Parmi les agents qui modulent la dynamique des populations, le parasitisme est important mais souvent négligé. Il est urgent non seulement d’inventorier les différentes espèces de parasites, mais aussi de comprendre la sensibilité des hôtes à l’infection (notamment des bivalves) et étudier les interactions entre les parasites et les autres facteurs environnementaux. Par conséquent, cette thèse avait comme objectif principal de caractériser et de quantifier les communautés de trématodes (les plus abondants et répandus des macroparasites de bivalves dans les eaux côtières) qui infectent Cerastoderma edule (coque) et Donax trunculus (telline), deux des bivalves les plus importants au Portugal et en France d’un point de vue écologique et économique.Dans un premier temps, la dynamique des populations de bivalves a été étudiée en tenant compte de la relation entre la température et la période de recrutement et des effets en retour du recrutement sur la biomasse adulte. Pour cela, une base de données a été analysée couvrant 17 ans d’observations mensuelles d’une population de coques dans une réserve nationale (Banc d’Arguin, Arcachon, France). Ces observations à long terme ont montré que la durabilité d’une population de coques dépend du succès du recrutement. Pour les coques, le succès du recrutement a été montré comme étant en partie, mais pas totalement, dépendant de la température. Ainsi, la durée de vie d’une cohorte pourrait être estimée plus tôt, grâce à des indices se produisant en amont du recrutement. Suite à ces résultats, le rôle du parasitisme dans la dynamique des populations de bivalves a été étudié.Premièrement, en raison de leur forte pathogénicité pour les bivalves, une attention particulière a été accordée aux parasites Bucephalus minimus et Bacciger bacciger qui utilisent C. edule et D. trunculus, respectivement, comme premier hôte intermédiaire (où se développe le stade parasitaire sporocyste). [...]Deuxièmement, cette étude s’est concentrée sur l’infection des bivalves par les métacercaires, c’est-à-dire lorsqu’ils servent de second hôte intermédiaire dans le cycle de vie du parasite. […]Enfin, la sensibilité des bivalves à l’infection parasitaire a été évaluée expérimentalement lorsqu’ils sont confrontés à des facteurs liés au changement climatique (salinité, température et pH) et à la contamination (arsenic). Les résultats ont montré que l’exposition de l’hôte à des conditions de stress liées à des scénarios de changement global peut modifier le succès de l’infection parasitaire et altérer les réponse biochimiques de l’hôte.Les résultats présentés dans cette thèse ont amélioré la connaissance des effets de différentes variables sur les bivalves, soulignant le rôle crucial du parasitisme. S’ils sont appliqués, ces nouveaux concepts peuvent promouvoir la gestion durable des bivalves, une ressource marine importante, en augmentant son potentiel de production et donc son potentiel économique. / Among population dynamics drivers, parasitism is significant but often neglected. Beyond inventory of the various parasites, it is urgent to understand the susceptibility of hosts, namely bivalves, to infection, and to investigate the interaction among parasites and other environmental conditions.In this way, the present study aimed to characterize and quantify the trematode macroparasites, the most abundant and prevalent in coastal waters, infecting Cerastoderma edule and Donax trunculus, which are among the most ecologically important and economically explored bivalve species in Portugal and France.The first step was to study bivalve population dynamics, evaluating the relationship between temperature and recruitment timing and the reciprocal effects of recruitment on adult biomass. For this, a large database spanning 17 years of monthly observations of a cockle population inhabiting a national protected area (Banc d’Arguin, Arcachon, France) was analysed. Long-term observations showed that the sustainability of a cockle population is recruitment-success dependent. In cockles, recruitment success showed to be partly, but not only, dependent on temperature. Hence, the sustainability of a cohort could be set earlier, i.e. by processes happening before recruitment. Following this clue, the role of parasitism on the bivalve host population dynamics was explored.Firstly, due to high pathogenicity for bivalves, special attention was given to the parasites Bucephalus minimus and Bacciger bacciger which use C. edule and D. trunculus, respectively, as first intermediate hosts (where their sporocysts parasitic stage develops). […]Then, the study focused on metacercariae infection in its bivalve second intermediate host, a relationship that is usually reported as less deleterious. […]Lastly, the susceptibility of bivalves to parasites infection when challenged by climate change related factors (salinity, temperature and pH) and contamination (Arsenic) was experimentally assessed. Main results showed that hosts exposure to stressful conditions related to global change scenarios can modify the parasite infection success and induced host biochemical response alterations.The findings presented in this thesis improved the knowledge on the effects of different constraints on bivalves, highlighting the crucial role of parasitism. If applied, these new insights can promote the sustainable management of bivalves, such an important marine resource, with greater production and economic potential. / Entre os agentes que modulam a dinâmica populacional, o parasitismo é significativo masmuitas vezes negligenciado. É urgente não só inventariar as várias espécies de parasitas, bem comocompreender a suscetibilidade dos hospedeiros à infeção (nomeadamente os bivalves) e investigar ainteração entre os parasitas e outras condições ambientais. Pelo que, esta tese teve como objetivoprincipal caracterizar e quantificar os macroparasitas trematodes (os mais abundantes e prevalentesem águas costeiras) que infetam Cerastoderma edule (berbigão) e Donax trunculus (conquilha), doisdos bivalves mais importantes em Portugal e França tanto do ponto de vista ecológico comoeconómico.Primeiramente, a dinâmica populacional dos bivalves foi estudada, tendo em conta a relaçãoentre a temperatura e o período de recrutamento e os efeitos recíprocos do recrutamento nabiomassa de adultos. Para isso, foi analisada uma base de dados abrangendo 17 anos deobservações mensais de uma população de berbigões que habitam uma área nacional protegida(Banc d’Arguin, Arcachon, França). Estas observações de longa duração mostraram que asustentabilidade de uma população de berbigão é dependente do sucesso do recrutamento. Emberbigões, o sucesso do recrutamento mostrou ser em parte, mas não totalmente, dependente datemperatura. Por esta razão, a sustentabilidade de uma coorte pode estar a ser estabelecida maiscedo, isto é, por processos que acontecem antes do recrutamento. Seguindo esta pista, o verdadeiropapel do parasitismo na dinâmica populacional dos bivalves foi mais explorado.De seguida e devido à elevada patogenicidade para os bivalves, foi dada especial atençãoaos parasitas Bucephalus minimus e Bacciger bacciger que usam C. edule e D. trunculus,respetivamente, como primeiros hospedeiros intermediários (onde o estádio parasítico esporocisto sedesenvolve). […].Depois, este estudo focou-se na infeção dos bivalves por metacercariae, ou seja, quandoservem de segundos hospedeiros intermediários no ciclo de vida do parasita. […]Por fim, foi experimentalmente avaliada a suscetibilidade dos bivalves à infeção por parasitasquando desafiados por fatores relacionados com as alterações climáticas (salinidade, temperatura epH) e contaminação (Arsénio). Os resultados mostraram que a exposição dos hospedeiros acondições de stress relacionadas com cenários de alterações globais podem modificar o sucesso dainfeção parasitária e induzir alterações na resposta bioquímica do hospedeiro.As descobertas apresentadas nesta tese melhoraram o conhecimento dos efeitos dediferentes variáveis nos bivalves, salientando o papel crucial do parasitismo. Se aplicados, estesnovos pontos de vista podem promover a gestão sustentável dos bivalves, um recurso marinho tãoimportante, aumentando o seu potencial de produção e económico.

A population of a critically endangered species Spiranthes spiralis was discovered in 1980 in the National Natural Monument Pastviště u Fínů near village Albrechtice, close to Sušice city. Since 1985 the number of flowering individuals in this population has been annually monitored. Since autumn 1998 all the specimen found there have been marked and biometrically measured. During these periods (12 or 26 years, respectively), large year-on-year fluctuations in the number of flowering plants and in the survival of the individual rosettes have been recorded. The main aim of my work was to assess the effect of weather conditions (temperature, precipitation, the number of days of snow) on the population dynamics and on the fitness of plants (leaf area, probability of flowering and probability of death). The year-round lower temperature and the wet end of autumn during the previous year (t-1) together with the wet spring of the following year (t) had a positive effect on the leaf area during the period of maximal rosette growth (end May in the year t). The probability of flowering was positively affected by the lower temperatures in May and June in the previous year (t-1) and in August just before flowering (year t). The probability of death (in the year t) was increased when the March precipitation (in t) and October temperatures (in t-1) were low. The average number of seeds in the capsule was 1528 ? 885 (s.d.). The number of flowers was positively correlated with the number of mature capsules. However, it did not affect the ratio of mature capsules. Capsules developed on average from 44% ? 24.6 % (s.d.) of the flowers. The average life time of individual plant cohorts was 4.7 years. The number of rosettes per each position was variable from 1 to 7 rosettes (73.2% positions had only 1 rosette). The annual life cycle of the underground organs is described at the end of the thesis.

Jusqu’à aujourd’hui, les traits démographiques du début de vie ont été peu étudiés relativement aux traits adultes chez une grande majorité d’espèces animales. Les jeunes individus sont généralement plus difficiles à étudier en milieu naturel du fait de leur taille plus petite, de leur comportement plus mobile et des forts taux de mortalité qu’ils subissent. Cependant, la bonne compréhension des processus démographiques requiert la prise en compte de l’ensemble des stades de vie. Le manque de connaissance concernant les plus jeunes individus est particulièrement préjudiciable pour les espèces longévives. En effet chez ces espèces, les individus immatures représentent une partie importante de la valeur reproductive totale et ont ainsi une forte influence sur l’ensemble de la dynamique de la population. Ainsi, ces lacunes affectent notre capacité à effectuer des projections démographiques réalistes dans un contexte de changements globaux et plus généralement limitent notre compréhension de l’évolution des traits d’histoire de vie. Afin de pallier à ce manque, cette thèse porte sur l’étude des traits d’histoire de vie en début de vie chez une espèce d’oiseau marin : l’albatros hurleur Diomedea exulans. Chez cette espèce particulièrement longévive, la période d’immaturité peut durer une dizaine d’années. En se basant sur un suivi individuel à long terme et des analyses de type capture-marquage-recapture, nous avons estimé la survie en début de vie ainsi que l’accès à la première reproduction en fonction de l’âge et du sexe. Nous avons également étudié les effets potentiels de facteurs extrinsèques (climat, pêcherie) et intrinsèques (densité dépendance, âge parental) sur ces paramètres. De nombreuses relations entre les taux vitaux de ces jeunes individus et leur environnement ont été décrites. Sur un plan plus théorique, nous avons également pu tester différentes prédictions comme la canalisation des traits d’histoire de vie ou l’existence de différentes stratégies d’histoire de vie au sein d’une même population. Au cours de ce travail, une attention particulière a été portée aux variations des traits démographiques à l’échelle individuelle. Notre étude montre que les taux vitaux d’individus de même âge et de même sexe peuvent être très variables. Nous avons pu associer les traits démographiques en début de vie aux performances futures au stade adulte et révéler certaines causes de ces variations interindividuelles. / To date, early life demographic traits have been poorly studied compare to adult traits in the vast majority of animal species. Young individuals are usually more difficult to study due to their small size, their mobile behavior and the high mortality rate that characterizes their life stage. However, the full understanding of the demographic processes requires the integration of all life stages. This lack of knowledge toward early-life stages is particularly detrimental for long lived species. Indeed for these species, the immature component represents a substantial part of the total reproductive value, having a high influence on the whole population dynamics. Hence, such limitations affect the accuracy of population projections in the context of global change and more generally our understanding of life history trait evolution. In order to fill in this gap, this PhD project focuses on early life demographic traits in a seabird species : the wandering albatross Diomedea exulans. In this very long-lived species, the immature period lasts around 10 years. Based on long-term individual monitoring and capture-recapture analyses, we estimated early-life survival and the access to reproduction according to age and sex. We also investigates the respective effects of extrinsic (e.g. climate, fisheries) and intrinsic factors (e.g. density dependence, parental effects) on these parameters. Many relationships between early-life vital rates and environmental variables have been described. From a theoretical perspective, we tested several predictions such as the canalization of life-history traits and the existence of different life-history strategies within a population. In this work, special attention was paid to demographic variations at the individual scale. Our study showed that vital rates of individuals of the same age and sex could be very different. We have linked early-life demographic traits with subsequent adult performances and identified some causes of these individual variations.

Commercialisées depuis 1996, les plantes génétiquement modifiées produisant une toxine insecticide (toxine Cry) dérivée de Bacillus thuringiensis et appelées plantes Bt ciblent certains Lépidoptères ou Coléoptères ravageurs. Au fil des ans, les surfaces cultivées en plantes Bt sont de plus en plus importantes et contrôlent de larges populations d'insectes. Pour limiter le risque de développement de populations résistantes, une stratégie agricole appelée 'Haute Dose / Zone Refuge' est actuellement recommandée aux Etats-Unis par l'Environmental Protection Agency. Cette stratégie préventive nécessite la plantation d'une 'zone refuge' composée de plantes non-Bt utilisables par le ravageur ciblé et plantée à proximité de la 'zone Bt' qui synthétise une haute dose de toxine Cry. <p><p>Mon projet de recherche s’inscrit dans le cadre de l’évaluation de l'efficacité de cette stratégie et s’articule en deux phases :une phase expérimentale et une phase théorique. La première se concentre sur la caractérisation en laboratoire de l'impact des toxines Cry sur la biologie d'un ravageur. Cette phase constitue un support au volet théorique :la mise au point d’un modèle mathématique évaluant l'efficacité de la stratégie HD/R. L'originalité de ce projet repose entre autre sur l'interactivité entre ces deux volets.<p><p>Volet expérimental. Impact des toxines Cry sur la biologie de Plodia interpunctella. Nous évaluons séparément l'impact d'une gamme de concentrations de deux toxines Cry (CryXX et CryYY) sur une série de paramètres comportementaux et biologiques d'un insecte commun des denrées stockées: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). Ces paramètres sont sélectionnés car leur variation pourrait avoir un impact sur l'efficacité de la stratégie HD/R dans le contrôle de la résistance. Il est donc pertinent de les quantifier pour intégrer dans le modèle des ordres de grandeur réalistes et générer des résultats qui ne sont pas uniquement basés sur des spéculations théoriques.<p><p>Volet théorique A. Efficacité de la stratégie HD/R pour des plantes Bt synthétisant une ou deux toxines simultanément. La stratégie 'HD/R' a été développée pour prévenir la résistance envers les plantes Bt synthétisant une seule toxine. Or, depuis 2003, de nouvelles variétés de coton Bt synthétisant simultanément deux toxines Cry sont commercialisées (BollgardII® et WidestrikeTM). Nous évaluons, grâce au modèle que nous avons développé, l'efficacité de cette stratégie lors d'une utilisation exclusive de plantes Bt synthétisant une ou deux toxines.<p><p>Volet théorique B. Impact du ralentissement du développement des insectes sur les plantes Bt sur l'efficacité de la stratégie HD/R. Le volet expérimental met en évidence un allongement de la durée du développement des larves se nourrissant sur une diète contaminée en toxine Cry. Ce ralentissement induit une séparation temporelle entre l'émergence des adultes de la zone Bt et de la zone refuge et perturbe une hypothèse principale de la stratégie HD/R: le croisement aléatoire entre adultes, indépendamment du génotype et de la zone d'origine. Dans ce troisième chapitre, nous étudions l'impact de la perturbation du croisement aléatoire sur l'efficacité de la stratégie HD/R. Nous testons également deux options pour optimiser la stratégie en cas d'asynchronie: l'utilisation de plantes Bt synthétisant une faible concentration en toxine (atténuant le décalage entre l'émergence des adultes) ou l'augmentation de la taille de la zone refuge (favorisant la survie des individus porteurs d'allèle de sensibilité et donc optimisant la dilution de la résistance à la génération suivante). <p><p>Ce travail s'intègre dans une problématique actuelle et utilise des outils de biologie théorique (théories de la dynamique et de la génétique des populations) ainsi que le développement d'un modèle mathématique. Il apporte des éléments de réponse et de réflexion sur l'optimisation de la gestion de la résistance des insectes mais c'est aussi une illustration de la complémentarité entre la biologie expérimentale et théorique.<p><p><p>/<p><p>On the market since 1996, genetically modified plants synthesizing an insecticidal toxin (Cry toxin) stemmed from Bacillus thuringiensis, called Bt plants, target several insect pests (Lepidoptera or Coleoptera). Bt crops cover increasingly larger areas and control important pest populations The Insect Resistance Management Strategy (IRM) strategy currently recommended in the U.S.A. to limit the development of resistant populations is the High Dose / Refuge zone (HD/R) strategy. This pre-emptive strategy requires a refuge zone composed by non-Bt plants, usable by the target insect and in close proximity of the Bt zone synthesizing a high toxin concentration.<p><p>My research project contributes to the effectiveness assessment of this HD/R strategy. It is structured on two main parts: an experimental, and a theoretical section. The first part characterizes the impact of Cry toxins on the biology of an insect pest. It is the basis of the theoretical part: the implementation of a mathematical model, which evaluates the effectiveness of the HD/R strategy.<p>The originality of this project is based on the interactivity of these two components.<p><p>Experimental section. Impact of the Cry toxins on the biology of Plodia interpunctella. We assess the impact of a range of concentrations of two Cry toxins (CryXX et CryYY) on several behavioural and biological parameters of a common pest of stored products: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). These parameters are selected because their variation could influence the effectiveness of a HD/R strategy. So, it is important to quantify these parameters so that realistic values can be integrated in our model. The results of the model are thus not based on theoretical assumptions alone.<p> <p>Theoretical section A. Effectiveness of a HD/R strategy with Bt plants synthesizing one or two toxins. Initially, the HD/R strategy has been developed to limit the resistance towards Bt plants synthesizing one toxin. However, since 2003, new Bt cotton varieties synthesize two toxins simultaneously (BollgardII® et WidestrikeTM). We assess, with our model, the effectiveness of this strategy for Bt plants synthesizing one or two toxins.<p><p>Theoretical section B. Impact of the slowing down of the insect development reared on Bt plants on the effectiveness of the HD/R strategy. The experimental part demonstrates that larvae reared on a Bt diet have a protracted development duration. The consequence of this is a temporal separation between adult emergence in the two zones (Bt zone and refuge zone). This could affect the main assumption of the HD/R strategy, i. e. random mating independently of the genotype and of the native zone. In this third chapter, we study the impact of random mating disruption on the effectiveness of a HD/R strategy. We test two options to optimise the strategy in case of asynchrony: the use of Bt plants synthesizing a lower toxin concentration (limiting emergence asynchrony) or increasing the refuge zone size (favouring the survival of insect carrying one or two susceptible allele and thus optimising the dilution of resistance at the next generation). <p><p>This work is applied to a current issue. It uses some of the tools of theoretical biology (theories of population dynamics and population genetics) and develops a mathematical model. It provides some responses and some elements of thought about insect resistance management. It is also an illustration of the complementarity between experimental and theoretical biology.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Modelling and simulation are essential to modern research in cell biology. This thesis follows a journey starting from the construction of new stochastic methods for discrete biochemical systems to using them to simulate a population of interacting haematopoietic stem cell lineages. The first part of this thesis is on discrete stochastic methods. We develop two new methods, the stochastic extrapolation framework and the Stochastic Bulirsch-Stoer methods. These are based on the Richardson extrapolation technique, which is widely used in ordinary differential equation solvers. We believed that it would also be useful in the stochastic regime, and this turned out to be true. The stochastic extrapolation framework is a scheme that admits any stochastic method with a fixed stepsize and known global error expansion. It can improve the weak order of the moments of these methods by cancelling the leading terms in the global error. Using numerical simulations, we demonstrate that this is the case up to second order, and postulate that this also follows for higher order. Our simulations show that extrapolation can greatly improve the accuracy of a numerical method. The Stochastic Bulirsch-Stoer method is another highly accurate stochastic solver. Furthermore, using numerical simulations we find that it is able to better retain its high accuracy for larger timesteps than competing methods, meaning it remains accurate even when simulation time is speeded up. This is a useful property for simulating the complex systems that researchers are often interested in today. The second part of the thesis is concerned with modelling a haematopoietic stem cell system, which consists of many interacting niche lineages. We use a vectorised tau-leap method to examine the differences between a deterministic and a stochastic model of the system, and investigate how coupling niche lineages affects the dynamics of the system at the homeostatic state as well as after a perturbation. We find that larger coupling allows the system to find the optimal steady state blood cell levels. In addition, when the perturbation is applied randomly to the entire system, larger coupling also results in smaller post-perturbation cell fluctuations compared to non-coupled cells. In brief, this thesis contains four main sets of contributions: two new high-accuracy discrete stochastic methods that have been numerically tested, an improvement that can be used with any leaping method that introduces vectorisation as well as how to use a common stepsize adapting scheme, and an investigation of the effects of coupling lineages in a heterogeneous population of haematopoietic stem cell niche lineages.

Durant les dernières années, la taille des systèmes ainsi que leur complexité ont pas mal évolué, entrainant le besoin d'approches distribuées pour la commande et l'aide à la décision. Cette thèse porte sur la résolution d'un problème incluant une commande distribuée et une aide à la décision, l'allocation dynamique de ressource dans un réseau.Pour résoudre ce problème, nous avons étudié un algorithme basé sur un consensus qui ne nécessite pas de calcul centralisé, et qui soit capable de traiter des applications modélisées par des systèmes dynamiques ou par des fonctions sans mémoires. La principale contribution de ce travail de thèse est d'avoir prouvé, en utilisant des outils issus de la théorie des graphes etl'analyse de la passivité, que le contrôleur atteint la solution optimale de façon asymptotique, sans obligation d'avoir une information complète.Afin d'illustrer la pertinence de notre résultat principal, plusieurs applications en ingénierie ont été étudiées, incluant la commande distribuée pour l'économie d'énergie dans des bâtiments intelligents, la gestion des clients dans un environnement de "smart grids", et le développement d'une méthode exacte d'optimisation distribuée pour un problème d'allocation de ressources soumis à des contraintes sur les bornes inférieures.Enfin, nous étudions les techniques d'allocation de ressources basées sur les modèlesde dynamique de populations. Pour les rendre distribuées, nous introduisons le concept dedynamique de populations "pas bien mélangées". Nous montrons que ces dynamiques peuventêtre utilisées pour des structures d'informations contraintes. Même si les dynamiquesde populations "pas bien mélangées" utilisent des informations partielles, ellesconservent des propriétés similaires aux dynamiques classiques qui utilisent desinformations complètes. Plus spécifiquement, la conservation de masse et la convergencevers l'équilibre de Nash sont prouvées. / Since the complexity and scale of systems have been growing in the last years, distributed approaches for control and decision making are becoming more prevalent. This dissertation focuses on an important problem involving distributed control and decision making, the dynamic resource allocation in a network. To address this problem, we explore a consensus--based algorithm that does not require any centralized computation, and that is capable to deal with applications modeled either by dynamical systems or by memoryless functions. The main contribution of our research is to prove, by means of graph theoretical tools and passivity analysis, that the proposed controller asymptotically reaches an optimal solution without the need of full information. In order to illustrate the relevance of our main result, we address several engineering applications including: distributed control for energy saving in smart buildings, management of the customers of an aggregating entity in a smart grid environment, and development of an exact distributed optimization method that deals with resource allocation problems subject to lower--bound constraints. Finally, we explore resource allocation techniques based on classic population dynamics models. In order to make them distributed, we introduce the concept of non--well--mixed population dynamics. We show that these dynamics are capable to deal with constrained information structures that are characterized by non--complete graphs. Although the proposed non--well--mixed population dynamics use partial information, they preserve similar properties of their classic counterpart, which uses full information. Specifically, we prove mass conservation and convergence to Nash equilibrium. / Dado que la complejidad y la escala de los sistemas sehan ido incrementando en los últimos años, las técnicas centralizadas de control y toma de decisiones están siendo reemplazadas por métodos distribuidos. Esta tesis se centra en un importante problema que involucra control y toma de decisiones distribuidas: la asignación dinámica de recursos en redes. Para abordar este problema, exploramos un algoritmo basado en consenso que no requiere computación centralizada, y que puede ser usado en aplicaciones modeladas ya sea por sistemas dinámicos o funciones sin memoria. La principal contribución de esta tesis es probar, por medio de teoría de grafos y pasividad, que el algoritmo propuesto alcanza asintóticamente una solución óptima sin la necesidad de usar información completa. Para ilustrar la relevancia del resultado principal de esta disertación, abordamos varias aplicaciones en ingeniería,incluyendo: el control distribuido en edificios inteligentes orientado a la eficiencia energética, la gestión de los clientes de un agregador en una red inteligente en la que se aplican estrategias de respuesta de la demanda, y el desarrollo de un método de optimización exacto que permite incluir restricciones de límite inferior. Finalmente, se exploran otras técnicas de asignación derecursos inspiradas en modelos de dinámicas poblacionales. Se introduce el concepto de poblaciones no—bien—mezcladas, y se muestra que las dinámicas asociadas a este tipo de poblaciones cuentan con una estructura de información local, caracterizada por grafos que no son completos. A pesar de que las dinámicas propuestas usan información parcial, ellas preservan características similares a las dinámicas poblacionales clásicas que usan información completa.

La rotation de cultures peut être utilisée pour empêcher la sélection continue d’espèces adventices adaptées à un type de culture. Elle pourrait favoriser la gestion des adventices, l’économie d’herbicides et la biodiversité. Les successions de cultures simples d’aujourd’hui pourraient être diversifiées par des cultures fourragères pérennes. Les impacts des ces cultures sur les adventices ont été étudié utilisant quatre approches : 1) Des relevés d’adventices sur 632 champs dans l’ouest de la France ont montré que la composition spécifique varie le plus entre des cultures fourragères pérennes et des cultures annuelles. Une comparaison des champs avant, pendant, et après des cultures fourragères pérennes a suggéré que la composition des communautés varie d’une manière cyclique pendant ces rotations. Plusieurs espèces problématiques dans des cultures annuelles ont été supprimées pendant et après les cultures pérennes, mais l’apparition d’autres espèces a produit une diversité de plantes comparable, voire supérieure. 2) Une expérimentation au champ de trois ans avec des modes de gestion contrastés a permis d’étudier les mécanismes sous-jacents: L’absence de travail du sol a réduit la levée des adventices, mais a augmenté la survie des plantes adultes. Le couvert végétal permanent et les fauches fréquentes ont réduit la croissance, la survie des plantes et la production de graines. 3) Des expérimentations sous serre analysant la croissance poste fauche de plantes individuelles ont montré des différences importantes entre espèces et groupes fonctionnels. Une expérimentation à deux facteurs a suggéré que les impacts négatifs de la fauche et de la compétition sur la croissance des adventices ont été additifs. 4) Des mesures spéciales de prédation de graines d’adventices sur l’expérimentation au champ ont montré des corrélations positives avec le couvert végétal et la prédation, indiquant une importance particulière de ce service écosystémique dans des cultures pérennes. La préférence des graines de certaines espèces montre que la prédation de graines peut être une autre cause des changements de communautés d’adventices. / Crop rotation may be used to prevent the continuous selection of particular weed species adapted to one crop type. This might be useful for weed management, economy in herbicide applications and promoting biodiversity. Common simple crop sequences might be diversified by introducing perennial forage crops. Impacts of such perennial crops on weeds were studied with four approaches : 1) Large-scale weed surveys in 632 fields in western France showed that weed species composition differed most strongly between perennial alfalfa crops and annual crops. Comparisons of fields before, during and after perennial alfalfa suggested that community composition varies in a cyclic way during such crop rotations. Several weed species problematic in annual crops were suppressed during and after perennial crops, but the appearance of other species led to equal or even higher plant diversities. 2) A 3-year field experiment with contrasting crop management options allowed an investigation of the underlying mechanisms for this: The absence of soil tillage reduced weed emergence but increased the survival of established plants. The permanent vegetation cover and frequent hay cuttings reduced weed growth, plant survival and seed production. 3) Greenhouse experiments testing the regrowth ability of individual plants after cutting showed strong differences between species and functional groups. An two-factorial experiment suggested that the negative impacts of cutting and competition on weed growth were mainly additive. 4) Special measurements of weed seed predation in the field experiment showed positive correlations with vegetation cover, indicating that this ecosystem service may be particularly fostered by perennial crops. Consistent preferences of seed predators for certain weed species indicates that seed predation may be another cause of the observed weed community shifts. / Fruchtfolgen können dazu dienen, die kontinuierliche Selektion von Unkrautarten zu verhindern, die an eine bestimmte Kultur angepasst sind. Dies könnte dem Unkrautmanagement, der Einsparung von Herbiziden, und der Biodiversität dienen. Heutige, sehr einfache Furchtfolgen könnten durch mehrjährige Futterkulturen diversifiziert werden. Die Einflüsse solcher mehrjähriger Kulturen auf Unkräuter wurden in vier Ansätzen untersucht : 1) Vegetationsaufnahmen auf 632 Feldern in Westfrankreich zeigten, dass die Unkrautzusammensetzung zwischen mehrjährigen Futterkulturen und einjährigen Kulturen stark variiert. Der Vergleich von Feldern vor, während und nach mehrjährigen Futterkulturen legte nahe, dass die Pflanzengemeinschaft während solcher Fruchtfolgen zyklisch variiert. Mehrere problematische Unkrautarten wurden während und nach den mehrjährigen Kulturen zurückgedrängt. Das Auftauchen anderer Arten führte jedoch zu einer gleichbleibenden oder leicht erhöhten Pflanzenvielfalt. 2) Ein dreijähriger Feldversuch mit verschiedenen Bearbeitungsoptionen ermöglichte es, die zugrunde liegenden Mechanismen zu untersuchen: Die fehlende Bodenbearbeitung hat das Auflaufen der Unkräuter reduziert und das Überleben der adulten Pflanzen erhöht. Die permanente Vegetationsbedeckung und die häufigen Heuschnitte haben das Wachstum, das Überleben und die Samenproduktion vermindert. 3) Gewächshausexperimente zum Nachwachsen von Unkrautpflanzen nach Heuschnitten zeigten große Unterschiede zwischen verschiedenen Arten und funktionellen Gruppen. Ein Experiment mit zwei Faktoren lässt vermuten, dass die negativen Effekte der Schnitte und der Konkurrenz auf das Unkrautwachstum sich addieren. 4) Spezielle Messungen der Prädation von Unkrautsamen auf den untersuchten Feldern zeigten positive Korrelationen mit der Vegetationsbedeckung, was auf eine besondere Wichtigkeit dieser Ökosystemdienstleistung in ausdauernden Kulturen hindeutet. Die Präferenz von bestimmten Samenarten deutet darauf hin, dass Samenprädation ein weiterer Grund für die beobachteten Änderungen der Unkrautgemeinschaften sein kann.

It appears to be unanimous that alien species in island environments tend to cause considerably more negative than positive impacts. To assess the potential level of threat aliens may pose to the native environment, understanding a species’ population structure and dynamics is of ultimate importance. Assessing both impacts and consequences of management interventions to alien species is likewise only possible through the comprehension of its population structure and dynamics. This can be achieved by estimating the number of individuals in the study site, as well as other population parameters through time, applying population models such as capture-recapture to the collected datasets. Nonetheless, alien species that have low capture rates, such as small mammals, might present a considerable obstacle for conservation, as available capturerecapture models need a relatively large dataset to precisely and accurately estimate population parameters. To improve accuracy and precision of estimates that use sparse datasets, the present study developed an integrated concurrent marking-observation capture-recapture model (C-MOM). The model proposed here, contrary to the commonly available mark-recapture and mark-resight models, allows for two different datasets (i.e. a capture-recapture and a population count) to be integrated, as well as for marking and observation (recapture) data to be collected simultaneously. While few models can integrate different datasets, no model is known to allow for concomitant capture-markobservation activities. To assess the performance of the C-MOM when estimating population parameters for sparse datasets, a virtual ecology study was carried out. The population dynamics of a small rodent, the rock cavy (Kerodon rupestris), as well as capture-recapture and population count datasets, were simulated under different scenarios. The sampled datasets were then analyzed by the C-MOM, and by two other established statistical models: a classical mark recapture (CMR) (based on the Jolly-Seber model), and a zero-truncated Poisson log-normal mixed effects (ZPNE), the only integrated mark-resight model that allows for recapture sampling with replacement. Estimates of population parameters provided by the three models were then compared in terms of bias, precision and accuracy. C-MOM and ZPNE models were afterwards applied to real data collected on a rock cavy colony in the island of Fernando de Noronha. The estimated parameters were used to extrapolate the number of individuals in the rock cavy colony to the whole population in the island. Subsequently, these results were used to develop a risk assessment for the species by modelling historical and management scenarios, simulating both the establishment of the species in the island, and the consequences of different management interventions applied to it. The virtual ecology study showed that, in comparison to the CMR and the ZPNE, the C-MOM presented improved accuracy without overestimating the precision of population parameter’s estimates. The last also presented reduced amplitude of the calculated credible interval at 95% when applied to real data in comparison to the ZPNE. While the extrapolation of C-MOM estimates suggests that the rock cavy population in Fernando de Noronha is 6,652 ± 1,587, ZPNE estimates are of 5,854 ± 3,269 individuals. In the risk assessment, historical simulation models demonstrated that even though different combinations of uncertainty in reproductive parameters of the rock cavy might be possible for the species, these did not interfere significantly in either establishment or spread of the rock cavy population in the island. Moreover, historical yearly mortality has most likely been under 30%. Regarding the species’ management simulations, the most effective management interventions to achieve population extinction were spaying and neutering of both sexes, although harvest effort presented the highest influence on this populations’ extirpation. Nonetheless, the relative influence of female and both sexes’ based interventions did not differ significantly regarding the frequency of extinction of stochastic replicates’. Moreover, none of the management interventions guaranteed the population extinction within the time span and harvest effort proposed for the management program. Neutering of both sexes was most inversely influential on time to extinction of this population, followed by removal of both sexes. Briefly, the C-MOM has proven to be a resourceful and precise model to estimate population parameters when low capture rates result in sparse datasets. Moreover, the rock cavy is well established in the island and likely at carrying capacity. In general, the risk assessment showed that the management interventions in the time span and harvest effort simulated in the present study were ineffective to extinguish the rock cavy population in Fernando de Noronha. Considering this, as well as the importance of investigating other vital factors to decide in favour of or contrary to the management of this species, it is recommended that both an impact assessment of the rock cavy and a cost-effectiveness analysis of the management interventions should be performed to complement the current study.:Acknowledgement III Abstract IV Zusammenfassung VI Resumen IX Table of Contents XII List of Tables and Figures XIV List of Abbreviations XIX 1. Introduction 1 1.1. Invasive alien species and their consequences 1 1.2. Population dynamics analysis 2 Capture-recapture models 3 Observation models 4 Integrated population models 5 Software 7 Model analysis 8 1.3. Fernando de Noronha and the rock cavy 10 1.4. Objectives 12 Overall Objectives 12 Specific Objectives 13 2. Study Framework 15 3. Methods 19 3.1. Study area 19 3.2. Study case species 21 3.3. Research Steps 24 RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 24 RESEARCH STEP II: C-MOM application to a real case study 40 RESEARCH STEP III: The rock cavy population in Fernando de Noronha 45 RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 47 4. Results 63 4.1. RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 63 4.2. RESEARCH STEP II: C-MOM application to a real case study 72 4.3. RESEARCH STEP III: The rock cavy population in Fernando de Noronha 73 4.4. RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 74 Sensitivity analysis 74 Simulation experiments 80 5. Discussion 83 5.1. Bias, precision and accuracy of population dynamic models for sparse datasets 85 Simulated data 85 Study case 90 5.2. Advantages and disadvantages of the C-MOM approach 93 5.3. Development and applications of the integrated models and the C-MOM 96 5.4. The reversed use of the PVA software Vortex to simulate AS and IAS populations’ extinction 97 5.5. Status of the rock cavy population in the island of Fernando de Noronha 100 The colonization of the rock cavy in Fernando de Noronha 101 Management of the rock cavy in Fernando de Noronha 104 Study case limitations and future researches 112 6. Conclusion 116 References 118 Appendices 124 APPENDIX I – Assessment of biological invasions 124 APPENDIX II – Population dynamics simulation and dataset sampling 125 APPENDIX III – CMR and C-MOM model codes in R 134 APPENDIX IV – ZPNE model code in R 138 APPENDIX V – C-MOM model used for real datasets 143 APPENDIX VI – Rock cavy colony sizes and number of individuals in Fernando de Noronha 145 APPENDIX VII – Parameter’s ranking of C-MOM, CMR and ZPNE models 148 APPENDIX VIII – Bias, precision and accuracy table 149

The general aim of my dissertation was to investigate the role of plant interactions in driving population dynamics. Both theoretical and empirical approaches were employed. All my studies were conducted on the basis of metabolic scaling theory (MST), because the complex, spatially and temporally varying structures and dynamics of ecological systems are considered to be largely consequences of biological metabolism. However, MST did not consider the important role of plant interactions and was found to be invalid in some environmental conditions. Integrating the effects of plant interactions and environmental conditions into MST may be essential for reconciling MST with observed variations in nature. Such integration will improve the development of theory, and will help us to understand the relationship between individual level process and system level dynamics. As a first step, I derived a general ontogenetic growth model for plants which is based on energy conservation and physiological processes of individual plant. Taking the mechanistic growth model as basis, I developed three individual-based models (IBMs) to investigate different topics related to plant population dynamics: 1. I investigated the role of different modes of competition in altering the prediction of MST on plant self-thinning trajectories. A spatially-explicit individual-based zone-of-influence (ZOI) model was developed to investigate the hypothesis that MST may be compatible with the observed variation in plant self-thinning trajectories if different modes of competition and different resource availabilities are considered. The simulation results supported my hypothesis that (i) symmetric competition (e.g. belowground competition) will lead to significantly shallower self-thinning trajectories than asymmetric competition as predicted by MST; and (ii) individual-level metabolic processes can predict population-level patterns when surviving plants are barely affected by local competition, which is more likely to be in the case of asymmetric competition. 2. Recent studies implied that not only plant interactions but also the plastic biomass allocation to roots or shoots of plants may affect mass-density relationship. To investigate the relative roles of competition and plastic biomass allocation in altering the mass-density relationship of plant population, a two-layer ZOI model was used which considers allometric biomass allocation to shoots or roots and represents both above- and belowground competition simultaneously via independent ZOIs. In addition, I also performed greenhouse experiment to evaluate the model predictions. Both theoretical model and experiment demonstrated that: plants are able to adjust their biomass allocation in response to environmental factors, and such adaptive behaviours of individual plants, however, can alter the relative importance of above- or belowground competition, thereby affecting plant mass-density relationships at the population level. Invalid predictions of MST are likely to occur where competition occurs belowground (symmetric) rather than aboveground (asymmetric). 3. I introduced the new concept of modes of facilitation, i.e. symmetric versus asymmetric facilitation, and developed an individual-based model to explore how the interplay between different modes of competition and facilitation changes spatial pattern formation in plant populations. The study shows that facilitation by itself can play an important role in promoting plant aggregation independent of other ecological factors (e.g. seed dispersal, recruitment, and environmental heterogeneity). In the last part of my study, I went from population level to community level and explored the possibility of combining MST and unified neutral theory of biodiversity (UNT). The analysis of extensive data confirms that most plant populations examined are nearly neutral in the sense of demographic trade-offs, which can mostly be explained by a simple allometric scaling rule based on MST. This demographic equivalence regarding birth-death trade-offs between different species and functional groups is consistent with the assumptions of neutral theory but allows functional differences between species. My initial study reconciles the debate about whether niche or neutral mechanisms structure natural communities: the real question should be when and why one of these factors dominates. A synthesis of existing theories will strengthen future ecology in theory and application. All the studies presented in my dissertation showed that the approaches of individual-based and pattern-oriented modelling are promising to achieve the synthesis.

Работа содержит исследования трех моделей живых систем с дискретным временем. В первой главе рассматривается одномерная модель нейронной активности, задаваемая кусочно-гладким отображением. Показывается, что в случае одномерного отображения наличие случайного возмущения приводит к появлению всплесков (спайкингу). Исследуются два механизма генерации спайков, вызванных добавлением случайного возмущения в один из параметров. Иллюстрируется, что сосуществование двух аттракторов является не единственной причиной возникновения спайкинга. Для прогнозирования уровня интенсивности шума, необходимого для генерации спайков, применяется метод доверительных областей, который основан на функции стохастической чувствительности. Также находятся основные характеристики межспайковых интервалов в зависимости от интенсивности шума. Вторая глава работы посвящена применению метода функции стохастической чувствительности к аттракторам кусочно-гладкого одномерного отображения, описывающего динамику численности популяции. Первым этапом исследования является параметрический анализ возможных режимов детерминированной модели: определение зон существования устойчивых равновесий и хаотических аттракторов. Для определения параметрических границ хаотического аттрактора применяется теория критических точек. В случае, когда на систему оказывает влияние случайное воздействие, на основе техники функции стохастической чувствительности дается описание разброса случайных состояний вокруг равновесия и хаотического аттрактора. Проводится сравнительный анализ влияния параметрического и аддитивного шума на аттракторы системы. С помощью техники доверительных интервалов изучаются вероятностные механизмы вымирания популяции под действием шума. Анализируются изменения параметрических границ существования популяции под действием случайного возмущения. В третьей главе проводится анализ возможных динамических режимов детерминированной и стохастической модели Лотки-Вольтерры. В зависимости от двух параметров системы строится карта режимов. Изучаются параметрические зоны существования устойчивых равновесий, циклов, замкнутых инвариантных кривых, а также хаотических аттракторов. Описываются бифуркации удвоения периода, Неймарка--Саккера и кризиса. Демонстрируется сложная форма бассейнов притяжения. Помимо детерминированной системы подробно изучается стохастическая, описывающая влияние внешнего случайного воздействия. В случае хаоса дан алгоритм нахождения критических линий, описывающих границу хаотического аттрактора. Опираясь на найденную чувствительность аттракторов, строятся доверительные полосы и эллипсы, позволяющие описать разброс случайных состояний вокруг детерминированного аттрактора. / The work contains study of three models of biological systems with discrete time. In the first chapter a one-dimensional model of neural activity defined by a piecewise-smooth map is considered. It is shown that in the case of a one-dimensional model, the presence of a random disturbance leads to a spike generation. Two mechanisms of spike generation caused by the presence of a random disturbance in one of the parameters are investigated. It is illustrated that the coexistence of two attractors is not the only reason of spiking. To predict the level of noise intensity needed to generate spikes, the confidence-domain method is used, which is based on the stochastic sensitivity function. The main characteristics of interspike intervals depending on the intensity of the noise are also described. The second chapter is devoted to the application of the method of the stochastic sensitivity function to attractors of a piecewise-smooth one-dimensional map, which describes the population dynamics. The first stage of the study is a parametric analysis of the possible regimes of the deterministic model: determining the zones of existence of stable equilibria and chaotic attractors. The theory of critical points is used to determine the parametric boundaries of a chaotic attractor. In the case where the system is affected by a random noise, based on the stochastic sensitivity function, a description of the spread of random states around equilibrium and a chaotic attractor is given. A comparative analysis of the influence of parametric and additive noise on the attractors is carried out. Using the technique of confidence intervals, the probabilistic mechanisms of extinction of a population under the influence of noise are studied. Changes in the parametric boundaries of the existence of population under the influence of random disturbance are analyzed. In the third chapter the possible dynamic modes of the Lotka-Volterra model in determi\-nistic and stochastic cases are analyzed. Depending on the two parameters of the system, bifurcation diagram is constructed. Parametric zones of the existence of stable equilibria, cycles, closed invariant curves, and also chaotic attractors are studied. The bifurcations of the period doubling, Neimark--Sacker and the crisis are described. The complex shape of the basins of attraction is demonstrated. In addition to the deterministic system, the stochastic system is studied in detail, which describes the influence of external random disturbance. In the case of chaos, an algorithm for finding critical lines describing the boundary of a chaotic attractor is given. Based on the stochastic sensitivity function, confidence bands and ellipses are constructed to describe the spread of random states around a deterministic attractor.