Tropical coral reefs are among the most diverse ecosystems of the world but facing increasing threats to their health. Over the last thirty years, many Caribbean coral reefs have undergone dramatic changes and experienced large losses in coral cover, due to direct and indirect anthropogenic disturbances. The results of which are reefs with low rugosity, changed trophic dynamics and low fish diversity. In recent times reefs have failed to recover from disturbances due to an increase in frequency and severity of disturbances and stresses. In the Caribbean on many coral reefs this has resulted in a shift towards macroalgal dominance by species of the phylum Phaeophyta. The processes and factors affecting the standing crop of macroalgae are many and complex. Two main hypotheses are identified in the literature as being the driving forces of algal dynamics: nutrient dynamics (availability, supply and uptake) and herbivory. However, many studies have been found to be inconclusive because of the complexity of the coral reef ecosystem, which makes it difficult if not impossible to control for all factors and processes influencing the standing crop of macroalgae such as light, water flow and sedimentation. The inherent characteristics of macroalgae, like morphology and life history, make them behave differently. Whilst herbivore characteristics, like size of mouth parts, feeding modes and preferences, will influence the amount of algal biomass removed. The spatial context (i.e. coral fore reef vs. back reef) will influence the effects of both bottom-up and top-down controls. Besides these inter-habitat differences, macroalgae within similar habitats but differing geographical locations may respond differently, for example, a forereef exposed to the open ocean or a forereef located in a sheltered bay. This thesis attempts to provide insight into the dynamics of two dominant brown macroalgae on Caribbean coral reefs, Dictyota spp. and Lobophora variegata. This aim was addressed by developing a model for the macroalga species Dictyota to model the various processes and factors on a coral forereef affecting percentage cover. Further, the patch dynamics of both Lobophora variegata and Dictyota were investigated to gain an insight into their dynamics under varying environmental conditions: the windward and leeward sides of an atoll. Finally, herbivory is identified as one of the key process affecting macroalgal cover. I investigated this process by deploying cages on both the windward and leeward side of the atoll to investigate the effects of grazing pressure under varying environmental conditions. A Bayesian Belief Network model was developed for Dictyota spp. to model the bottom-up and top-down processes on a coral forereef determining the percentage cover. The model was quantified using relationships identified in the scientific literature and from field data collected over a nine moth period in Belize. This is the first BBN model developed for brown macroalgae. The fully parameterized model identified areas of limited knowledge and because of its probabilistic nature it can explicitly communicate the uncertainties associated with the processes and interactions on standing crop. As such the model may be used as a framework for scientific research or monitoring programmes and it is expected that the model performance to predict macroalgal percentage cover will improve once new information becomes available. Size-based transition matrices were developed for both Dictyota spp. and Lobophora variegata to investigate the patch dynamics under varying environmental conditions: the windward and leeward sides of an atoll. The matrices reveal that standard measures of algal percent cover might provide a misleading insight into the underlying dynamics of the species. Modelling the patch dynamics with matrices provided insight into the temporal behaviour of macroalgae. This is an important process to understand because patch dynamics are determining competitive interactions with other coral reef benthic organisms. The outcome of competitive interactions will differ with macroalgal species. This study indicate that Dictyota spp. responded strongly to differing environmental conditions in that it has reduced growth rates and lower percent cover on the leeward side of the atoll, whilst Lobophora variegata showed far less sensitivity to environmental conditions. The patch dynamics of Dictyota spp. also showed a higher temporal variation than Lobophora variegata but only on the exposed forereef. A caging experiment was set up to investigate the response of both macroalgal species to different grazing pressure scenarios, under varying environmental conditions. Dictyota spp. had a significant response to environmental conditions in that a higher percentage cover was found on the exposed side of the atoll, whilst for Lobophora variegata the response was far less obvious. The less clear response of Lobophora variegata was very likely caused by competition of Dictyota with Lobophora due to the very high cover Dictyota obtained in the cages where all herbivores were excluded. The low grazing pressure treatments also showed an increase in cover of Dictyota, whilst for Lobophora, only a reduction in the rate of increase could be observed. The results indicate that on the leeward side of the atoll, fish grazing alone seems sufficient to control the standing crop of Dictyota and Lobophora variegata. Retrospective analysis of the experimental design showed that the limited size of the experimental set up could have confounded the results for Lobophora as well. In future experiments it is recommended to increase number replicates. Management of coral reef habitats is frequently constrained by a lack of funds and resources. The BBN Model once fully parameterized can provide a useful tool for coral reef management, because the model allows exploration of different reef scenario’s, which in turn can aid in prioritizing management strategies. Furthermore, the thesis provided an insight into the complexities of macroalgal dynamics. The responses of macroalgae to physiological factors and ecological processes are species specific and dependent on the location, and caution against generalizing on what controls the standing crop of macroalgae. Therefore it is argued that future investigations into algal ecology should clearly define the species, habitat and location. This can help to make informed management decisions.

<p>Population viability analysis (PVA) is commonly used in conservation biology to predict population viability in terms of population growth rate and risk of extinction. However, large data requirements limit the use of PVA for many rare and threatened species. This thesis examines the possibility of conducting a matrix model-based PVA for plants with limited data and provides some practical recommendations for reducing the amount of work required. Moreover, the thesis applies different forms of matrix population models to species with different life histories. Matrix manipulations on 37 plant species revealed that the amount of demographic data required can often be reduced using a smaller matrix dimensionality. Given that an individual’s fitness is affected by plant density, linear matrix models are unlikely to predict population dynamics correctly. Estimates of population size of the herb <i>Melampyrum sylvaticum</i> were sensitive to the strength of density dependence operating at different life stages, suggesting that in addition to identifying density-dependent life stages, it is important to estimate the strength of density dependence precisely. When a small number of matrices are available for stochastic matrix population models, the precision of population estimates may depend on the stochastic method used. To optimize the precision of population estimates and the amount of calculation effort in stochastic matrix models, selection of matrices and Tuljapurkar’s approximation are preferable methods to assess population viability. Overall, these results emphasize that in a matrix model-based PVA, the selection of a stage classification and a model is essential because both factors significantly affect the amount of data required as well as the precision of population estimates. By integrating population dynamics into different environmental and genetic factors, matrix population models may be used more effectively in conservation biology and ecology in the future.</p>

Population viability analysis (PVA) is commonly used in conservation biology to predict population viability in terms of population growth rate and risk of extinction. However, large data requirements limit the use of PVA for many rare and threatened species. This thesis examines the possibility of conducting a matrix model-based PVA for plants with limited data and provides some practical recommendations for reducing the amount of work required. Moreover, the thesis applies different forms of matrix population models to species with different life histories. Matrix manipulations on 37 plant species revealed that the amount of demographic data required can often be reduced using a smaller matrix dimensionality. Given that an individual’s fitness is affected by plant density, linear matrix models are unlikely to predict population dynamics correctly. Estimates of population size of the herb Melampyrum sylvaticum were sensitive to the strength of density dependence operating at different life stages, suggesting that in addition to identifying density-dependent life stages, it is important to estimate the strength of density dependence precisely. When a small number of matrices are available for stochastic matrix population models, the precision of population estimates may depend on the stochastic method used. To optimize the precision of population estimates and the amount of calculation effort in stochastic matrix models, selection of matrices and Tuljapurkar’s approximation are preferable methods to assess population viability. Overall, these results emphasize that in a matrix model-based PVA, the selection of a stage classification and a model is essential because both factors significantly affect the amount of data required as well as the precision of population estimates. By integrating population dynamics into different environmental and genetic factors, matrix population models may be used more effectively in conservation biology and ecology in the future.

In this thesis, I examine variation in occurrence and performance of glabrous and trichome-producing plants of the perennial herb Arabidopsis lyrata. I combine field studies and genetic analysis to (1) examine the function of trichomes as a resistance character in natural populations, (2) compare the magnitude of population differentiation in trichome-production and at putatively neutral marker loci, (3) examine the molecular genetic basis of trichome-production, and (4) quantify the effects of herbivore removal on population growth and relative performance of glabrous and trichome-producing plants. In a survey of 30 populations of A. lyrata in Norway and Sweden, I documented spatiotemporal variation in damage from insect herbivores. With few exceptions, glabrous plants were more damaged by herbivorous insects than trichome-producing plants in polymorphic populations. Damage levels varied substantially among populations and among years. The intensity of herbivory quantified as mean leaf removal to glabrous plants was higher in polymorphic populations than in monomorphic glabrous populations. Within the Swedish range, populations were more strongly differentiated at the locus coding for glabrousness than at eight putatively neutral isozyme loci. This is consistent with the hypothesis that trichome production is subject to divergent selection. A study of the genetic basis of trichome production showed that glabrousness was associated with mutations in an orthologue to GLABROUS1, a regulatory gene known to cause glabrousness in A. thaliana. Comparative data indicate that the genetic basis of glabrousness varies among populations. Experimental removal of insect herbivores in a natural A. lyrata population increased population growth rate and the relative fitness of the glabrous morph. The results suggest that insect herbivory may influence both population dynamics and selection on trichome production in A. lyrata.

Plants can interact with many different organisms on many trophic levels in their life. In this thesis I investigated how three biotic inertactions, powdery mildew infection, caused by Podosphaera ferruginea, predispersal seed predation by Dusky Large Blue (Phengaris nausithous) and Scarce Large Blue (P. teleius) and deer grazing affect life cycle and population biology of the Great Burnet (Sanguisorba officinalis L.). I also analysed their preferences of environmental conditions. Most of studied plant populations growth rates (λ) were lower than 1 and population decreased, but quite surprisingly for more populations vegetative reproduction was more important than reproduction by seeds. All intraction mentioned above affects more generative reproduction, and thus their influence on Great Burnet population dynamics is low, even with modelled maximal possible effect. Environment conditions analysis showed that powdery mildew occurs on sites with more flowering individuals, where spreading is very easy, butterflies preferred high, well noticeable flower heads grown high above other vegetation and host ant presence. For host ants' presence model locality was only significant variable.

A juçara (Euterpe edulis Mart.) é uma palmeira importante ecologicamente e considerada fonte de produtos valiosos culturalmente e economicamente. Há mais de duas décadas tem sido considerada ameaçada de extinção pelo corte de palmito, e atualmente surge uma nova oportunidade para reduzir sua vulnerabilidade por meio da valorização de seus frutos. Nesta pesquisa investigamos se o manejo de juçara para produção de polpa de frutos pode funcionar como catalisador da conservação da biodiversidade e da melhoria dos meios de vida das populações humanas locais. Algumas questões foram elaboradas e organizadas em quatro eixos convergentes a questão central: (I) Quais os principais aspectos socioeconômicos e práticas de manejo de E. edulis para produção de polpa nas áreas de estudo? Qual o potencial da atividade para o fortalecimento local e conservação da espécie? (II) Como varia a composição e a estrutura florestal ao longo de gradientes de manejo e altitude? Quais as espécies vegetais nativas mais valorizadas por estas comunidades locais? (III) Como a produção e a colheita de frutos variam através de diferentes sistemas de manejo ao longo dos anos? Quais os principais fatores que explicam essa variação? (IV) De que maneira o manejo de frutos de juçara afeta sua dinâmica populacional? Qual a taxa máxima sustentável de remoção de frutos? Quais as estratégias de manejo sustentável recomendada para diferentes condições? Para isso, foi realizado o monitoramento de populações de E. edulis em áreas manejadas por quatro populações humanas que habitam o entorno e interior do Parque Estadual da Serra do Mar (PESM), Núcleos Santa Virgínia e Picinguaba, nos municípios de Natividade da Serra e Ubatuba, SP. Também amostramos populações de E. edulis em áreas de proteção integral no interior do PESM, entrevistamos os moradores de cada comunidade local, assim como usamos dados de fontes secundárias sobre a vegetação do PESM e sobre a atividade de manejo da juçara nos últimos anos. Verificamos que existe uma nova possibilidade de trabalho e renda nas comunidades, inclusive para mulheres e jovens, possibilitando diversificação da economia local. As práticas não destrutivas de colheita dos frutos e as características do sistema reprodutivo da espécie não implicam em severas consequências ecológicas adversas, permitindo considerar o potencial de conservação circa situm, principalmente diante as mudanças climáticas e pressão do mercado de palmito. A diversidade arbórea reduziu localmente com o aumento da intensidade de manejo agroflorestal, mas permite a manutenção de espécies arbóreas de interesse para a conservação, além de proporcionar sustento às famílias dos produtores. As práticas de manejo realizadas nos sistemas agroflorestais tradicionais podem favorecer a manutenção do conhecimento ecológico local, além de aumenta a produtividade de frutos e reduzir a variação interanual da frutificação. A colheita de frutos de juçara em si não representa prejuízos em termos populacionais. Sendo o novo manejo de juçara uma das estratégias recomendadas para manter a viabilidade das populações em longo prazo, desde que o corte de palmito seja controlado e a regeneração seja promovida. / Juçara (Euterpe edulis Mart.) is a palm source of various culturally and economically valued products. It has been considered threatened of extinction for more than two decades. The simple opposition between strategies to obtain its different products arises a new opportunity to reduce its vulnerability. In this research we investigated if the management for fruit production could act as a catalyst to biodiversity conservation and local livelihood improvement. Some questions were elaborated and organized into four axes convergent to the central question: (I) How do the management systems of E. edulis for fruit production are characterized at the study area? Which is the activity potential to improve local livelihoods? (II) How does the forest structure and composition vary along management and altitude gradients? What native plant species are most valued by these communities? (III) How do fruit production and harvest vary through different management systems along different years? What are the main factors explaining such variation? (IV) How do juçara management for fruit production affect its population dynamics? What is the maximum sustainable rate of fruit removal? Which sustainable management strategies are recommended for different conditions? We built empirical evidences through monitoring E. edulis populations managed by four local human populations living around and inside Parque Estadual da Serra do Mar (PESM), Nuclei Santa Virgínia and Picinguaba. We also sampled E. edulis populations in strictly protected areas inside PESM, as well as used secondary data about juçara management activities in the last years. The opportunity for work and income, inclusive for women and young people, the stimulus for social organization, production diversification, among other aspects recorded in this study promote community resilience in the face of political and economic change. Juçara fruit harvest allows frugivorous foraging and indicates the potential for in situ and circa situm conservation approach, mainly in the face of climate change and market pressure for palm heart. Arboreal diversity reduced locally with increasing agroforesty management intensity, which in turn raised diversity at the landscape level. Management practices, performed at the traditional agroforestry systems, could strengthen local cognitive systems, enhance fruit productivity and reduce fruiting inter annual variation. Juçara fruit harvest benefits recruitment and could even induce population increase at the long term. Neverheless, other factors affected negatively affected the population negatively. The protection of adult palms for fruit harvest is one of the recommended strategies to keep population viability in the long term and could function as in situ and circa situm conservation strategies.

A juçara (Euterpe edulis Mart.) é uma palmeira importante ecologicamente e considerada fonte de produtos valiosos culturalmente e economicamente. Há mais de duas décadas tem sido considerada ameaçada de extinção pelo corte de palmito, e atualmente surge uma nova oportunidade para reduzir sua vulnerabilidade por meio da valorização de seus frutos. Nesta pesquisa investigamos se o manejo de juçara para produção de polpa de frutos pode funcionar como catalisador da conservação da biodiversidade e da melhoria dos meios de vida das populações humanas locais. Algumas questões foram elaboradas e organizadas em quatro eixos convergentes a questão central: (I) Quais os principais aspectos socioeconômicos e práticas de manejo de E. edulis para produção de polpa nas áreas de estudo? Qual o potencial da atividade para o fortalecimento local e conservação da espécie? (II) Como varia a composição e a estrutura florestal ao longo de gradientes de manejo e altitude? Quais as espécies vegetais nativas mais valorizadas por estas comunidades locais? (III) Como a produção e a colheita de frutos variam através de diferentes sistemas de manejo ao longo dos anos? Quais os principais fatores que explicam essa variação? (IV) De que maneira o manejo de frutos de juçara afeta sua dinâmica populacional? Qual a taxa máxima sustentável de remoção de frutos? Quais as estratégias de manejo sustentável recomendada para diferentes condições? Para isso, foi realizado o monitoramento de populações de E. edulis em áreas manejadas por quatro populações humanas que habitam o entorno e interior do Parque Estadual da Serra do Mar (PESM), Núcleos Santa Virgínia e Picinguaba, nos municípios de Natividade da Serra e Ubatuba, SP. Também amostramos populações de E. edulis em áreas de proteção integral no interior do PESM, entrevistamos os moradores de cada comunidade local, assim como usamos dados de fontes secundárias sobre a vegetação do PESM e sobre a atividade de manejo da juçara nos últimos anos. Verificamos que existe uma nova possibilidade de trabalho e renda nas comunidades, inclusive para mulheres e jovens, possibilitando diversificação da economia local. As práticas não destrutivas de colheita dos frutos e as características do sistema reprodutivo da espécie não implicam em severas consequências ecológicas adversas, permitindo considerar o potencial de conservação circa situm, principalmente diante as mudanças climáticas e pressão do mercado de palmito. A diversidade arbórea reduziu localmente com o aumento da intensidade de manejo agroflorestal, mas permite a manutenção de espécies arbóreas de interesse para a conservação, além de proporcionar sustento às famílias dos produtores. As práticas de manejo realizadas nos sistemas agroflorestais tradicionais podem favorecer a manutenção do conhecimento ecológico local, além de aumenta a produtividade de frutos e reduzir a variação interanual da frutificação. A colheita de frutos de juçara em si não representa prejuízos em termos populacionais. Sendo o novo manejo de juçara uma das estratégias recomendadas para manter a viabilidade das populações em longo prazo, desde que o corte de palmito seja controlado e a regeneração seja promovida. / Juçara (Euterpe edulis Mart.) is a palm source of various culturally and economically valued products. It has been considered threatened of extinction for more than two decades. The simple opposition between strategies to obtain its different products arises a new opportunity to reduce its vulnerability. In this research we investigated if the management for fruit production could act as a catalyst to biodiversity conservation and local livelihood improvement. Some questions were elaborated and organized into four axes convergent to the central question: (I) How do the management systems of E. edulis for fruit production are characterized at the study area? Which is the activity potential to improve local livelihoods? (II) How does the forest structure and composition vary along management and altitude gradients? What native plant species are most valued by these communities? (III) How do fruit production and harvest vary through different management systems along different years? What are the main factors explaining such variation? (IV) How do juçara management for fruit production affect its population dynamics? What is the maximum sustainable rate of fruit removal? Which sustainable management strategies are recommended for different conditions? We built empirical evidences through monitoring E. edulis populations managed by four local human populations living around and inside Parque Estadual da Serra do Mar (PESM), Nuclei Santa Virgínia and Picinguaba. We also sampled E. edulis populations in strictly protected areas inside PESM, as well as used secondary data about juçara management activities in the last years. The opportunity for work and income, inclusive for women and young people, the stimulus for social organization, production diversification, among other aspects recorded in this study promote community resilience in the face of political and economic change. Juçara fruit harvest allows frugivorous foraging and indicates the potential for in situ and circa situm conservation approach, mainly in the face of climate change and market pressure for palm heart. Arboreal diversity reduced locally with increasing agroforesty management intensity, which in turn raised diversity at the landscape level. Management practices, performed at the traditional agroforestry systems, could strengthen local cognitive systems, enhance fruit productivity and reduce fruiting inter annual variation. Juçara fruit harvest benefits recruitment and could even induce population increase at the long term. Neverheless, other factors affected negatively affected the population negatively. The protection of adult palms for fruit harvest is one of the recommended strategies to keep population viability in the long term and could function as in situ and circa situm conservation strategies.

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