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.

Die Gattung Daphnia nimmt eine zentrale Position im pelagischen Nahrungsnetz vieler Standgewässern (Seen, Talsperren) ein. Aufgrund hoher Filtrierleistungen sind Daphnien für das integrierte Gewässermanagement, z.B. im Rahmen einer Nahrungskettenmanipulation (Biomanipulation), von großem Interesse. Ihre relativ einfache Kultivierbarkeit machte sie außerdem zu einen weit verbreiteten Modellorganismus limnologischer Grundlagenforschung. Das Ziel dieser Arbeit besteht darin, ein umfassendes Modellsystem für die Gattung Daphnia zu entwickeln, das wesentliche Kenntnisse der Ökologie von Daphnia miteinander verknüpft, um eine Vernetzung des Wissens zu realisieren. Bestehende Modellansätze konnten diese Aufgabe nur unzureichend erfüllen, weil sie in der Regel einem "Problem-orientierten Ansatz" folgen und somit sehr unterschiedliche inhaltliche Ausrichtungen und verschiedene Modellstrukturen aufweisen. Eine Kopplung bzw. ein direkter Vergleich dieser Modelle ist deshalb in der Regel schwierig. Dieses Modellsystem wurde entwickelt, um ein Instrument zur Synthese des vorhandenen Prozesswissens bereitzustellen, und nicht, um ein spezifisches, abgegrenztes Problem zu bearbeiten; es steht somit diametral zu existierenden Ansätzen. Aus diesem Grunde wird der gewählte Ansatz als ein "Spezies-orientierter Ansatz" bezeichnet. Drei Eigenschaften charakterisieren diesen Ansatz. (i) Das Modellsystem umfasst mehrere hierarchische Ebenen biologischer Organisation, wobei der Schwerpunkt auf den Ebenen des Individuums und der Population liegt. Interaktionen zwischen diesen Organisationsebenen sind ausgeprägt und in Feld- und Laborstudien gut belegt, in existierenden Modellen aber noch unzureichend miteinander verknüpft. (ii) Da eine quantitative Interpretation der Ergebnisse beabsichtigt ist, wurden die Modellausgaben einer umfangreichen Validation an unabhängigen und bereits publizierten Daten unterzogen. (iii) Das Modellsystem zeichnet sich durch einen geschachtelten Aufbau aus (nested design), wodurch eine einfache Erweiterbarkeit des Modells oder auch die separate Anwendung bestimmter Modellkomponenten gewährleistet ist. / The scope of this thesis was to develop a comprehensive model system of the genus Daphnia, a key organism in the pelagic food web of lakes and reservoirs and a widely used model organism in experimental and theoretical ecology. Although its central role in applied and basic research in aquatic ecology is obvious, there are still fundamental problems in modelling the observed dynamics of Daphnia (for details see chapter 2). Therefore, a basic motivation of this work was to use scientific results obtained in independently conducted research for developing a model that brings these results into context. Instead of following a "problem-oriented" paradigm applicable to a single, well defined problem or scientific hypothesis, the underlying concept of the emerging model system was considered to be "species-oriented". Thus, various relevant processes are included into the framework in order to simulate the dynamics of daphnids displayed on different levels of biological organization. To facilitate its application to various problems in ecological research on the genus Daphnia, the model system fulfills the following three important properties: (1) model outputs are thoroughly validated on experimental data in order to guarantee sound quantitative outputs of the model system (2) the system spans over different levels of biological organization with special emphasis laid upon the individual level and the population level (3) the model´s architecture follows a nested design with a defined individual level model that is integrated into a population level model The whole model system is able to describe an individual´s development over time on basis of physiological properties of the organism and, furthermore, how these individual level processes interact with the dynamics on the population level. Due to its nested design, applications of separate submodels (e.g. the individual-level model) are possible.