations. The recovery of green spiny lobster populations in the ETP and the future maintenance of a sustainable fishery will depend on effective management decisions and on taking in account environmental factors that influence the population dynamics of the lobsters. In the first study (Chapter 2), the B52 Spiny Lobster individual based simulation model was used for conducting a population viability analysis to quantify the effect of current fishing practices and the effect of varying management regulations on minimum landing size (MLS) and fishing effort. The best suit of regulations to maintain the highest abundance, production of offspring and catch is to protect juveniles and egged females, and to establish a MLS that assures the reproduction of individuals before being extracted. This study revealed regional variations, however the patterns and the causes for variation were not yet clear. This led to the next chapters in this dissertation. In Chapter 3, I used a meta-analysis to explore regional lobster variability by comparing published studies from the ETP. The objective was to identify patterns of variation related to geographic and environmental factors of the region that can inform the establishment and evaluation of coordinated regulations. Morphological relationships showed to be more variable at northern latitudes, where the mean annual sea surface temperatures are higher than at lower temperatures at the Equator. In terms of management, MLS regulations should be adapted accounting for the effect of sea surface temperature and its variation. Additionally, it was observed that monitoring methodologies are not standardized within the region and even in some cases, neither within countries. Furthermore, in most places monitoring of the spiny lobster fishery happens sporadically, only in Galapagos takes place every year. Identifying patterns of variations can improve the accuracy of prediction models which can help to explore, design, and apply more effective management measures, as well as promote regional coordination to support the recovery and maintenance of spiny lobsters. In Chapter 4, I contrast current Ecuadorian minimum landing size (MLS) regulation to lobster empirical measurements within Ecuador in order to recognize potential pitfalls for management enforcement. I used linear regression and multiple regression models with the objective of identifying potential relative size variations of the individuals caught in the wild over time and in the different fishing areas in Ecuador, as well as to analyse the effect of locality, sex, age and mean SST on the tail length/total length ratio. Morphological relations were significantly different among sexes, in time and by all sites. Most importantly, this study shows that current minimum size regulations are not applicable to all sites. Additionally, I found that water temperature has a significant effect on morphological relationship variations. However, it was not the main site-specific variable responsible for explaining such variations. In general, this work emphasizes the need for length data collection standardization and the consideration of temporal and spatial variation implications in national and regional fishery management planning, enforcement and evaluation.

L’étude des interactions entre les plantes au sein de couverts hétérogènes pourrait permettre une meilleure utilisation des associations variétales de blé, car nous manquons de connaissances sur la manière dont les complémentarités, synergies et compétitions entre variétés affectent leurs performances dans ces conditions. Notre étude s'est focalisée sur la compréhension de l'impact de la compétition pour la lumière sur l'architecture aérienne du blé, en couplant une analyse expérimentale et une approche par modélisation. Nous avons dans un premier temps, caractérisé la plasticité de l’architecture aérienne en réponse à la modification de la densité de semis, pour 20 génotypes contrastés de blé tendre. Ainsi, nous avons déterminé que le nombre d’axes par plante était le trait le plus plastique pour tous les génotypes. Nous avons ensuite développé un modèle individu-centré représentant le développement du blé du semis à la floraison. Ce modèle est composé de deux parties : une partie descriptive du développement foliaire basée sur un modèle existant (ADEL-blé) et une partie plus mécaniste où nous avons intégré une régulation du tallage par la ressource lumineuse. Cette régulation du tallage se fait selon deux hypothèses simples : (1) la plante arrête d'émettre des talles dès que le Green Area Index (GAI) de son voisinage atteint une valeur seuil et (2) une talle meurt si la quantité de lumière qu'elle intercepte est inférieure à un seuil critique. La dynamique de tallage simulée par le modèle sur une large gamme de densité de semis est proche de la dynamique de tallage observée expérimentalement. Nous avons également caractérisé expérimentalement la plasticité de l’architecture aérienne de huit génotypes de blé en réponse à la compétition dans différentes associations variétales binaires. Ces analyses ont révélé des réponses assez différentes de celles mesurées en culture pure, soulignant la spécificité de certaines interactions entre plantes de génotypes différents. Ces essais ont confirmé que les associations contribuaient généralement à une augmentation de la production, en particulier dans des itinéraires techniques économes en intrants. Nous avons montré que des associations variétales comprenant des génotypes avec des hauteurs différentes permettaient d’avantager fortement le génotype haut sans trop pénaliser le génotype court. Ce travail a permis de développer un formalisme simplifié des processus régulant le tallage, qui va permettre d'explorer et optimiser les complémentarités/compétitions entre variétés dans des peuplements multi-variétaux. A terme le modèle pourra être couplé à des modèles génétiques pour mieux décrire l'impact de l'interaction plate-plante dans la valeur sélective des individus dans des populations hétérogènes. / The understanding of the interactions between plants within heterogeneous crops could allow for a more efficient use of wheat varietal mixtures, as there is a gap of knowledge on the complementarity, synergy and competition that develop among varieties within these systems. Our study is focused on competition for light, and its impact on the above ground architecture of wheat, coupling experimental analysis and model development. We first characterized the plasticity of the aerial architecture in response to different sowing densities, for 20 contrasting genotypes of winter wheat. The number of axes per plant was shown to be the most plastic trait for all genotypes. We developed an individual-based model representing wheat growth, from the sowing to flowering. The model is composed of two parts: a descriptive part of the foliar development based on the ADEL-wheat model and a mechanistic part which accounts for the regulation of tillering by light. Tillering is regulated by two simple hypotheses: (1) tillering stops when a critical value of local Green Area Index (GAI) is reached, (2) a tiller dies if the amount of intercepted light falls below a critical threshold. A realistic tillering dynamics was simulated by our model over a wide range of sowing densities, with a good fit with experimental data. We also experimentally characterized the plasticity of plant architecture for eight wheat genotypes observed in various two-components varietal mixtures. Contrasted plastic responses were observed when compared to those expressed in pure stands, underlining the specificity of certain plant-plant interactions. These experiments confirmed that the cultivar mixtures generally contribute to an overyielding, particularly in low-input agriculture . Finally, our results revealed that variety mixtures including genotypes with different heights may provide an advantage to the taller genotype with limited tradeoff on the short genotype. This work contributed to the development of a simplified formalism for tillering process, allowing to explore and optimize complementarities / competitions between plants within variety mixtures. Ultimately, the model could be coupled with a genetic model, in order to better describe the impact of plant-to-plant interactions in the selective value of individuals in heterogeneous populations.

Cette thèse est consacrée à la modélisation mathématique de l'hématopoïèse et des maladies sanguines. Plusieurs modèles traitant d'aspects différents et complémentaires de l'hématopoïèse y sont étudiés.Tout d'abord, un modèle multi-échelle de l'érythropoïèse est analysé, dans lequel sont décrits à la fois le réseau intracellulaire, qui détermine le comportement individuel des cellules, et la dynamique des populations de cellules. En utilisant des données expérimentales sur les souris, nous évaluons les rôles des divers mécanismes de retro-contrôle en réponse aux situations de stress.Ensuite, nous tenons compte de la distribution spatiale des cellules dans la moelle osseuse, question qui n'avait pas été étudiée auparavant. Nous décrivons l'hématopoïèse normale à l'aide d'un système d'équations de réaction-diffusion-convection et nous démontrons l'existence d'une distribution stationnaire des cellules. Puis, nous introduisons dans le modèle les cellules malignes. Pour certaines valeurs des paramètres, la solution "disease-free" devient instable et une autre solution, qui correspond à la leucémie, apparaît. Cela mène à la formation d'une tumeur qui se propage dans la moelle osseuse comme une onde progressive. La vitesse de cette propagation est étudiée analytiquement et numériquement. Les cellules de la moelle osseuse échangent des signaux qui régulent le comportement cellulaire. Nous étudions ensuite une équation integro-différentielle qui décrit la communication cellulaire et nous prouvons l'existence d'une solution du type onde progressive en utilisant la théorie du degré topologique et la méthode de Leray et Schauder. L'approche multi-agent est utilisée afin d'étudier la distribution des différents types de cellules dans la moelle osseuse.Finalement, nous étudions un modèle de type "Physiologically Based Pharmacokinetics-Pharmacodynamics" du traitement de la leucémie par l'AraC. L'AraC agit comme chimiothérapie et induit l'apoptose de toutes les cellules proliférantes, saines et malignes. La pharmacocinétique donne accès à la concentration intracellulaire d'AraC. Cette dernière, à son tour, détermine la dynamique des populations cellulaires et, par conséquent, l'efficacité de différents protocoles de traitement. / This PhD thesis is devoted to mathematical modelling of haematopoiesis and blood diseases. We investigate several models, which deal with different and complementary aspects of haematopoiesis.The first part of the thesis concerns a multi-scale model of erythropoiesis where intracellular regulatory networks, which determine cell choice between self-renewal, differentiation and apoptosis, are coupled with dynamics of cell populations. Using experimental data on anemia in mice, we evaluate the roles of different feedback mechanisms in response to stress situations. At the next stage of modelling, spatial cell distribution in the bone marrow is taken into account, the question which has not been studied before. We describe normal haematopoiesis with a system of reaction-diffusion-convection equations and prove existence of a stationary cell distribution. We then introduce malignant cells into the model. For some parameter values the disease free solution becomes unstable and another one, which corresponds to leukaemia, appears. This leads to the formation of tumour which spreads in the bone marrow as a travelling wave. The speed of its propagation is studied analytically and numerically. Bone marrow cells exchange different signals that regulate cell behaviour. We study, next, an integro-differential equation which describes cell communication and prove the existence of travelling wave solutions using topological degree and the Leray-Schauder method. Individual based approach is used to study distribution of different cell types in the bone marrow. Finally, we investigate a Physiologically Based Pharmacokinetics-Pharmacodynamics model of leukaemia treatment with AraC drug. AraC acts as chemotherapy, inducing apoptosis of all proliferating cells, normal and malignant. Pharmacokinetics provides the evolution of intracellular AraC. This, in turn, determines cell population dynamics and, consequently, efficacy of treatment with different protocols.

L'objectif de cette thèse était d'anticiper les effets de l'Obligation de Débarquement (OD) mise en place en UE depuis début 2015 en Manche Orientale (MO). Pour accomplir ces objectifs, il a été prévu de : i) mieux comprendre la distribution spatiale saisonnière d'espèces commerciales à l'aide d'observations embarquées sur des navires commerciaux, ii) les comparer avec la distribution de l'effort de pêche à fine échelle des chalutiers de fonds (OTB), et iii) développer un modèle individu-centré de dynamique des flotilles, DSVM, à intégrer avec le modèle écosystémique OSMOSE pour simuler l'OD. L'utilité des données d'observations embarquées a été prouvée pour une majeure partie des espèces échantillonnées, en utilisant une validation par la bibliographie et un indicateur géostatique. Ensuite la comparaison de l'effort de pêche à fine échelle a fourni une amélioration de la quantification de l'effort de pêche effectif et mis en valeur l'importance de la seiche et du rouget barbet pour la distribution des OTB en MO. De plus, l'intensité de ciblage des OTB a été quantifiée en octobre à l'aide d'un nouvel indicateur, et démontré l'intérêt pour les mêmes espèces, mais aussi la contrainte d'un faible quota de cabillaud pour les pêcheurs. Les résultats du couplage OSMOSE-DSVM montrent que k'OD aurait des effets négatifs à court terme pour le revenu des pêcheurs, induits par le déplacement de l'effort de pêche afin d'éviter les dépassements de quota, mais serait profitable à moyen terme. Cependant, l'OD provoquerait une hausse de la pression de prédation produite par le cabillaud et le merlan sur les autres espèces, ce qui n'améliorerait pas l'état global de l'écosystème. / The objective of this thesis was to anticipate the effects if the EU Landing Obligation (LO) implemented since the beginning of 2015 in the Eastern English Channel (EEC). To achieve these objectives, it was planned to : i) better understand seasonal spatial distribution of commercial species using on-board commercial vessels observation data, ii) compare them with the final scale fishing effort distribution of EEC bottom otter trawlers (OTB), and iii) develop an individual-based model of fleet-dynamics, DSVM, to be integrated within the ecosystem model OSMOSE to simulate a LO. The usefulness of on-board observation data was proved for a main part of a species sample, using validation from the literature and a geostatistical indicator. Then the comparison of fine scale fishing effort provided an improvement of the quantification of effective fishing effort and emphasized the importance of cuttlefish and red mullet for the global distribution of EEC OTB. In addition, the targeting intensity of OTB was quantified in October using a newly-developed indicator, and demonstrated the attractiveness of the same species, but also the constraint of low cod quota for fishers. Results of the OSMOSE-DSVM coupling show that the LO would have short-term negative effects on fishers' revenue, induced by a large reallocation of their fishing effort to avoid quota over-shooting, but would be profitable in the medium-term. However, the LO would induce an increase of the predatory pressure operated by cod and withing on the other species, which would not improve the overall ecosystem health.