Le modèle Aevol est un modèle d'évolution expérimentale in silico développé par Carole Knibbe et Guillaume Beslon pour étudier l'évolution de la structure des génomes. Aevol a permis d'identifier une très forte pression de sélection indirecte vers un certain niveau de variabilité mutationnelle du phénotype : la survie à long terme d'une lignée étant conditionnée à sa capacité à produire des mutations avantageuses sans pour autant produire trop de mutations délétères, un certain compromis entre robustesse et évolvabilité est indirectement sélectionné. Une conséquence de cette pression de sélection indirecte est le rôle central joué par le taux spontané de réarrangements chromosomiques dans la détermination de la structure du génome. Dans ce travail, nous avons modifié le modèle Aevol pour introduire d'une part un processus explicite de régulation de l'expression des gènes et d'autre part, une sensibilité aux similarités entre séquences dans les événements de recombinaison de l'ADN. Nous avons ainsi pu étudier l'effet de ces variations sur la sélection de second-ordre. Nous avons en particulier observé que celle-ci est extrêmement robuste aux choix de modélisation : les effets liés aux réarrangements sont en effet observés de la même façon lorsque les organismes possèdent un réseau de régulation (qui plus est, ces effets sont visibles sur le réseau lui-même), lorsque les réarrangements se produisent préférentiellement entre séquences similaires et lorsque les transferts horizontaux sont possibles. De plus, les effets de cette pression de sélection de second-ordre ne sont pas limités au niveau génomique : de forts taux de réarrangements tendent à donner lieu à des génomes présentant beaucoup d'opérons, très peu d'ARNs non-codants et des réseaux de régulation très simples. Au contraire, chez les organismes ayant évolué avec de faibles taux de réarrangement, la plupart des gènes sont transcrits sur des ARNs monocistroniques. Ces organismes possèdent un grand nombre d'ARNs non-codants et présentent des réseaux de régulation très complexes. Ces effets observés dans le modèle à différents niveaux d'organisation peuvent s'apparenter à de nombreuses caractéristiques observées chez les organismes réels. Ainsi les pressions sélectives indirectes observées grâce au model Aevol permettent de reproduire un large spectre de propriétés biologiques connues en ne modifiant que le seul taux de réarrangements dans le modèle. Ces mécanismes de sélection indirecte apparaissent donc comme de bons candidats pour expliquer ces mêmes observations sur les organismes réels. / The Aevol model is an in silico experimental evolution model that was specifically developped by Carole Knibbe to study the evolution of the structure of the genome. Using Aevol, a very strong second-order selective pressure towards a specific level of mutational variability of the phenotype was revealed: it was shown that since the survival of a lineage on the long term is conditionned to its ability to produce beneficial mutations while not loosing those previously found, a specific trade-off between robustness and evolvability is indirectly selected. A consequence of this indirect selective pressure is the central role played by the spontaneous rate of chromosomal rearrangements in determining the structure of the genome. More specifically, it was shown that because some rearrangements (large duplications and large deletions) have an impact not only arround their breakpoints but on the whole sequence between them, non-coding sequences are actually mutagenic for the coding sequences they surround. The consequence is a clear trend for organisms having evolved under high rearrangement rates to have very short genomes with hardly any non-coding sequences while organisms evolving in the context of low rearrangement rates have huge, mostly non-coding genomes. Here, we modified the Aevol model to introduce an explicit regulation of gene expression as well as a sensitivity to sequence similarity in DNA recombination events. We observed that the effects of the second-order pressure mentioned above are very robust to modelling choices: they are similarly observed when gene regulation is made available, when rearrangements occur preferentially between similar sequences and even when a biologically plausible process of horizontal transfer is allowed. Moreover, the effects of this second-order selective pressure are not limited to the genomic level: high rearrangement rates usually lead to genomes that have many polycistronic RNAs, almost no non-coding RNAs and very simple regulation networks. On the contrary, at low rearrangement rates organisms have most of their genes transcribed on monocistronic RNAs, they own a huge number of coding RNAs and present very complex and intricate regulation networks. These astounding effects at different levels of organization can account for many features found on real organisms. Thus, the indirect selective pressure that was identified thanks to the Aevol model allows to reproduce a large panel of known biological properties by changing the sole spontaneous rearrangement rate, making this pressure a good candidate for explaining these observations on real organisms.

Variation et sélection sont au coeur de l'évolution Darwinienne. Cependant, ces deux mécanismes dépendent de processus eux-mêmes façonnés par l'évolution. Chez les micro-organismes, qui font face à des environnements souvent variables, ces propriétés adaptatives sont particulièrement bien exploitées, comme le démontrent de nombreuses expériences en laboratoire. Chez ses organismes, l'évolution semble donc avoir optimisé sa propre capacité à évoluer, un processus que nous nommons évolution de l'évolution (EvoEvo). La notion d'évolution de l'évolution englobe de nombreux concepts théoriques, tels que la variabilité, l'évolvabilité, la robustesse ou encore la capacité de l'évolution à innover (open-endedness). Ces propriétés évolutives des micro-organismes, et plus généralement de tous les organismes vivants, sont soupçonnées d'agir à tous les niveaux d'organisation biologique, en interaction ou en conflit, avec des conséquences souvent complexes et contre-intuitives. Ainsi, comprendre l'évolution de l'évolution implique l'étude de la trajectoire évolutive de micro-organismes — réels ou virtuels —, et ce à différents niveaux d'organisation (génome, interactome, population, …). L'objectif de ce travail de thèse a été de développer et d'étudier des modèles mathématiques et numériques afin de lever le voile sur certains aspects de l'évolution de l'évolution. Ce travail multidisciplinaire, car impliquant des collaborations avec des biologistes expérimentateur•rice•s, des bio-informaticien•ne•s et des mathématicien•ne•s, s'est divisé en deux parties distinctes, mais complémentaires par leurs approches : (i) l'extension d'un modèle historique en génétique des populations — le modèle géométrique de Fisher — afin d'étudier l'évolution du bruit phénotypique en sélection directionnelle, et (ii) le développement d'un modèle d'évolution in silico multi-échelles permettant une étude plus approfondie de l'évolution de l'évolution. Cette thèse a été financée par le projet européen EvoEvo (FP7-ICT-610427), grâce à la commission européenne. / Variation and selection are the two core processes of Darwinian Evolution. Yet, both are directly regulated by many processes that are themselves products of evolution. Microorganisms efficiently exploit this ability to dynamically adapt to new conditions. Thus, evolution seems to have optimized its own ability to evolve, as a primary means to react to environmental changes. We call this process evolution of evolution (EvoEvo). EvoEvo covers several aspects of evolution, encompassing major concepts such variability, evolvability, robustness, and open-endedness. Those phenomena are known to affect all levels of organization in bacterial populations. Indeed, understanding EvoEvo requires to study organisms experiencing evolution, and to decipher the evolutive interactions between all the components of the biological system of interest (genomes, biochemical networks, populations, ...). The objective of this thesis was to develop and exploit mathematical and numerical models to tackle different aspects of EvoEvo, in order to produce new knowledge on this topic, in collaboration with partners from diverse fields, including experimental biology, bioinformatics, mathematics and also theoretical and applied informatics. To this aim, we followed two complementary approaches: (i) a population genetics approach to study the evolution of phenotypic noise in directional selection, by extending Fisher's geometric model of adaptation, and (ii) a digital genetics approach to study multi-level evolution. This work was funded by the EvoEvo project, under the European Commission (FP7-ICT-610427).

Nos estudos de populações pesqueiras é comum o uso de modelos hidrodinâmicos acoplados a modelos biológicos e, um tipo de modelo merece destaque: o baseado no indivíduo (IBM). A Plataforma Continental do Atlântico Sudoeste comporta uma importante atividade pesqueira e, a influência da circulação na distribuição de ovos/larvas nessa região é pouco entendida. Estudos anteriores sugerem que o transporte de Ekman em direção à costa e o deságue de água fluvial impedem a perda de ovos e larvas da área costeira. Este trabalho apresenta resultados de um estudo englobando os padrões de circulação e de transporte de larvas nessa área, realizado através do desenvolvimento de um IBM para os estágios iniciais da Engraulis anchoita e o acoplamento deste a dois campos de velocidade superficial: a de Ekman, e a saída de um modelo hidrodinâmico 3D. Os resultados mostram que somente a deriva de Ekman não é suficiente para explicar o padrão de retenção larval observado na região. Os valores de retenção encontrados com a utilização da saída do modelo estão próximos aos observados. Maiores concentrações larvais foram obtidas no outono/inverno e menores na primavera/verão. Estes resultados estão diretamente relacionados à combinação dos efeitos dos padrões de vento da área com a influência das Correntes do Brasil e das Malvinas e do deságue continental na circulação sobre a plataforma. / Recruitment of pelagic fishes is the net result a series of continuous events in their life cycle. Most of the variability in natural mortality is thought to occur during the early stages of development and is related to environmental factors. The use of coupled physical-biological modeling in the study of fisheries populations is very common and a particular type of model deserves special mention: the Individual Based Model (IBM). The Atlantic Southwestern Continental Shelf is one of the most productive fishing sites in the Western South Atlantic, but the processes involving the circulation in this area and its influence on eggs/larvae transport and retention are still poorly understood. Recent studies describe the spawning activity of anchovy and its relationship to oceanographic processes and suggest that predominant onshore Ekman transport, during the austral winter/spring, keeps the eggs and larvae in coastal areas. According to these studies, the river runoff contributes to the formation of a retention zone for planktonic organisms over the area. This work presents results of a study that considers both the circulation pattern and larval transport, throught the development of an IBM for the early stages of anchovy Engraulis anchoita. The model is coupled to two surface velocity fields: the Ekman drift, and the output of a 3D hydrographic model. The results show that just Ekman surface velocities are not able to explain the larval dispersion observed in this region. Retention values obtained with the model output are much closer to observed values. Autumn and winter seasons present the highest values of retention. These results are due to the combined effect of the wind patterns registered in the area with the influence of the river runoff and the Brazil-Malvinas shelf circulation.

Le déplacement animal joue un rôle déterminant dans la structuration spatiale et la dynamique des populations biologiques, en particulier des espèces fortement mobiles. L’espace et l’environnement font ainsi partie intégrante du cycle de vie des tortues marines. Ce travail de thèse propose de caractériser l’écologie spatiale des tortues marines, du stade juvénile au stade adulte, dans le Sud-ouest de l’océan Indien, principalement par l’usage de deux méthodes : la télémétrie satellitaire et la modélisation individu-centrée. Il montre en premier lieu que la phénologie de la reproduction de la tortue verte à travers la région est principalement liée à la température de surface de la mer au voisinage des sites de reproduction. Sont ensuite étudiés les patrons de dérive des nouveau-nés générés par les courants océaniques qui impacteraient inégalement leurs traits d’histoire de vie selon l’emplacement du site de naissance. Concernant le stade immature, les résultats suggèrent un cycle de développement trans-équatorial pour la tortue caouanne dans l’océan Indien. Pour le stade adulte, cette étude caractérise les couloirs et la connectivité migratoires de la tortue verte dans la région. Enfin, l’intégration de ces résultats permet de comprendre la structuration des patrons migratoires régionaux et leur influence sur la dynamique des populations. L’ensemble des connaissances acquises fournit un support concret d’aide à la décision pour la mise en place de plans de gestion et de conservation des tortues marines dans le Sud-ouest de l’océan Indien. Cela souligne l’importance d’une approche à grande échelle pour la protection d’un patrimoine biologique partagé par plusieurs nations. / Animal movement is crucial to the ecology of spatially structured population, particularly for highly mobile species. Marine turtles’ life cycle is indeed closely related to spatial and environmental factors. This work analyses the spatial ecology of marine turtles, from early juvenile to adult stages, in the Southwest Indian Ocean, primarily through the use of two methods: satellite tracking and individual-based modeling. Firstly, this analysis argues that green turtle’s reproductive phenology across the region is mainly related to the sea surface temperature in the vicinity of the nesting site. Then, it shows how drifting trajectories of hatchlings in oceanic currents unevenly influence their life history traits depending on the position of the natal site. By tracking late juvenile stage, this work also suggests a trans-equatorial developmental cycle for loggerhead turtle in the Indian Ocean. At adult stage, it describes migratory corridors and connectivity for green turtle across the region. Finally, an integrative approach considering all these results allows for an understanding of the regional migratory patterns and their influence on population dynamics. The results of this work provide a practical policy decision tool for management and conservation of marine turtles in the Southwest Indian Ocean and highlight the need for a large-scale approach in the protection of biological resources and heritage shared by multiple nations.

Nos estudos de populações pesqueiras é comum o uso de modelos hidrodinâmicos acoplados a modelos biológicos e, um tipo de modelo merece destaque: o baseado no indivíduo (IBM). A Plataforma Continental do Atlântico Sudoeste comporta uma importante atividade pesqueira e, a influência da circulação na distribuição de ovos/larvas nessa região é pouco entendida. Estudos anteriores sugerem que o transporte de Ekman em direção à costa e o deságue de água fluvial impedem a perda de ovos e larvas da área costeira. Este trabalho apresenta resultados de um estudo englobando os padrões de circulação e de transporte de larvas nessa área, realizado através do desenvolvimento de um IBM para os estágios iniciais da Engraulis anchoita e o acoplamento deste a dois campos de velocidade superficial: a de Ekman, e a saída de um modelo hidrodinâmico 3D. Os resultados mostram que somente a deriva de Ekman não é suficiente para explicar o padrão de retenção larval observado na região. Os valores de retenção encontrados com a utilização da saída do modelo estão próximos aos observados. Maiores concentrações larvais foram obtidas no outono/inverno e menores na primavera/verão. Estes resultados estão diretamente relacionados à combinação dos efeitos dos padrões de vento da área com a influência das Correntes do Brasil e das Malvinas e do deságue continental na circulação sobre a plataforma. / Recruitment of pelagic fishes is the net result a series of continuous events in their life cycle. Most of the variability in natural mortality is thought to occur during the early stages of development and is related to environmental factors. The use of coupled physical-biological modeling in the study of fisheries populations is very common and a particular type of model deserves special mention: the Individual Based Model (IBM). The Atlantic Southwestern Continental Shelf is one of the most productive fishing sites in the Western South Atlantic, but the processes involving the circulation in this area and its influence on eggs/larvae transport and retention are still poorly understood. Recent studies describe the spawning activity of anchovy and its relationship to oceanographic processes and suggest that predominant onshore Ekman transport, during the austral winter/spring, keeps the eggs and larvae in coastal areas. According to these studies, the river runoff contributes to the formation of a retention zone for planktonic organisms over the area. This work presents results of a study that considers both the circulation pattern and larval transport, throught the development of an IBM for the early stages of anchovy Engraulis anchoita. The model is coupled to two surface velocity fields: the Ekman drift, and the output of a 3D hydrographic model. The results show that just Ekman surface velocities are not able to explain the larval dispersion observed in this region. Retention values obtained with the model output are much closer to observed values. Autumn and winter seasons present the highest values of retention. These results are due to the combined effect of the wind patterns registered in the area with the influence of the river runoff and the Brazil-Malvinas shelf circulation.

Nous connaissons depuis plus d’un siècle des bouleversements climatiques, socio-économiques et sociétaux de plus en plus fréquents et intenses. L’adaptation à ce contexte incertain, pour envisager l’avenir de façon durable, est un défi particulièrement important. L’agriculture est au cœur de ce défi et de la réflexion sur les modes d’adaptation. Les anthropologues ont récemment identifié deux types de changements de l’agriculteur: le changement mineur (en accord avec le comportement normatif de référence), et le changement majeur (changement profond, remise en cause des normes majoritaires permettant l’adoption de comportements innovants). Ces deux types de changement sont très proches de l’adaptation incrémentale et de l’adaptation transformationnelle qui sont définis tant pour des individus que pour des institutions locales, nationales ou internationales … Nous proposons un modèle individu-centré de l’adaptation des agriculteurs qui intègre dynamiquement changements mineurs et majeurs, en nous focalisant sur la dimension psycho-sociale de ces changements. Nous appliquons notre modèle à la question, de la conversion à l’agriculture biologique des éleveurs laitiers français. Cette transition a en effet été généralement caractérisée comme un changement majeur, ou une adaptation transformationnelle, et s’avère donc pertinente pour tester notre modèle. Le modèle d’agriculteur est en général dans un régime stable durant lequel seuls des changements mineurs sont opérés. Ces changements sont menés en imitant des comportements adoptés par les agriculteurs les plus crédibles. La crédibilité d’un agriculteur pour un autre est d’autant plus forte que son volume produit est supérieur à celui de cet agriculteur. Ces changements se traduisent concrètement par des modifications des volumes produits qui correspondent à des choix de pratiques plus ou moins intensifs.Le modèle peut passer d’un régime stable à un autre en transitant par un changement majeur impliquant de changer la hiérarchie des importances, accordées aux dimensions « productiviste » et « environnementale », qui pondèrent son évaluation des résultats de son mode de production (par exemple : conventionnel ou biologique). Le calcul de son évaluation utilise la théorie de l’action raisonnée. Il permet à l’agriculteur de déterminer sa satisfaction, à partir de ses résultats précédents, et de ses résultats comparés à ceux de ses pairs crédibles, en tenant compte de l’importance accordées à chaque dimension d’évaluation. Lorsqu’un agriculteur est insatisfait de son mode de production courant, il évalue sa satisfaction potentielle pour un autre mode de production, et adopte ce dernier si son gain de satisfaction est supérieur à un seuil. Il change alors la hiérarchie des importances accordées à ses dimensions d’évaluation pour être en accord avec le mode adopté. Un agriculteur biologique accordera ainsi par exemple une importance plus forte à la dimension environnementale qu’à la dimension productiviste. Ce changement implique alors une réévaluation tant de la crédibilité de ses pairs que de leurs pratiques. (...) / For more than a century, climatic, socio-economic and societal changes are more and more frequent and intense. Adapting to this uncertain context to envisage a sustainable future is a particularly important challenge. Agriculture is at the heart of this challenge and the reflection on the modes of adaptation. Anthropologists have recently identified two types of farmer changes: minor change (consistent with normative behavior), and major change (deep change, challenge the majority norms allowing adoption of innovative behaviors). These two types of change are very close to the incremental adaptation and the transformational adaptation that are defined for individuals as well as for local, national or international institutions.We propose an individual-based model to study farmers’ adaptations that dynamically integrates minor and major changes. We focus on the social-psychological dimension of these changes. Our model is applied to the question of French dairy farmers’ conversions to organic farming. This transition has been characterized as a major change, or a transformational adaptation, and is therefore relevant to test our model.A farmer stays generally in a stable regime doing only minor changes. These changes are carried out by imitating the practices of the most credible farmers. The credibility of one farmer given to another is larger if his (her) produced volume is greater than that of this farmer. These changes are shown by concrete changes of produced volumes, which correspond to more or less intensive choices of practice.In the model, a farmer passes from one stable regime to another through a major change involving a change of his (her) hierarchy of importance over the "productivist" and "environmental" evaluative dimensions. The importance weights his (her) evaluation of the results according to the mode of production (for example: conventional or organic). The computation of the evaluation is based on the theory of reasoned action. This evaluation shows a farmer’s satisfaction that is based on his (her) previous results and his (her) results compared to those of his (her) credible peers, taking into account the importance given to each dimension of evaluation. When a farmer is dissatisfied with his (her) current mode of production, he (she) evaluates his (her) potential satisfaction with another mode of production, and adopts the latter if his (her) satisfaction gain is above a threshold. He (she) then changes the importance hierarchy given to the evaluation dimensions to be in agreement with the adopted mode. For example, an organic farmer will given more importance to the environmental dimension than to the productivist dimension. This change implies a reassessment of both the credibility given to his (her) peers and their practices. (...)

Biological invasions are major threats to any nation’s economy and biodiversity. To detect new biological incursions of some species biosecurity agencies deploy pheromone sentinel traps for targeted species at high risk sites such as airports, seaports and transitional facilities. A good example is the gypsy moth surveillance program in New Zealand. Following the detection of an incursion by an unwanted organism, ground-based searches to locate the source can be very expensive, but are essential to identify the introduction pathway and to increase the chances of success eradicating the unwanted organism. In such circumstances, the possibility of better targeting the search for the source of the incursion using a modelling approach is worthy of investigation A stochastic mechanistic model to hindcast moth flight from a recapture location to the release location was developed based on insect behaviour in response to wind and pheromones. The model was composed of two main processes, 1) downwind dispersal, assumed to result from an appetitive behaviour, indicated by an analysis of a previous mark-release-recapture experiment on painted apple moth (Teia anartoides, Walker) and, 2) anemotaxic dispersal inspired by pheromone anemotaxis theory but up-scaled from a fine-scaled behaviour model to a 2 m scale. A genetic algorithm was used to fit some model parameters. A specialised fitness function was developed to allow the genetic algorithm to identify parameters that resulted in models that reflected both the spread and density patterns in the trapping data. The resulting function allowed the stochastic model results to be compared with the inherently stochastic trapping data. The resulting individual based model simulates the spatio-temporal dispersal pattern of painted apple moth recorded during a previous mark-release-recapture experiment. While the proposed model is shown to have limitations with respect to accuracy and precision it is also demonstrated to greatly improve biosecurity incursion response capability, by more efficient targeting of search effort for the proximal source of an incursion.

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.

Despite their important ecosystem benefits for terrestrial and marine flora and fauna and the human livelihood mangrove forests suffer a high loss rate mainly due to human activity. Aside from these impacts, natural forest disturbances exist more commonly in mangroves compared to other forests as a direct consequence of their exposed coastal location. Within this thesis I investigate the influence of natural disturbance regimes on the mangrove forest dynamics focusing in particular on the ecological role of disturbances, disturbance patterns, forest structure, succession behavior and long-term vulnerability evaluation. The study areas were set in the Indian River Lagoon in Florida (USA) and in Can Gio an UNESCO Biosphere Reserve (Vietnam). In addition, theoretical simulation studies were carried out to complement the field studies. Thereby, in our study at the Indian River Lagoon site I investigated the ecosystem response to hurricane events of an artificially impounded mangrove forest. In Can Gio, the suitability of lightning strike – caused gaps for setting a homogenous plantation into more natural-like state according to species composition and forest structure was analyzed. Finally, a theoretical simulation study was carried out to compare lightning strike and hurricane events regarding their homogenization and heterogenization effects on the spatio-temporal forest structure. The findings of the field study in the Indian River Lagoon indicate that hurricane events had a severe impact on forest areas in higher successional stages by creating open patches, whereas areas in lower successional stages remained largely undisturbed. Furthermore, the impoundment determines the species selection of the post-hurricane succession by favoring flooding-tolerant species. However, regeneration was found to be impaired by the artificially high inundation regime at some disturbed patches. The lightning-strike disturbances enhance the species composition in the monospecific plantation in Can Gio by providing a sufficient light regime for entering seeds to establish. In addition, lightning-strike gaps increased the plantation structure complexity. Regenerating lightning-strike gaps remained as “green islands” within windthrow sites in the plantation due to their low stature and provided seeds for surrounding disturbed areas thereby accelerating their recolonization. The results of the simulation analysis of a theoretical landscape showed that in the simulated highly complex natural mature forests all disturbance regimes entail homogenization on the spatial structure compared to an undisturbed scenario. The hurricane scenario showed an increased temporal variation of the forest dynamics whereas lightning-strike gaps were not able to contribute to additional heterogeneity in the simulated area, despite of having the same tree mortality probability during disturbances. The interaction of the large-scale impoundment in the Indian River Lagoon and medium-sized hurricane events is characterized by partially impeded post-hurricane regeneration. In contrast, small-scaled lightning strikes influenced the regeneration of medium-sized windthrow sites positively within the homogenous plantation. We therefore suggest management activities aimed at creating small clearances within the plantation in Can Gio to simulate additional small-scale disturbances in order to facilitate heterogenization of the plantation structure. Natural disturbances are found to be able to enhance the species diversity and the interactions of ecological processes. In particular, where sustainable management strategies focused on maintaining ecosystem services especially in restored sites or plantations act as a supportive part. Natural disturbances are an integral component of mangrove forests and fulfill specific ecological functions. However, our findings indicate that these disturbances, on top of altered environmental conditions associated with climate change and direct human impacts, might jeopardize the natural development in unnatural forest structures as on plantations or restored sites. This thesis gives an extensive overview about the effect of various disturbances in different mangrove forest systems, including semi-natural forests and strongly modified plantations, on species composition and forest structure. Field studies and simulation analyses contribute in equal parts to the results of the thesis.

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.