The central question addressed in this thesis is whether descriptions of the dynamics of ecological systems at one scale may be effectively used as descriptions of the dynamics of ecological systems at larger scales. This question is addressed in the context of the dynamics of fungal communities. A simple experimental system and complementary theoretical approach, in the form of an individual-based (cellular automaton) model, is presented. Experimental results derived from small-scale systems are used to quantify parameters of the model; results from large-scale experimental systems serve to test the model. The theoretical analyses clearly demonstrate that the dynamics observed are a result of both local and non-local features of the experimental system. In cases such as this the immediate extrapolation of results derived from xperiments conducted out of the context of the community to represent system scale behaviour is not possible. In response to this observation a generic framework is developed to allow the consideration of effects at a range of scales through contextual parameterisation of localised dynamics. The framework is directed toward plant systems where a large body of experimental data exists, and may be parameterised by that experimental data. It represents the essential features of individual interactions in terms of competition for space and resource, and the behaviour of a given plant is described in terms of functional traits. Model runs demonstrate complex community patterns suggestive of a known biological phenomena, succession, that arises as a consequence of the coupling between the community and environment. This coupling may allow the long-term coexistence of species through some particular balance in individual function (traits) across the community. A search mechanism is determined to allow combinations of trait values at the scale of the individual to be assessed for a particular community-scale phenomenon. Initial results demonstrate that this mechanism may identify and converge on combinations of trait values that give rise to, in this case, a simple measure of diversity. The manner in which the generic framework developed may be applied to further the investigation into fungal community dynamics is addressed.

A perda e fragmentação de habitats são, atualmente, as principais ameaças à conservação da biodiversidade. Espécies que outrora tinham sua distribuição contínua são forçadas a sobreviver de forma segmentada, em populações menores e mais susceptíveis à extinção. Segundo a teoria de metapopulações, se extinções locais em fragmentos específicos puderem ser compensadas por recolonizações provenientes de populações adjacentes, uma espécie pode persistir apesar da fragmentação. Extinções e recolonizações são processos que dependem da estrutura da paisagem. Fragmentos pequenos e com baixa qualidade de habitat possuem maior probabilidade de extinção, assim como paisagens pouco conectadas e com alta resistência à dispersão de indivíduos têm menores taxas de recolonização. Modelos de dinâmica populacional espacialmente explícitos (MVPEE) possibilitam a análise da influência de diferentes tipos de paisagens sobre a persistência de espécies, contribuindo na decisão de estratégias para sua conservação. Esta tese teve o objetivo de identificar os fatores que afetam a persistência de três espécies de aves florestais endêmicas à Mata Atlântica (Chiroxiphia caudata, Xiphorhyncus fuscus e Pyriglena leucoptera) através de um MVPEE. Foram estudadas quatro paisagens do Planalto Atlântico de São Paulo que possuem florestas fragmentadas. A técnica de play-back foi utilizada para atestar a presença ou ausência das aves em 80 fragmentos dispersos por essas paisagens. Esses dados foram utilizados para gerar modelos logísticos de incidência capazes de estimar sua probabilidade de ocorrência de acordo com a cobertura e arranjo espacial da paisagem circundante. Ademais, o padrão de movimentação das aves entre fragmentos florestais foi determinado através de experimentos de play-back que as induziu a transpor a matriz, e pela translocação de indivíduos acompanhados por radio-telemetria. Os modelos de incidência indicaram que a probabilidade de ocorrência das aves em locais de matas fragmentadas depende em larga escala da distribuição espacial dos remanescentes florestais, sendo maior em locais onde o isolamento dos fragmentos é baixo. Esse efeito torna-se ainda mais importante em locais onde os fragmentos não são grandes o suficiente para prover as aves com todos os recursos necessários, forçando-as a buscá-los em matas adjacentes, mas não muito distantes entre si a ponto de coibir sua movimentação. Essa capacidade das aves de transpor a matriz inter-habitat, alcançando florestas próximas, foi confirmada pelos estudos de movimentação. As espécies estudadas são capazes de se movimentar entre fragmentos florestais próximos, mostrando-se ainda capazes de utilizar corredores de habitat ou árvores isoladas para facilitar sua passagem pela paisagem. Esses resultados indicam que os territórios das espécies estudadas podem incluir fragmentos isolados, porém funcionalmente conectados pela movimentação das aves, sendo que as condições mínimas para o estabelecimento destes territórios em termos de quantidade e espaçamento das florestas variam em função da espécie. Esses resultados, somados às informações bibliográficas sobre a biologia das espécies estudadas, foram utilizados para guiar a construção de um MVPEE ecologicamente calibrado, onde as células da paisagem foram definidas como sendo os territórios potenciais das aves. Esse modelo de viabilidade se mostrou de grande utilidade para avaliar os efeitos de variações estruturais da paisagem sobre a persistência de populações de pequenas aves territoriais. Simulações conduzidas tanto com paisagens artificiais como reais indicaram que, em uma escala espacial ampla, a persistência dessas espécies está em grande parte sujeita à quantidade de territórios que a paisagem pode suportar, mas não à sua agregação. No entanto, o aumento da densidade de florestas na paisagem leva a um aumento na quantidade de territórios possíveis, afetando positivamente a persistência das espécies. O MVPEE desenvolvido para esta tese permitiu conciliar uma análise estrutural de paisagens com a modelagem de dinâmicas populacionais, o que é considerado como um dos assuntos prioritários de pesquisa em ecologia de paisagens. / Habitat loss and fragmentation are currently the most important threats to the conservation of biodiversity. These processes may generate patchy landscapes where several species are forced to survive in small and isolated populations, which are very susceptible to local extinctions. According to the metapopulation theory, if local extinctions in specific patches can be compensated by re-colonization from surrounding populations, a species can persist despite fragmentation. Extinctions and re-colonizations are processes that depend directly on landscape structure. Small patches with low habitat quality have increased extinction probabilities, while poorly connected landscapes with high resistance to the dispersal of individuals have decreased re-colonization rates. Spatially explicit population viability models (SEPVM) allow analyses of the influence of different types of landscapes on the persistence of species, contributing to conservation strategies decision making. The objective of the current thesis was to identify the factors which affect the persistence of three forest bird species endemic to the Atlantic forest (Chiroxiphia caudata, Xiphorhynchus fuscus and Pyriglena leucoptera) through a SEPVM. Four different fragmented landscapes of the Atlantic plateau of São Paulo were chosen for this study. The playback technique was used to assess the incidence of the birds inside 80 forest fragments in these landscapes. These data were used to derive logistic incidence models to estimate their occurrence probabilities according to the cover and spatial pattern of the surrounding landscape. Furthermore, the movement pattern of the birds between forest fragments was inferred from playback experiments which induced birds to overcome the matrix, and through the translocation of individual birds which were followed by radio-telemetry. The incidence models indicated that the occurrence probability of the birds in places of fragmented habitat depends in large scale on the spatial distribution of forest remnants, being higher where patch isolation is low. This effect becomes even more important in places where habitat patches are not big enough to provided the birds with sufficient resources, forcing them to search for it in nearby forests, which shall not be further away than the birds\' aptitude to move through the landscape. Their ability to overcome the inter-habitat matrix, reaching close by forests, was confirmed by the experiments on individuals\' movements. The studied species are able to move between nearby forest patches, being even able to use habitat corridors or isolated trees to ease their passage through the landscape. These results indicate that the territories of the studied species can include isolated patches which are connected by birds\' movement. Also, the minimum conditions to the establishment of these territories in terms of amount and aggregation of forests varies according to the species. These results, added to bibliographical information on the studied birds\' biology, were used to guide the development of an ecologically scaled SEPVM, in which the landscape cells were defined as potential bird territories. This viability model was greatly useful to assess the effects of landscape structural changes on the persistence of small territorial birds\' populations. Simulations using both artificial and real landscapes indicated that, in a wide landscape scale, the persistence of these species is largely subjected to the amount of territories the landscape can bear, but not to its aggregation. Nevertheless, increases of forest density lead to a higher amount of possible territories, positively affecting the persistence of the species. The SEPVM developed for the current thesis allowed the reconciliation of a structural analysis of the landscape to dynamical population modeling, what is considered as a top priority research subject in landscape ecology.

Um dos maiores impactos antrópicos aos ecossistemas terrestres é a fragmentação do habitat. Este processo afeta fortemente os padrões de movimentação das espécies, implicando em alterações consideráveis na conectividade entre as manchas de habitat remanescentes. Por sua vez, isso interfere na distribuição espacial e na dinâmica das populações de uma espécie. Nesta dissertação, foram estudados alguns aspectos dos movimentos rotineiros e dispersivo de Pyriglena leucoptera, uma espécie de ave endêmica da Mata Atlântica. Estes dois tipos de movimentação atuam em escalas distintas, afetando diferentemente os parâmetros que regulam a estrutura das populações. Com o uso da técnica de playback, foi verificado se a capacidade desta espécie atravessar áreas abertas, em movimentos rotineiros entre fragmentos, é afetada pela distância entre eles. A partir desta relação, foram obtidas probabilidades de cruzar áreas abertas, as quais foram usadas para parametrizar índices de conectividade funcional (um binário e outro probabilístico) baseados na teoria dos grafos. Em uma abordagem de seleção de modelos, estes dois índices de conectividade mais um outro estrutural (i.e. área do fragmento) foram comparados para se estabelecer qual deles melhor prediz a incidência de P. leucoptera em fragmentos florestais. Quanto aos movimentos dispersivos, foram realizados experimentos de translocação e telemetria para verificar se a dispersão desta espécie em áreas fragmentadas é afetada pela distância entre os fragmentos, assim como para averiguar se este efeito é diferente entre os sexos. Os resultados mostraram que distância entre os fragmentos florestais limita tanto a movimentação rotineira, quanto a dispersiva para esta espécie. Na escala dos movimentos rotineiros, verificou-se que fragmentos distanciados a mais de 45 m estão totalmente isolados. A incidência da espécie foi melhor descrita pelo índice de conectividade funcional probabilístico (PCS), mostrando que a conectividade é fundamental para se compreender a distribuição espacial da espécie, sendo que este atributo da paisagem deve ser visto de forma probabilística. Ademais, a dispersão foi enviesada para fêmeas, as quais possuíram maior propensão a emigrar, assim como foram mais eficientes em sua movimentação pela matriz. As conseqüências deste viés foram discutidas, destacando-se que, em áreas altamente fragmentadas, a probabilidade de colonização de áreas desocupadas diminui, bem como o fluxo gênico entre as populações da espécie pode estar comprometido. Portanto, ambos os tipos de movimento devem ser considerados para que se possa compreender mais precisamente os efeitos da conectividade do habitat para a sobrevivência de uma espécie em paisagens fragmentadas. Por fim, foi sugerido um modelo hierárquico de estrutura populacional, a fim de integrar as informações obtidas pelos dois tipos de movimentação em uma única estrutura conceitual. Esse modelo possui um grande potencial para ser usado no planejamento e manejo ambiental. / Habitat fragmentation is one of the major human impacts on terrestrial ecosystems. This process highly affects the species movement pattern, implying in considerable alterations on the connectivity between the remaining habitat patches. Consequently, it interferes in the spatial distribution and in the population dynamics of species. In this dissertation, some aspects of the routine and dispersal movements of Pyriglena leucoptera, an endemic bird of the Atlantic rainforest, were studied. These two movement types act in distinct scales, affecting, differently, the parameter regulating the structure of the populations. Using the playback technique, we verified if the gap-crossing capacity of this species, by routine movements, is affected by gap width. From this relation, we obtained gap-crossing probabilities, which were used to parameterize functional connectivity indices (one binary and one probabilistic) based on graph theory. In a model selection approach, these two indices plus another structural one (i.e. patch area) were compared to establish which one is the best to predict P. leucopteras incidence in forest fragments. About the dispersal movements, we done translocation and telemetry experiments to investigate if the species dispersal ability in fragmented landscapes is affected by the distance between forest patches, and to verify if there are sexual differences in this effect. The results showed that distance between forest patches limits both the routine movements and the dispersal one to this species. In the routine movements scale, we verified that patches are completely isolated when the gap width is higher than 45 m. The species incidence was better described by the probabilistic connectivity index (PCS), evincing that it is essential to consider connectivity to understand the spatial distribution of P. leucoptera, and this attribute must be viewed in its probabilistic form. Furthermore, dispersal is female-biased, since females are more prone to emigrate and were more efficient in their movement in the matrix. We discussed the consequences of this sex-bias, highlighting that, in severely fragmented landscapes, the colonization probability of empty patches is decreased and the genetic flux between populations should be imperiled. Thus, to comprehend the effects of habitat connectivity on species survival in fragmented landscapes, both movement types must be considered. Finally, we suggested a hierarchically structured population model in order to integrate the two movement type information in one conceptual framework. This model has a great potential to be used in environmental planning and management.

In the management of agricultural insect pests, short-term costs must be balanced against long-term benefits. Controls should be selected to account for both their immediate and downstream effects upon the demography and genetics of the pest, enabling suppression today without threatening suppression tomorrow. The iterative, algorithmic method of dynamic programming can provide optimal solutions to problems of this type, in which actions are taken sequentially and each action may influence those which follow it. However, this approach is fundamentally constrained with regards to the magnitude of the problems it may solve. As questions of insect pest management can be subject to ecological and evolutionary complexities, this may place them beyond the scope of dynamic programming. When it is the intricacies of a problem that are of interest, it may be more productive to utilise approximate dynamic programming (ADP) methods which can attempt problems of arbitrary complexity, although at the expense of no longer guaranteeing optimality. In this thesis I first challenge a dynamic programming algorithm with the management of a hypothetical insect pest feeding upon a transgenic insecticidal crop. The model explores how different realisations of fitness costs to resistance influence the algorithms suggested actions. I then apply a brute-force variant of ADP, a lookahead policy, to the management of a stage-structured, continuously reproducing pest population. This was to explore the extent to which an algorithm with a limited temporal perspective is able to balance the timetable of pest demography against the timescale over which insecticidal sprays and bisex-lethal sterile insect releases unfold. This same decision framework is then applied to a modified problem in which resistance to insecticidal toxins may evolve and releases are now male-selecting. This was used to assess the efficacy with which simple lookahead policies utilise a control with delayed benefits (the male-selecting releases) and possible constraints on their capacity to respond to resistance evolution. Dynamic programming and ADP methods offer a versatile toolbox for accounting for the potential impacts of the evolutionary and ecological peculiarities of particular pests upon control decisions.

Um dos maiores impactos antrópicos aos ecossistemas terrestres é a fragmentação do habitat. Este processo afeta fortemente os padrões de movimentação das espécies, implicando em alterações consideráveis na conectividade entre as manchas de habitat remanescentes. Por sua vez, isso interfere na distribuição espacial e na dinâmica das populações de uma espécie. Nesta dissertação, foram estudados alguns aspectos dos movimentos rotineiros e dispersivo de Pyriglena leucoptera, uma espécie de ave endêmica da Mata Atlântica. Estes dois tipos de movimentação atuam em escalas distintas, afetando diferentemente os parâmetros que regulam a estrutura das populações. Com o uso da técnica de playback, foi verificado se a capacidade desta espécie atravessar áreas abertas, em movimentos rotineiros entre fragmentos, é afetada pela distância entre eles. A partir desta relação, foram obtidas probabilidades de cruzar áreas abertas, as quais foram usadas para parametrizar índices de conectividade funcional (um binário e outro probabilístico) baseados na teoria dos grafos. Em uma abordagem de seleção de modelos, estes dois índices de conectividade mais um outro estrutural (i.e. área do fragmento) foram comparados para se estabelecer qual deles melhor prediz a incidência de P. leucoptera em fragmentos florestais. Quanto aos movimentos dispersivos, foram realizados experimentos de translocação e telemetria para verificar se a dispersão desta espécie em áreas fragmentadas é afetada pela distância entre os fragmentos, assim como para averiguar se este efeito é diferente entre os sexos. Os resultados mostraram que distância entre os fragmentos florestais limita tanto a movimentação rotineira, quanto a dispersiva para esta espécie. Na escala dos movimentos rotineiros, verificou-se que fragmentos distanciados a mais de 45 m estão totalmente isolados. A incidência da espécie foi melhor descrita pelo índice de conectividade funcional probabilístico (PCS), mostrando que a conectividade é fundamental para se compreender a distribuição espacial da espécie, sendo que este atributo da paisagem deve ser visto de forma probabilística. Ademais, a dispersão foi enviesada para fêmeas, as quais possuíram maior propensão a emigrar, assim como foram mais eficientes em sua movimentação pela matriz. As conseqüências deste viés foram discutidas, destacando-se que, em áreas altamente fragmentadas, a probabilidade de colonização de áreas desocupadas diminui, bem como o fluxo gênico entre as populações da espécie pode estar comprometido. Portanto, ambos os tipos de movimento devem ser considerados para que se possa compreender mais precisamente os efeitos da conectividade do habitat para a sobrevivência de uma espécie em paisagens fragmentadas. Por fim, foi sugerido um modelo hierárquico de estrutura populacional, a fim de integrar as informações obtidas pelos dois tipos de movimentação em uma única estrutura conceitual. Esse modelo possui um grande potencial para ser usado no planejamento e manejo ambiental. / Habitat fragmentation is one of the major human impacts on terrestrial ecosystems. This process highly affects the species movement pattern, implying in considerable alterations on the connectivity between the remaining habitat patches. Consequently, it interferes in the spatial distribution and in the population dynamics of species. In this dissertation, some aspects of the routine and dispersal movements of Pyriglena leucoptera, an endemic bird of the Atlantic rainforest, were studied. These two movement types act in distinct scales, affecting, differently, the parameter regulating the structure of the populations. Using the playback technique, we verified if the gap-crossing capacity of this species, by routine movements, is affected by gap width. From this relation, we obtained gap-crossing probabilities, which were used to parameterize functional connectivity indices (one binary and one probabilistic) based on graph theory. In a model selection approach, these two indices plus another structural one (i.e. patch area) were compared to establish which one is the best to predict P. leucopteras incidence in forest fragments. About the dispersal movements, we done translocation and telemetry experiments to investigate if the species dispersal ability in fragmented landscapes is affected by the distance between forest patches, and to verify if there are sexual differences in this effect. The results showed that distance between forest patches limits both the routine movements and the dispersal one to this species. In the routine movements scale, we verified that patches are completely isolated when the gap width is higher than 45 m. The species incidence was better described by the probabilistic connectivity index (PCS), evincing that it is essential to consider connectivity to understand the spatial distribution of P. leucoptera, and this attribute must be viewed in its probabilistic form. Furthermore, dispersal is female-biased, since females are more prone to emigrate and were more efficient in their movement in the matrix. We discussed the consequences of this sex-bias, highlighting that, in severely fragmented landscapes, the colonization probability of empty patches is decreased and the genetic flux between populations should be imperiled. Thus, to comprehend the effects of habitat connectivity on species survival in fragmented landscapes, both movement types must be considered. Finally, we suggested a hierarchically structured population model in order to integrate the two movement type information in one conceptual framework. This model has a great potential to be used in environmental planning and management.

Lake Erie has undergone a substantial amount of ecosystem changes over the past century; including cultural eutrophication and several invasions by industrious exotic species. Simple mass balance models for phosphorus have been useful in guiding policy decisions that led to reduced eutrophication, but new, confounding threats to the ecological health of Lake Erie continue to appear and lake managers continue to need useful tools to better understand the lake. As more complex ecological questions are asked to guide future management decisions, more complex ecological models are developed in an effort to provide some clues. The walleye fishery in Lake Erie is economically very important. Walleye recruitment has been highly variable from year to year since the 1990s. Modelling zooplankton is desired as a diagnostic tool for elucidating the quality of habitat – spatially and temporally – that is available to walleye in their vulnerable larval state. ELCOM-CAEDYM (or ELCD) is a 3-dimensional, coupled hydrodynamic and ecological model, which has been successfully applied to Lake Erie to model the nutrients and phytoplankton. The objectives of this study were to better understand the ELCOM-CAEDYM model of Lake Erie through a sensitivity analysis (SA), which has not been done before, and to explicitly simulate zooplankton in this model. An SA is important for determining which of the uncertain parameters have the greatest impact on the output variables. Due to the complexity of the CAEDYM model and the highly interdependent functions and variables modelled, a local SA (comparing changes in output by perturbing parameters one-at-a-time from some baseline configuration) was not desirable. Local SA’s ignore the possibility of a parameter’s effects being correlated to the status of other parameters. However, quantitative global methods are enormously computationally expensive for a complex model. The Lake Erie ELCD model simulates temperature, mixing, nutrient cycles, and phytoplankton dynamics. Phytoplankton are represented by 5 functional groups. With the explicit inclusion of 2 functional groups of zooplankton (copepods and cladocerans), the model uses over 300 function parameters in addition to requiring meteorological data and river inflow characteristics throughout the simulation. The model is set up with a 2-km grid over 40 layers with a 5-minute timestep from April 11 to September 1. This full simulation takes 6 days to complete. A quantitative global method to evaluate all parameters potentially significant to zooplankton would be impossible. The Morris method was selected for its streamlined global sampling procedure combined with the manageable computational demands of a one-at-a-time analysis. This method provides the relative sensitivity of diagnostic outputs to perturbed parameters. Ninety-one parameters were selected to be evaluated in 3680 simulations for the Morris SA. The selection of which parameters to evaluate and their assigned ranges are critical components in any SA. The ranges for parameters that represent a measurable quantity were assessed based on observed values in Lake Erie and other relevant studies. For some parameters, a measured realistic range was unknown. In these cases, values from relevant published models or judgements based on experience with the ELCD-Erie model were used to choose a suitable range. To assess the sensitivity of CAEDYM variables to parameters, DYRESM was substituted for ELCOM to vastly decrease the computation time of a single run. DYRESM is not suitable to model the entire lake due to the large size and irregular shape of the entire lake. Therefore, only the West Basin was modelled and analysed using DYCD. The West Basin was of special interest for a sensitivity analysis of CAEDYM parameters with respect to zooplankton because it is an important area for walleye larval development. DYCD output profiles for temperature, total chlorophyll a (TChla as a surrogate for total phytoplankton concentration) were similar in magnitudes and seasonal dynamics compared to ELCD outputs in deep West Basin stations. The sensitivity of zooplankton, TChla and TP to each parameter was assessed using two single value diagnostics: the simulated seasonal maximum and the simulated day on which peak maximum was reached. Zooplankton were sensitive to almost all of the zooplankton parameters perturbed in the analysis. This may indicate that modelling zooplankton is extremely complex, relying on many dynamic processes, or that evaluated ranges were not constrained well enough. An example of sensitivity to a poorly known parameter is the messy feeding coefficient. Reducing the uncertainty of this parameter would improve the confidence in the zooplankton assimilation submodel. Other parameters that stood out for being especially significant to zooplankton were: the respiration rate, mortality rate, internal phosphorus to carbon ratio, the temperature multiplier and standard temperature for feeding dynamics, and the half saturation constant. Most of these are easily explained as they directly aid or impede growth or they directly affect zooplankton losses. The most significant phytoplankton parameters on TChla and zooplankton outputs were, not surprisingly, the maximum growth rate and the mortality and respiration coefficient. Some particulate matter parameters proved to be important to outputs as well. More than 2500 of the 3680 parameter configurations resulted in unrealistic zooplankton simulations: peak values that did not much exceed initial conditions on the first day of the simulation. The SA exercise pinpointed a few configurations that resulted in reasonable peak zooplankton values and timing; these runs were used as a starting point for calibrating the ELCD model. Parameters were further manually adjusted by quickly checking their impacts on DYCD before applying them to ELCD. Post SA and minor calibration, the modelled zooplankton results were dramatically better than initial modelling attempts prior to the SA. Zooplankton concentrations throughout the lake were close to measured ranges and in some parts of the lake seasonal patterns were also similar to measured patterns. Modelled zooplankton results were least consistent with observations in the south west area of the lake: zooplankton were overestimated in late June-early July and they subsequently crashed and were underestimated in late July-August. It is supposed that this is due to higher grazing pressure from fish larvae in that area of the lake, which is not explicitly modelled. Although it is not anticipated that the south west seasonal zooplankton patterns will improve through parameter calibration (since predator effects are uniformly characterized throughout the lake by the same mortality factor) , further calibration is needed to improve results in the rest of the lake since copepods are generally overestimated and cladocerans generally underestimated. Phytoplankton groups must also be calibrated simultaneously to ensure that they are still operating within reasonable concentrations given more successful zooplankton simulations.

Lake Erie has undergone a substantial amount of ecosystem changes over the past century; including cultural eutrophication and several invasions by industrious exotic species. Simple mass balance models for phosphorus have been useful in guiding policy decisions that led to reduced eutrophication, but new, confounding threats to the ecological health of Lake Erie continue to appear and lake managers continue to need useful tools to better understand the lake. As more complex ecological questions are asked to guide future management decisions, more complex ecological models are developed in an effort to provide some clues. The walleye fishery in Lake Erie is economically very important. Walleye recruitment has been highly variable from year to year since the 1990s. Modelling zooplankton is desired as a diagnostic tool for elucidating the quality of habitat – spatially and temporally – that is available to walleye in their vulnerable larval state. ELCOM-CAEDYM (or ELCD) is a 3-dimensional, coupled hydrodynamic and ecological model, which has been successfully applied to Lake Erie to model the nutrients and phytoplankton. The objectives of this study were to better understand the ELCOM-CAEDYM model of Lake Erie through a sensitivity analysis (SA), which has not been done before, and to explicitly simulate zooplankton in this model. An SA is important for determining which of the uncertain parameters have the greatest impact on the output variables. Due to the complexity of the CAEDYM model and the highly interdependent functions and variables modelled, a local SA (comparing changes in output by perturbing parameters one-at-a-time from some baseline configuration) was not desirable. Local SA’s ignore the possibility of a parameter’s effects being correlated to the status of other parameters. However, quantitative global methods are enormously computationally expensive for a complex model. The Lake Erie ELCD model simulates temperature, mixing, nutrient cycles, and phytoplankton dynamics. Phytoplankton are represented by 5 functional groups. With the explicit inclusion of 2 functional groups of zooplankton (copepods and cladocerans), the model uses over 300 function parameters in addition to requiring meteorological data and river inflow characteristics throughout the simulation. The model is set up with a 2-km grid over 40 layers with a 5-minute timestep from April 11 to September 1. This full simulation takes 6 days to complete. A quantitative global method to evaluate all parameters potentially significant to zooplankton would be impossible. The Morris method was selected for its streamlined global sampling procedure combined with the manageable computational demands of a one-at-a-time analysis. This method provides the relative sensitivity of diagnostic outputs to perturbed parameters. Ninety-one parameters were selected to be evaluated in 3680 simulations for the Morris SA. The selection of which parameters to evaluate and their assigned ranges are critical components in any SA. The ranges for parameters that represent a measurable quantity were assessed based on observed values in Lake Erie and other relevant studies. For some parameters, a measured realistic range was unknown. In these cases, values from relevant published models or judgements based on experience with the ELCD-Erie model were used to choose a suitable range. To assess the sensitivity of CAEDYM variables to parameters, DYRESM was substituted for ELCOM to vastly decrease the computation time of a single run. DYRESM is not suitable to model the entire lake due to the large size and irregular shape of the entire lake. Therefore, only the West Basin was modelled and analysed using DYCD. The West Basin was of special interest for a sensitivity analysis of CAEDYM parameters with respect to zooplankton because it is an important area for walleye larval development. DYCD output profiles for temperature, total chlorophyll a (TChla as a surrogate for total phytoplankton concentration) were similar in magnitudes and seasonal dynamics compared to ELCD outputs in deep West Basin stations. The sensitivity of zooplankton, TChla and TP to each parameter was assessed using two single value diagnostics: the simulated seasonal maximum and the simulated day on which peak maximum was reached. Zooplankton were sensitive to almost all of the zooplankton parameters perturbed in the analysis. This may indicate that modelling zooplankton is extremely complex, relying on many dynamic processes, or that evaluated ranges were not constrained well enough. An example of sensitivity to a poorly known parameter is the messy feeding coefficient. Reducing the uncertainty of this parameter would improve the confidence in the zooplankton assimilation submodel. Other parameters that stood out for being especially significant to zooplankton were: the respiration rate, mortality rate, internal phosphorus to carbon ratio, the temperature multiplier and standard temperature for feeding dynamics, and the half saturation constant. Most of these are easily explained as they directly aid or impede growth or they directly affect zooplankton losses. The most significant phytoplankton parameters on TChla and zooplankton outputs were, not surprisingly, the maximum growth rate and the mortality and respiration coefficient. Some particulate matter parameters proved to be important to outputs as well. More than 2500 of the 3680 parameter configurations resulted in unrealistic zooplankton simulations: peak values that did not much exceed initial conditions on the first day of the simulation. The SA exercise pinpointed a few configurations that resulted in reasonable peak zooplankton values and timing; these runs were used as a starting point for calibrating the ELCD model. Parameters were further manually adjusted by quickly checking their impacts on DYCD before applying them to ELCD. Post SA and minor calibration, the modelled zooplankton results were dramatically better than initial modelling attempts prior to the SA. Zooplankton concentrations throughout the lake were close to measured ranges and in some parts of the lake seasonal patterns were also similar to measured patterns. Modelled zooplankton results were least consistent with observations in the south west area of the lake: zooplankton were overestimated in late June-early July and they subsequently crashed and were underestimated in late July-August. It is supposed that this is due to higher grazing pressure from fish larvae in that area of the lake, which is not explicitly modelled. Although it is not anticipated that the south west seasonal zooplankton patterns will improve through parameter calibration (since predator effects are uniformly characterized throughout the lake by the same mortality factor) , further calibration is needed to improve results in the rest of the lake since copepods are generally overestimated and cladocerans generally underestimated. Phytoplankton groups must also be calibrated simultaneously to ensure that they are still operating within reasonable concentrations given more successful zooplankton simulations.

The Western Honeybee (Apis mellifera) is an important species, not only ecologically and economically, but as a source of recreation to many. The pollination services the species provides benefit a number of crops worldwide, and, as the honeybee is domesticated and kept in hives, can be directed commercially. Recently, although overall global stocks are growing, there have been reports of high colony losses worldwide. Due to the value of this species, this is a worrying trend. There are many stressors facing the honeybee, both natural and anthropogenic in origin. Two of the most prevalent, both in the popular media and in monitoring studies of colonies are insecticidal pesticides and the parasitic mite Varroa destructor. Due to the difficulties and expense of carrying out large-scale field studies required to properly investigate the multiple stressors and their interaction, the use of modelling to explore the problem and direct field work is a vital resource. In this thesis, I present research using the BEEHAVE model and a novel model to explore the exposure and potential impacts of pesticides and the varroa mite. The results show that the timing of a pesticide exposure in the year greatly changes the resultant impact on the colony. Pesticides can have many impacts on different stages of the honeybee, and I show that increased mortalities of different life stages of the honeybee (larvae, in-hive adults, foragers) and decreasing egg-laying rate, affect the development of the colony to different extents at different times of the year, with the colony being highly sensitive to losses of in-hive bees during the summer, and the over-wintering bees at the beginning and end of the year. A novel model is presented exploring the in-hive distribution of pesticide-containing nectar and the effect it has on the exposure of in-hive receiving bees and larvae. The results from this model show that, in-hive distribution is not important to consider for the adults, but may be for the larvae. The landscape, specifically the distance to pesticide-treated forage in relation to untreated forage also has an impact on the result of a pesticide exposure, and this is a potential avenue for the mitigation of pesticide impacts. I also present work towards the validation of BEEHAVE with regards to varroa mite infestation, finding that the model results are close to empirical data, both for datasets from the UK and USA, but the impact of varroa is underestimated. The results are discussed in the context of pesticide risk assessment, the mitigation of potential stressors and the modelling of the varroa mite. The BEEHAVE model is a vital tool for many applications, one being the risk assessment of pesticides. A review of the model by the European Food Security Agency (EFSA) highlighted extensions to the model required before it can be incorporated. This research begins to answer some questions asked in that review.

A perda e fragmentação de habitats são, atualmente, as principais ameaças à conservação da biodiversidade. Espécies que outrora tinham sua distribuição contínua são forçadas a sobreviver de forma segmentada, em populações menores e mais susceptíveis à extinção. Segundo a teoria de metapopulações, se extinções locais em fragmentos específicos puderem ser compensadas por recolonizações provenientes de populações adjacentes, uma espécie pode persistir apesar da fragmentação. Extinções e recolonizações são processos que dependem da estrutura da paisagem. Fragmentos pequenos e com baixa qualidade de habitat possuem maior probabilidade de extinção, assim como paisagens pouco conectadas e com alta resistência à dispersão de indivíduos têm menores taxas de recolonização. Modelos de dinâmica populacional espacialmente explícitos (MVPEE) possibilitam a análise da influência de diferentes tipos de paisagens sobre a persistência de espécies, contribuindo na decisão de estratégias para sua conservação. Esta tese teve o objetivo de identificar os fatores que afetam a persistência de três espécies de aves florestais endêmicas à Mata Atlântica (Chiroxiphia caudata, Xiphorhyncus fuscus e Pyriglena leucoptera) através de um MVPEE. Foram estudadas quatro paisagens do Planalto Atlântico de São Paulo que possuem florestas fragmentadas. A técnica de play-back foi utilizada para atestar a presença ou ausência das aves em 80 fragmentos dispersos por essas paisagens. Esses dados foram utilizados para gerar modelos logísticos de incidência capazes de estimar sua probabilidade de ocorrência de acordo com a cobertura e arranjo espacial da paisagem circundante. Ademais, o padrão de movimentação das aves entre fragmentos florestais foi determinado através de experimentos de play-back que as induziu a transpor a matriz, e pela translocação de indivíduos acompanhados por radio-telemetria. Os modelos de incidência indicaram que a probabilidade de ocorrência das aves em locais de matas fragmentadas depende em larga escala da distribuição espacial dos remanescentes florestais, sendo maior em locais onde o isolamento dos fragmentos é baixo. Esse efeito torna-se ainda mais importante em locais onde os fragmentos não são grandes o suficiente para prover as aves com todos os recursos necessários, forçando-as a buscá-los em matas adjacentes, mas não muito distantes entre si a ponto de coibir sua movimentação. Essa capacidade das aves de transpor a matriz inter-habitat, alcançando florestas próximas, foi confirmada pelos estudos de movimentação. As espécies estudadas são capazes de se movimentar entre fragmentos florestais próximos, mostrando-se ainda capazes de utilizar corredores de habitat ou árvores isoladas para facilitar sua passagem pela paisagem. Esses resultados indicam que os territórios das espécies estudadas podem incluir fragmentos isolados, porém funcionalmente conectados pela movimentação das aves, sendo que as condições mínimas para o estabelecimento destes territórios em termos de quantidade e espaçamento das florestas variam em função da espécie. Esses resultados, somados às informações bibliográficas sobre a biologia das espécies estudadas, foram utilizados para guiar a construção de um MVPEE ecologicamente calibrado, onde as células da paisagem foram definidas como sendo os territórios potenciais das aves. Esse modelo de viabilidade se mostrou de grande utilidade para avaliar os efeitos de variações estruturais da paisagem sobre a persistência de populações de pequenas aves territoriais. Simulações conduzidas tanto com paisagens artificiais como reais indicaram que, em uma escala espacial ampla, a persistência dessas espécies está em grande parte sujeita à quantidade de territórios que a paisagem pode suportar, mas não à sua agregação. No entanto, o aumento da densidade de florestas na paisagem leva a um aumento na quantidade de territórios possíveis, afetando positivamente a persistência das espécies. O MVPEE desenvolvido para esta tese permitiu conciliar uma análise estrutural de paisagens com a modelagem de dinâmicas populacionais, o que é considerado como um dos assuntos prioritários de pesquisa em ecologia de paisagens. / Habitat loss and fragmentation are currently the most important threats to the conservation of biodiversity. These processes may generate patchy landscapes where several species are forced to survive in small and isolated populations, which are very susceptible to local extinctions. According to the metapopulation theory, if local extinctions in specific patches can be compensated by re-colonization from surrounding populations, a species can persist despite fragmentation. Extinctions and re-colonizations are processes that depend directly on landscape structure. Small patches with low habitat quality have increased extinction probabilities, while poorly connected landscapes with high resistance to the dispersal of individuals have decreased re-colonization rates. Spatially explicit population viability models (SEPVM) allow analyses of the influence of different types of landscapes on the persistence of species, contributing to conservation strategies decision making. The objective of the current thesis was to identify the factors which affect the persistence of three forest bird species endemic to the Atlantic forest (Chiroxiphia caudata, Xiphorhynchus fuscus and Pyriglena leucoptera) through a SEPVM. Four different fragmented landscapes of the Atlantic plateau of São Paulo were chosen for this study. The playback technique was used to assess the incidence of the birds inside 80 forest fragments in these landscapes. These data were used to derive logistic incidence models to estimate their occurrence probabilities according to the cover and spatial pattern of the surrounding landscape. Furthermore, the movement pattern of the birds between forest fragments was inferred from playback experiments which induced birds to overcome the matrix, and through the translocation of individual birds which were followed by radio-telemetry. The incidence models indicated that the occurrence probability of the birds in places of fragmented habitat depends in large scale on the spatial distribution of forest remnants, being higher where patch isolation is low. This effect becomes even more important in places where habitat patches are not big enough to provided the birds with sufficient resources, forcing them to search for it in nearby forests, which shall not be further away than the birds\' aptitude to move through the landscape. Their ability to overcome the inter-habitat matrix, reaching close by forests, was confirmed by the experiments on individuals\' movements. The studied species are able to move between nearby forest patches, being even able to use habitat corridors or isolated trees to ease their passage through the landscape. These results indicate that the territories of the studied species can include isolated patches which are connected by birds\' movement. Also, the minimum conditions to the establishment of these territories in terms of amount and aggregation of forests varies according to the species. These results, added to bibliographical information on the studied birds\' biology, were used to guide the development of an ecologically scaled SEPVM, in which the landscape cells were defined as potential bird territories. This viability model was greatly useful to assess the effects of landscape structural changes on the persistence of small territorial birds\' populations. Simulations using both artificial and real landscapes indicated that, in a wide landscape scale, the persistence of these species is largely subjected to the amount of territories the landscape can bear, but not to its aggregation. Nevertheless, increases of forest density lead to a higher amount of possible territories, positively affecting the persistence of the species. The SEPVM developed for the current thesis allowed the reconciliation of a structural analysis of the landscape to dynamical population modeling, what is considered as a top priority research subject in landscape ecology.

Namaqualand is world renowned for its mass displays of annual wildflowers occurring in highly disturbed areas. Leysera gnaphalodes is a short-lived perennial shrub that encroaches into this wildflower display, lessening the aesthetic appeal. For this reason populations of L. gnaphalodes need to be kept as small as possible. This is usually achieved by tilling the area regularly, but a less disruptive method would be preferable. Alternatives to this approach are explored. The effect of many interacting factors needed to be examined over long periods of time so that alternative management strategies could be evaluated. Ecological modelling was used as it is ideally suited to this purpose. A review of modelling and its application in ecology is given, which includes a description of the modelling process and a discussion of different types of models and their applications. It was hypothesised that grazing and low rainfall, in addition to tilling, could control the population size of L. gnaphalodes. Data was used from an eight-year study conducted to determine the effects of tilling, grazing and environmental factors on the seedbank and population size of L. gnaphalodes. A rule-based mechanistic mathematical model based on the logistic growth curve was constructed to describe the population dynamics of this species. The model-fit was evaluated using Pearson’s correlation coefficients and graphs, and it proved to be a good model. Tilling and low rainfall were both found to be effective in reducing populations of L. gnaphalodes but grazing had no reducing effect. Simulations based on the model were run to test three different basic management strategies under stochastic rainfall conditions. The management strategy, which most effectively controlled the population was to till the lands whenever the population of L. gnaphalodes reaches of exceeds a relative frequency of 45%. Multivariate statistical models were constructed to determine the effects of all of these factors on the population of L. gnaphalodes. Tilling was confirmed to be effective in reducing the population, but grazing was found to have no effect. Low rainfall was also effective in controlling the population but has the disadvantages of being out of management control and also affecting the desirable wildflowers. / Dissertation (MSc (Botany))--University of Pretoria, 2005. / Plant Science / unrestricted