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.

This thesis is presented as a collection of five papers and one report, each of which has been either published after peer review or submitted for publication. It covers a broad range of applied statistical methods, from deterministic modelling to integrated Bayesian modelling using MCMC, via bootstrapping and stochastic simulation. It also covers a broad range of subjects, from analysis of recreational fishing diaries, to genetic mark recapture for wombats. However, it focuses on practical applications of statistics to the management of wild populations. The first chapter (Hoyle and Jellyman 2002, published in Marine and Freshwater Research) applies a simple deterministic yield per recruit model to a fishery management problem: possible overexploitation of the New Zealand longfin eel. The chapter has significant implications for longfin eel fishery management. The second chapter (Hoyle and Cameron 2003, published in Fisheries Management and Ecology) focuses on uncertainty in the classical paradigm, by investigating the best way to estimate bootstrap confidence limits on recreational harvest and catch rate using catch diary data. The third chapter (Hoyle et al., in press with Molecular Ecology Notes) takes a different path by looking at genetic mark-recapture in a fisheries management context. Genetic mark-recapture was developed for wildlife abundance estimation but has not previously been applied to fish harvest rate estimation. The fourth chapter (Hoyle and Banks, submitted) addresses genetic mark-recapture, but in the wildlife context for estimates of abundance rather than harvest rate. Our approach uses individual-based modeling and Bayesian analysis to investigate the effect of shadows on abundance estimates and confidence intervals, and to provide guidelines for developing sets of loci for populations of different sizes and levels of relatedness. The fifth chapter (Hoyle and Maunder 2004, Animal Biodiversity and Conservation) applies integrated analysis techniques developed in fisheries to the modeling of protected species population dynamics - specifically the north-eastern spotted dolphin, Stenella attenuata. It combines data from a number of different sources in a single statistical model, and estimates parameters using both maximum likelihood and Bayesian MCMC. The sixth chapter (Hoyle 2002, peer reviewed and published as Queensland Department of Primary Industries Information Series) results directly from a pressing management issue: developing new management procedures for the Queensland east coast Spanish mackerel fishery. It uses an existing stock assessment as a starting point for an integrated Bayesian management strategy evaluation. Possibilities for further research have been identified within the subject areas of each chapter, both within the chapters and in the final discussion chapter.

Research Doctorate - Doctor of Philosophy (PhD) / The original contribution of this thesis is to demonstrate the use of a generalised and parsimonious approach to building individual-based computer models of ecological systems with the objective of advancing our mechanistic understanding of these systems. Two models are presented; the first, a model of predator-prey interaction, produces the expected non-linear dynamics and illustrates the importance of the timing of variable updating and individual variation for the persistence of the populations. This model is applied to two near-exclusive, cycling predator-prey systems, those of the Canadian lynx and snowshoe hare and the Fennoscandian mustelid predators and their microtine prey. The reproduction of the patterns found in the empirical data of these systems by the model suggests that the underlying mechanism of these predator-prey systems may be more simple than is suggested by other more complex models reported in the literature. The second model describes a system similar to that of a grazing herbivore in a two-dimensional space. The emergence of complex behaviour resulting from the use of space in the model, including metapopulation-like local extinction and re-population and the effects of corridors and edge qualities on the species are demonstrated. The inclusion of a graphical display of the two-dimensional space in the computer interface to the model reveals important details of system behaviour not evident in the population means, including herding behaviour. The latter is dependent on herbivore mobility and the re-growth of resources in an heterogeneous environment, and emerges in the absence of social behaviour. The problem of detecting herding behaviour automatically is addressed, including the development of qualitative and quantitative definitions of herding in the model.

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

No description available.

La faible représentation de la biodiversité dans les modèles de végétation a longtemps été un obstacle à la compréhension et à la projection des processus écosystémiques. La forte biodiversité des forêts tropicales, leur rôle clé dans les cycles biogéochimiques globaux, ainsi que leur vulnérabilité aux perturbations anthropiques directes et indirectes, amplifient les difficultés et enjeux de ces questions de recherche. En particulier, l'augmentation prédite de la fréquence et de l'intensité des sécheresses pourrait impacter la structure et composition floristique de ces forêts, comme dors et déjà observé au cours d'expériences naturelles et artificielles. Cette thèse explore ces questions de recherche à travers deux approches complémentaires, de modélisation et de mesures écophysiologiques. Dans le premier chapitre, je décris un simulateur de croissance forestière individu-centré et spatialement-explicite, TROLL, qui intègre les progrès récents en physiologie des plantes. Les processus sont paramétrés à l'aide de traits fonctionnels espèce-spécifiques, pour une forêt tropicale amazonienne. Une régénération forestière est simulée, et validée par des observations faites en Guyane française. La sensibilité du modèle à plusieurs paramètres globaux clés est évaluée. Enfin, l'influence de la variation de la richesse et composition spécifiques sur les propriétés écosystémiques est explorée. La réponse des forêts tropicales à la sécheresse est mal connue, empêchant la représentation pertinente des processus en jeu dans les modèles de végétation. Les chapitres 2 à 5 de cette thèse ont ainsi pour but de documenter la tolérance à la sécheresse et sa diversité dans une forêt amazonienne. Une méthode récente et rapide de détermination d'un trait de tolérance des feuilles à la sécheresse, le potentiel hydrique des feuilles au point de perte de turgescence (ptlp), est validée et utilisée, permettant de quantifier pour la première fois un tel trait de tolérance à la sécheresse dans une forêt amazonienne à l'échelle de la communauté. Ce jeu de données permet l'exploration des déterminants de la tolérance à la sécheresse des feuilles, à travers les espèces d'arbres, les tailles des individus, les stades de succession, les expositions à la lumière, ainsi que les lianes. La variabilité de ptlp observée suggère une large diversité de réponses à la sécheresse au sein des communautés de plantes amazoniennes. Ceci est confirmé par le suivi direct du flux de sève au cours d'une saison sèche sur divers arbres de canopée. Enfin, je discute les implications de ces résultats pour le développement des futurs modèles de végétation. / A great part of uncertainties in our current understanding and projections of the carbon cycle lies in the vegetation compartment. The problem of biodiversity representation in vegetation models has long been an impediment to a detailed understanding of ecosystem processes. The high biodiversity of tropical forests, their disproportionate role in global biogeochemical cycles, together with their vulnerability to direct and indirect anthropogenic perturbations, amplify the relevance of this research challenge. In particular, the predicted increase in drought intensity and frequency in the tropics may impact forest structure and composition, as already observed in natural and artificial experiments. This thesis explores how new advances in modelling and ecophysiology should help improve our understanding of these processes in the future. In the first chapter, I describe an individual-based and spatially-explicit forest growth simulator, TROLL, that integrates recent advances in plant physiology. Processes are linked to species-specific functional traits parameterized for an Amazonian tropical rainforest. This model is used to simulate a forest regeneration, which is validated against observations in French Guiana. Model sensitivity is assessed for a number of key global parameters. Finally, we test the influence of varying the species richness and composition on ecosystem properties. Tropical forest response to drought is not well understood, and this hampers attempts to model these processes. In chapters 2 to 5 I aimed at documenting drought-tolerance and its diversity in an Amazonian forest. A rapid method of determination of a leaf drought tolerance trait, the leaf water potential at turgor loss point (ptlp), was validated and applied to a range of plant species. We established the first community-wide assessment of drought tolerance in an Amazonian forest. These results inform on the drivers and determinants of leaf drought tolerance, across tree species and lianas, tree size, successional stages, light exposition, and seasons. Variability in ptlp among species indicates the potential for a range of species responses to drought within Amazonian forest communities. This is further confirmed by direct monitoring of whole-plant water use on diverse canopy trees during a marked dry season. Finally, I discuss the implications of these results to increase the dialogue between the vegetation modeling community and ecology, to enhance model's predictive ability, and to inform policy choices.

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.

Les changements climatiques ont un impact certain sur les écosystèmes marins. Un déplacement vers le sud des principaux systèmes de front servant de sites de nourrissage pour de nombreuses espèces de prédateurs supérieurs est susceptible de se produire dans les zones subantarctiques. Les « central place foragers », tels que les pinnipèdes, sont susceptibles de faire face à une augmentation de la distance entre leurs lieux d'alimentation et leurs colonies d'élevage. Nous avons étudié l’impact des changements climatiques sur le succès d’élevage et la dynamique de population des otaries à fourrure (Arctocephalus gazella) des Îles Kerguelen par le biais du développement du modèle individu centré, MarCPFS (Marine Central Place Foragers Simulator) qui montre que la survie du couple femelle-jeune est particulièrement sensible à la répartition des proies (abondance et structure), à la capacité de mémorisation des meilleurs sites de nourrissages trouvés par la femelle pendant la période d'élevage, à la taille des femelles et à la distance qu'il faut parcourir pour trouver la ressource. Les résultats suggèrent qu’au cours des trois prochaines décennies un déplacement vers le sud supérieur à 2km an 1 pourrait compromettre la survie et la durabilité des populations. Un couplage avec un modèle de simulation de la dynamique océanique et de la ressource (SEAPODYM) a permis des projections jusqu’à la fin de ce siècle basées sur le scénarios RCP8.5 du GIEC (2014), confirmant les tendances mises à jour précédemment. Ces travaux montrent que les perspectives de maintien des populations sont pessimistes y compris en envisageant une adaptation de la taille des individus. / Climate change has certain impact on the marine ecosystems. A southward shift in productive frontal systems serving as the main foraging sites for many top predator species is likely to occur in the Subantarctic areas. Central place foragers, as seabirds and pinnipeds, are thus likely to cope with an increase in the distance between foraging locations and their land-based breeding colonies. We studied the impact of climate change on the breeding success and population dynamics of Antarctic fur seals (Arctocephalus gazella) at Kerguelen Islands by means of an individual based model we developped, MarCPFS (Marine Central Place Foragers Simulator) which showed that the survival of the female-pup pair is particularly sensitive to the distribution of preys (abundance and structure), to the memorization abilities of the best resource sites found by the female during the rearing period, to the female size and to the foraging distance which it is necessary to cover at each trip. The results suggest that during the next three decades a southward shift greater than 2 km year-1 could compromise the survival and the sustainability of the populations. A coupling with a model of simulation of the oceanic dynamics and the resource (SEAPODYM) allowed projections till the end of this century based on scenarios RCP8.5 of the IPCC (2014), confirming the trends previously obtained. Globally, these works lead us to conclude with pessimistic perspectives about the sustainability of populations even when considering an evolution through time towards individuals of greater sizes.

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

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