The main goal of this study was to evaluate the effectiveness of two biological control agents in reducing population growth and spread of the invasive tree Melaleuca quinquenervia, a subtropical tree native to Australia, and invasive in Florida, Puerto Rico, and the Bahamas. While in Florida two insects Oxyops vitiosa (weevil), and Boreioglycaspis melaleucae (psyllid) have been established as biocontrol agents, in Puerto Rico only psyllids are present, and in the Bahamas no biocontrol agents are present. This study combined demographic data, experiments and mathematical models to investigate the influence of the biocontrol agents on M. quinquenervia's spatial population dynamics. In the field, permanent plots were established and demographic data was collected in populations in the native and exotic ranges. Australian populations are comprised mostly of tall adult trees, while in the exotic ranges populations are comprised mostly of short trees (<1.3m in height), and small adult trees. In a shade-house, I performed an experiment to investigate the effects of insect type and density on survival and growth of M. quinquenervia seedlings. I found that high density of insects, independently or in combination, reduce seedling performance, thus having the potential to alter the seedling-short plant transition of the M. quinquenervia life cycle. Based on the demographic data, I developed integral projection models (IPMs) to determine population growth rates in each region. Populations in Australia and the Bahamas are increasing, while populations in Florida and Puerto Rico are decreasing. Population growth is most sensitive to the seedling-short plant transition in all regions, except Florida, where it is most sensitive to survival of tall plants. Simulations combining the results of the IMPs and experiment indicated the biocontrol damage results in reductions in population growth rate in Puerto Rico and the Bahamas. Seed dispersal and demographic data was combined to develop an integrodifference structured model of population spread. Simulations indicated that by reducing seedling performance, insects have the potential to reduce the rate of population spread. Overall this study shows that individual-level effects of biocontrol agents have translated into reductions in population growth rate and rate of spread of M. quinquenervia.

A device capable of continuously monitoring an individual’s levels of alertness in real-time is highly desirable for preventing drowsiness and lapse related accidents. This thesis presents the development of a non-intrusive and light-insensitive video-based system that uses computer-vision methods to localize face, eyes, and eyelids positions to measure level of eye closure within an image, which, in turn, can be used to identify visible facial signs associated with drowsiness and behavioural microsleeps. The system was developed to be non-intrusive and light-insensitive to make it practical and end-user compliant. To non-intrusively monitor the subject without constraining their movement, the video was collected by placing a camera, a near-infrared (NIR) illumination source, and an NIR-pass optical filter at an eye-to-camera distance of 60 cm from the subject. The NIR-illumination source and filter make the system insensitive to lighting conditions, allowing it to operate in both ambient light and complete darkness without visually distracting the subject. To determine the image characteristics and to quantitatively evaluate the developed methods, reference videos of nine subjects were recorded under four different lighting conditions with the subjects exhibiting several levels of eye closure, head orientations, and eye gaze. For each subject, a set of 66 frontal face reference images was selected and manually annotated with multiple face and eye features. The eye-closure measurement system was developed using a top-down passive feature-detection approach, in which the face region of interest (fROI), eye regions of interests (eROIs), eyes, and eyelid positions were sequentially localized. The fROI was localized using an existing Haar-object detection algorithm. In addition, a Kalman filter was used to stabilize and track the fROI in the video. The left and the right eROIs were localized by scaling the fROI with corresponding proportional anthropometric constants. The position of an eye within each eROI was detected by applying a template-matching method in which a pre-formed eye-template image was cross-correlated with the sub-images derived from the eROI. Once the eye position was determined, the positions of the upper and lower eyelids were detected using a vertical integral-projection of the eROI. The detected positions of the eyelids were then used to measure eye closure. The detection of fROI and eROI was very reliable for frontal-face images, which was considered sufficient for an alertness monitoring system as subjects are most likely facing straight ahead when they are drowsy or about to have microsleep. Estimation of the y- coordinates of the eye, upper eyelid, and lower eyelid positions showed average median errors of 1.7, 1.4, and 2.1 pixels and average 90th percentile (worst-case) errors of 3.2, 2.7, and 6.9 pixels, respectively (1 pixel 1.3 mm in reference images). The average height of a fully open eye in the reference database was 14.2 pixels. The average median and 90th percentile errors of the eye and eyelid detection methods were reasonably low except for the 90th percentile error of the lower eyelid detection method. Poor estimation of the lower eyelid was the primary limitation for accurate eye-closure measurement. The median error of fractional eye-closure (EC) estimation (i.e., the ratio of closed portions of an eye to average height when the eye is fully open) was 0.15, which was sufficient to distinguish between the eyes being fully open, half closed, or fully closed. However, compounding errors in the facial-feature detection methods resulted in a 90th percentile EC estimation error of 0.42, which was too high to reliably determine extent of eye-closure. The eye-closure measurement system was relatively robust to variation in facial-features except for spectacles, for which reflections can saturate much of the eye-image. Therefore, in its current state, the eye-closure measurement system requires further development before it could be used with confidence for monitoring drowsiness and detecting microsleeps.

The rock outcrop plants are neglected group of plants, even though they include endangered or endemic species. Despite this fact, there is only a few of studies focusing at this topic. The aim of this thesis is to focus on this group of plants in terms of its population dynamics. Aurinia saxatilis ssp. saxatilis was chosen as a model species. It is a species of the Czech thermophyticum. Three populations were chosen and studied over three years. The population dynamics was compared between the populations by integral projection modelling (IPM) and matrix population modelling (MPM). The results of these two analytical approaches were compared to one another, too. The population growth rate (λ) predicts that one of the populations is stable, whereas the other two populations are declining. The highest elasticity is mostly for the seeds survival in the seed bank. The population growth rate does not differ distinctly between the two statistical approaches, IPM and MPM. In all cases the IPM λ is lower than the MPM λ. Within the IPM analysis, the influence of the substrate type was also studied. The analyses, however, did not indicate any major differences between the substrates. For maintaining the populations, it is necessary to protect the new seeds and seedling recruitment and to create the new space...

Explicar os padrões de diversidade de espécies e entender os processos que geram e mantêm essa diversidade na natureza é um dos grandes objetivos da Ecologia. A teoria clássica de competição prevê que duas espécies só podem coexistir quando há divergência no uso de recursos. Portanto, há um limite de similaridade imposto pela competição entre as espécies, que leva à co-ocorrência de espécies com estratégias ecológicas mais diferentes entre si. Por outro lado, o ambiente físico pode impor restrições às possíveis estratégias ecológicas das espécies. Ambientes com limitações de recursos ou condições desfavoráveis permitem apenas a sobrevivência de espécies com estratégias mais similares, um processo conhecido como filtro ambiental. Dois processos podem então gerar padrões antagônicos na estrutura das comunidades, selecionando estratégias ecológicas mais parecidas ou mais diferentes entre si. Há ainda a possibilidade de que os dois processos ou mesmo nenhum dos dois seja importante na estruturação das comunidades, levando a um padrão aleatório ou neutro. Utilizando-se das contribuições proporcionais (elasticidades) das três taxas vitais demográficas - sobrevivência, crescimento e fecundidade - para a taxa de crescimento populacional para inferir as estratégias ecológicas das espécies de árvores de uma comunidade, nos propusemos a responder a pergunta: \"Qual processo é responsável pela estruturação de comunidades de árvores tropicais?\". O trabalho foi realizado em uma parcela permanente de 10,24 hectares na Restinga da Ilha do Cardoso, São Paulo. Todos os indivíduos com mais de 15cm de perímetro à altura do peito foram marcados, identificados e tiveram seus diâmetros à altura do peito registrados para dois censos. As elasticidades das três taxas vitais para 89 espécies de árvores foram obtidas por meio de um modelo de projeção integral (IPMs). Os IPMs são ferramentas modernas mais robustas que os clássicos modelos matriciais, comumente utilizados em estudos demográficos. Definimos um espaço ecológico no triângulo onde as estratégias ecológicas das espécies são classificadas de acordo com as elasticidades das três taxas demográficas. Construímos também uma filogenia molecular específica para a comunidade baseada nos marcadores cloroplásticos rbcL e matK, com a qual obtivemos as distâncias entre todos os pares de espécies. Calculamos o sinal filogenético das estratégias ecológicas por meio da correlação entre a distância entre as espécies no espaço ecológico e suas distâncias filogenéticas. Aceitamos a premissa de conservação das estratégias ecológicas na filogenia. As espécies puderam ser classificadas em quatro grupos demográficos distintos no espaço ecológico, distribuídos principalmente no eixo crescimento-sobrevivência, o que é esperado para árvores. Não há sinal filogenético para as estratégias ecológicas, o que indica que ambos os processos ou nenhum dos dois processos é importante na estruturação dessa comunidade. Nosso trabalho traz uma nova abordagem metodológica e resultados que contradizem a literatura recente, em que a importância dos filtros ecológicos na estruturação de comunidades tropicais é repetidamente encontrada. A confirmação deste padrão para outras comunidades poderá colaborar para o melhor entendimento dos processos estruturadores das comunidades tropicais. / One of Ecology\'s biggest goals is to explain the patterns of species\' diversity and to understand the processes that generate and maintain this diversity in natural communities. Classical competition theory predicts that two species will be able to coexist only when there is divergence in the use of resources, i.e., competition imposes a limiting similarity among species that allows co-occurrence of species with divergent ecological strategies. On the other hand, the physical environment may impose restrictions to the range of possible ecological strategies of species. Environments with limited resources or adverse conditions will allow the survival of species with more specific strategies, a process known as environmental filtering. These two processes will generate opposite effects on the structure of communities, as more similar or more different ecological strategies will be selected. There is still the possibility that both processes are occurring simultaneously, or neither are important for the community. In both cases, a neutral or random pattern is expected. Using the proportional contribution (elasticities) of the three demographic vital rates - survival, growth and fecundity - to the finite rate of increase of population as a mean of inferring the ecological strategy of trees in a community, we intended to answer the question: \"What process is responsible for the structuring of tropical tree communities?\". Data was collected in a Restinga forest 10.24 ha permanent plot. All individuals with more than 15cm of perimeter at breast height were marked, identified and had their diameters at breast height registered for two censes. Elasticities of the three vital rates for 89 tree species were obtained with an Integral Projection Model (IPM). IPMs are modern tools more robust than classical matrix models, commonly used in demographic studies. We defined an ecological space in the triangle where ecological strategies are plotted according to elasticities of the three vital rates. We also generated a molecular phylogeny based on rbcL and matK chloroplast markers, and used it to obtain the phylogenetic distance between all pairs of species. We calculated the phylogenetic signal of ecological strategies using the correlation between ecological distances in the ecological space and phylogenetic distances. We assumed ecological strategies to be conserved in the phylogeny. Species could be classified into four demographic groups in ecological space, distributed mainly in a growth-survival axis. This is expected for trees. No phylogenetic signal was found for the ecological strategies. This can mean that either both processes are structuring this community, or neither is important. Our study uses a new methodological approach and presents new results that contradict recent literature, on which environmental filtering is repeatedly accounted as the main process structuring tropical communities. Confirmation of this pattern for other communities may bring further understanding of structuring of tropical communities.

This diploma thesis is studying population dynamics of endangered species Silene acaulis in the High Tatra Mountains in Slovakia. Silene acaulis is a species of extreme alpine habitats creating cushions that provide a microclimate acting as a facilitator of establishment of other species in the alpine communities. This dome-like structure has one woody taproot making it easier to distinguish each individual. It is thus a perfect model species for determining the population dynamics drivers. The findings help in understanding future behaviour of the species and whole alpine ecosystems. Population data have been collected since 2013 or 2014 in two valleys in the High Tatras providing a database suitable to study various effects on species performance. Data collection includes marking, measuring, counting of flowers and capsules, viability and new seedlings recording, gender identification and comparison of vegetation structure within and in close proximity of a cushion. The data on vegetation were analysed using CCA ordination and the population data were analysed using Integral Projection Models. The results show that the breeding system of Slovak S. acaulis is gynodioecious and the gender affects the size of cushions, individuals with both female and hermaphrodite flowers being the biggest. The...

La région méditerranéenne, hot-spot de biodiversité avec un fort taux d'endémisme, est classée parmi les zones les plus touchées par le changement climatique. La conservation des espèces nécessite de comprendre finement leur démographie face à ces changements, mais aussi leur capacité à s’adapter à ces nouvelles conditions. Au cours de cette thèse, deux espèces végétales rares méditerranéennes ont été étudiées, Centaurea corymbosa et Brassica insularis, en utilisant des modèles mathématiques récents pour analyser des suivis démographiques de long-terme (22 ans et 18 ans). Dans la première partie de cette thèse, des modèles de projection matriciels ont été construits afin d’analyser la variation spatio-temporelle des taux d’accroissement des populations de C. corymbosa. Cela a permis d'identifier les facteurs climatiques clefs qui impactent les taux d’accroissement des populations, et plus finement, les paramètres de survie, de floraison et de fécondité. Une analyse de viabilité des populations a été réalisée sous différents scénarios climatiques. Dans un second temps, une analyse de la capacité des populations de C. corymbosa à répondre à ces changements climatiques a été effectuée avec un modèle de projection intégral. Les changements des traits d’histoire de vie au cours du temps ont montré que la stratégie de floraison observée répond aux variations climatiques en suivant la même direction que la stratégie optimale. Ceci montre que les populations sont capables de s’adapter au changement climatique. Enfin, des modèles de capture-recapture (CR) ont été construits afin de déterminer l’influence de la faible détectabilité des individus sur l’estimation des paramètres démographiques chez B. insularis. Les probabilités de survie estimées par l’approche classique sont inférieures à celles estimées par les modèles CR. Les paramètres estimés par les deux approches sont en général très corrélés, à l'exception d'une population montrant des problèmes d'identification des individus. L'ensemble de cette thèse est replacé dans le cadre de la biologie de la conservation des espèces végétales, notamment en suggérant de prendre en compte leur capacité de réponse au changement climatique. / Mediterranean region is a biodiversity hot-spot with a high endemism rate and is classified among the areas most sensitive to climate change. Deep understanding of demography and evolution following these changes is a necessity for species conservation. During this thesis, two rare Mediterranean plant species have been studied, Centaurea corymbosa and Brassica insularis, using recent mathematical models to analyse long term demographic datasets (22 and 18 years). In the first part of this thesis, matrix projection models have been used to analyse spatio-temporal variation in population growth rate in C. corymbosa. Major climatic parameters that impact population growth rate and survival, flowering and fecundity have been identified. A population viability analysis has been performed under various climatic scenarios. In a second part, an analysis of the population ability of C. corymbosa to response to these climatic changes has been performed using integral projection models. Temporal variation of life-history traits showed that the realized flowering strategy varied with climatic conditions following the same direction than the optimal flowering strategy. It can thus be concluded that the studied populations can adapt to climatic changes. Finally, capture-recapture models have been applied on the Brassica insularis dataset to analyse the effect of plant detectability on demographic parameter estimations. Survival probabilities obtained with the classical approach are lower than the ones estimated using the CR models. However, the parameters estimated using both methods are highly correlated, except for one population where individual identification is problematic. Results of this thesis are linked to some considerations in conservation biology of plants, particularly in link to their ability to respond to climatic changes.

Linking environmental variation to population dynamics is necessary to understand and predict how the environment influences species abundances and distributions. I used demographic, environmental and trait data of forest herbs to study effects of spatial variation in environmental factors on populations as well as environmental change in terms of effects of forest succession on field layer plants. The results show that abundances of field layer species during forest succession are correlated with their functional traits; species with high specific leaf area increased more in abundance. I also found that soil nutrients affect vegetative and flowering phenology of the forest herb Actaea spicata. The effect of nutrients shows that a wider range of environmental factors than usually assumed can influence plant phenology. Moreover, local environmental factors affected also the demography of A. spicata through effects on vital rates. An abiotic factor, soil potassium affecting individual growth rate, was more important for population growth rate than seed predation, the most conspicuous biotic interaction in this system. Density independent changes in soil potassium during forest succession, and to a lesser extent plant population size dependent seed predation, were predicted to alter population growth rate, and thereby the abundance, of A. spicata over time. Because these environmental factors had effects on population projections, they can potentially influence the occupancy pattern of this species along successional gradients. I conclude that including deterministic, as opposed to stochastic, environmental change in demographic models enables assessments of the effects of processes such as succession, altered land-use, and climate change on population dynamics. Models explicitly incorporating environmental factors are useful for studying population dynamics in a realistic context, and to guide management of threatened species in changing environments.

Codakia orbicularis est un mollusque bivalve appartenant à la famille des Lucinidae et établissant des symbioses avec des bactéries sulfo-oxydantes (symbiotes) au sein de ses branchies. Dans l’hypothèse où toute symbiose nécessite une régulation par des molécules de dialogue, une étude chimique exhaustive pourrait aboutir à la mise en évidence des métabolites impliqués. Le travail de ce manuscrit porte donc sur l'isolement de métabolites secondaires à partir des branchies de ce bivalve et sur l'évaluation de l'activité antibactérienne des molécules isolées. Douze composés ont été isolés des branchies de Codakia orbicularis et leurs structures ont été déterminées par les méthodes spectroscopiques usuelles. Parmi ces molécules, une seule est nouvelle et a été nommée orbicularisine. Elle présente un squelette indolone spirotetracyclique inédit. Parmi les molécules isolées, seules quatre d’entre elles présentent une activité antibactérienne à savoir le soufre S8, la 4-hydroxybenzaldéhyde et deux monoglycérolipides. L'orbicularisine est inactive contre un panel de lignées cellulaires cancéreuses et de kinases. Le nouveau squelette de l’orbicularisine pourrait permettre d'aboutir à une nouvelle famille de molécules par synthèse organique et ainsi d'accroître la diversité moléculaire autour de ce motif inédit. Il sera également intéressant de déterminer l'origine des molécules isolées (procaryote ou eucaryote), particulièrement pour l’orbicularisine, et leurs rôles dans le cadre de la symbiose. Les résultats chimiques obtenus sur C. orbicularis et sur les Lucinidae en général sont intéressants puisque les espèces côtières appartenant aux bivalves ont été peu exploitées en chimie jusqu’à ce jour. / Codakia orbicularis is a bivalve mollusk belonging to the family Lucinidae harboring sulfur-oxidizing bacterial endosymbionts within its gills. Considering that any symbiosis is most likely regulated by dialogue molecules, an exhaustive chemical study could lead to identify the involved metabolites. Thus, the aim of this thesis focuses on the isolation of secondary metabolites from the gills of this bivalve and the evaluation of the antibacterial activity of the isolated molecules. Twelve compounds were isolated from the gills of Codakia orbicularis and their structures were determined by usual spectroscopic methods. Among these molecules, only one presented a new structure and has been named orbicularisine. The latter presents an undescribed spirotetracyclic indolone skeleton. Regarding the biological activities, among the isolated molecules, only four of them identified as S8 sulfur, 4-hydroxybenzaldehyde and two monoglycerolipids presented an antibacterial activity. Orbicularisine was inactive against a panel of cell lines and kinase. The orbicularisine new skeleton is an interesting start for the synthesis of new family of molecules, thus enhancing its molecular diversity. It will be interesting to determine the origin of the isolated molecules (prokaryotic or eukaryotic), especially for the new orbicularisine, and their roles in the frame of the symbiosis. The chemical results obtained on C. orbicularis and on lucinids in general are interesting since the coastal species belonging to Bivalves have not been chemically explored.

In present thesis, I treat the topic of impacts of plant-animal interactions, namely herbivory and pollination, on plant life cycle and lifetime fitness. First, I identify the components of the impact of plant-animal interactions: i) interaction frequency; ii) per-interaction effect; iii) sensitivity of the plant's life cycle to the changes in vital rate impacted by the animals. Furthermore, I also classify other causes changing the outcome of a plant-animal interaction into two categories: i) plant's traits; ii) plant's environment. A review of extant literature on the topic revealed that especially the role of plant's environment in changing the outcome of plant-animal interactions is largely understudied and I attempt to reduce this gap in knowledge in the five detailed studies encompassed in this thesis. The detailed studies focus on a model system of Central European wet grasslands and especially on three species typical to it: Succisa pratensis, Achillea millefolium and A. ptarmica. The first two studies examine the effects of environment on frequency of plant- animal interactions. The next two studies are more integrative, one focusing on the impacts of different herbivore groups on the complete life cycle and the other on interaction of herbivory and pollination on plant lifetime fitness....