Forests are a critical biome but are under threat from unprecedented global change. The need to understand forest dynamics across spatial, temporal and biological scales has never been greater. Critical to this will be understanding how the demographic rates of individuals translate into patterns of species diversity, biomass and carbon turnover at much larger scales. In this thesis, I present a modelling framework focussed on demography. In Chapter 2, I introduce methods for translating forest inventory data into population models that account for the size-dependency of vital rates and persistent differences in individual performance. Outbreaks of forest pest and pathogens are increasing in frequency and severity, with consequences for biodiversity and forest structure. In Chapter 3, I explore the impact of ash dieback on the community dynamics of a British woodland, describing a spatially explicit individual based model that captures the effect of an opening of the canopy on local competitive interactions. Chapter 4 introduces methods to infer the impact of historical deer herbivory on the juvenile survival of forest trees. The approach is generalisable and could be applied to any forest in which patterns of regeneration and community structure have been impacted by periodic disturbance (e.g. forest fires). Finding meaningful ways of incorporating species diversity into global vegetation models is increasingly recognised as a research priority. In Chapter 5, I explore the diversity of demographic rates in a tropical forest community and identify groups of species with similar life history strategies. I discuss the potential of integrating demographic and physiological traits as a way to aggregate species for inclusion in global models. In summary, translating measurements of individuals into population dynamics provides opportunities to both explore small-scale community responses to disturbance events, and to feed into much larger scale vegetation models.

In the face of unprecedented anthropogenic change, we increasingly turn to emergent technologies and extensive data sets for solutions that complement much needed systemic changes in our societies. These technological solutions, however, must be approached with care. We must recognize and address biases in the way data has been accumulated. In demographic studies, dormant life stages, such as seed banks, and other cryptic factors have often been neglected. The potential consequences of these omissions have been extensively described in the literature. In the first chapter, I analyze patterns of seed bank omissions in demographic models, finding unjustified omissions are widespread across ecoregions, growth forms, and taxonomic groups. More importantly, studies with longer duration and accounting for a greater range of conditions were less likely to neglect the seed bank. Unfortunately, most demographic studies are conducted for relatively short periods and are limited to one or a few sites. In addition, modeling tools often focus on mean behavior and do not properly characterize variability. In the second chapter, I explore the use of Bayesian generalized linear mixed models to characterize vital rates and compare their variation across growing conditions. Using wild and translocated populations of Dicerandra christmanii,this study tests the ability of this approach to evaluate early translocation success and site suitability.In chapter 3, I expand the demographic analysis of Dicerandra christmaniiand provide an example of the use of Bayesian-fitted Integral Projection Models (IPMs) to combine data sources and incorporate seed dynamics into demographic models. By propagating uncertainty from vital rates to derived population metrics, this study illustrates the consequences of accounting for the seed bank stage and site condition to our assessment of population viability. In the final part of this work, I present potential routes to expand field and modeling tools to help address the inclusion of dormant and cryptic life stages into demographic studies. Among these, I recommend exploring more complex sampling schemes, informed priors, and expanded IPMs.

Understanding factors limiting population growth is crucial to evaluating species persistence in changing environments. I used Integral Projection Models (IPMs) to elucidate the role of biotic interactions and disturbance on population growth rate in two plants: Helianthemum squamatum, a perennial endemic to gypsum habitats in central Spain, and Liatris ohlingerae, a long-lived perennial endemic to the Lake Wales Ridge of central Florida. In H. squamatum, there was a strong positive effect of trampling in the site with the highest plant density and moderate positive effects of seed addition in the site with the lowest plant density. Differences in treatment effectiveness between sites may represent a shift from seed to microsite limitation at increasing densities. Additionally, a distinct drop in population growth rate occurred in the hottest and driest year (2009-10). In Liatris ohlingerae, roadside populations had consistently higher population growth rates than scrub populations. A modest negative effect of time-since-fire was observed in plants that did not experience herbivory. Both habitat and time-since-fire showed distinct interactions with vertebrate herbivory, with herbivory increasing the difference in growth rate between habitats and decreasing the difference between time-since-fire classes. The direct effect of herbivory was negative in all environmental combinations except in long unburned populations. These results demonstrate the importance of considering environmental interactions when constructing population models, as well as the validity of using IPMs to assess interactions in species with differing life histories.

Over the past 40 years, coral cover has reduced by as much as 80%. At the same time, Coral Reefs are coming under increasing threat from hurricanes, as climate change is expected to increase the intensity of hurricanes. Therefore, it has become increasingly important to understand the effect of hurricanes on a coral population. This Thesis focuses on the reef-building coral Montastraea annularis. This species once dominated Caribbean Coral Reefs, but is fast being replaced by faster growing more opportunistic species. It is important that the underlying dynamics of the decline is understood, if managers stand any chance of reversing this decline. The aim of this Thesis is to investigate the effect of hurricane activity on the dynamics of the reef-building coral Montastraea annularis. To achieve this the Integral Projection Model (IPM) method was adopted and the results compared to those produced using the more traditional method of Population Projection Matrix (PPM) method. The models were fitted using census data from June 1998 to January 2003, which described the area of individual coral patches on a sample of ramets on Glovers Reef, Belize. Glovers Reef is a marine reserve that lies 30km off the coast of Belize and 15km east of the main barrier reef. Three hurricanes struck Glovers Reef during the study: Hurricane Mitch (October 1998), Hurricane Keith (September 2000) and Hurricane Iris (October 2001). The data have been divided by two different methods in order to test two research questions, firstly if the initial trauma following a hurricane affects the long term dynamics of a population and, secondly, if the dynamics exhibited during a hurricane varied with hurricane strength. In this Thesis five main results are shown: 1. All models for all divisions of data are in long term decline. 2. As initial trauma increased, the long term growth rates decreased, conversely the short term extremes increased. 3. Fragmentation is more likely as patch size increased and more likely under stronger hurricanes. 4. Integral Projection Modelling painted a similar picture to Population Projection Matrix models and should be a preferred method of analysis.5. Interaction of the IPMs can be used to model the changing occurrence of hurricanes under climate change. It is shown that with increased intensity, the population could become extinct 6.3 years sooner. This research is the first step in modelling coral patch populations by the IPM method. It suggests possible functional forms and compares the results with the PPM method. Further research is required into the biological functions which drive fragmentation, the method by which large patches divide into groups of smaller patches. The conclusions from this Thesis add to the growing body of knowledge concerning the response of coral species to hurricanes, focusing on the importance of understanding patch dynamics, in order to understand colonial dynamics.

Biologists have long used demographic approaches to answer questions in ecology and evolution. The utility of these approaches has meant a constant development and refinement of methods. A key milestone has been the development of phenotype structured population models that link ecology and evolution. Moreover, biostatistical research steadily improves methods to coax demographic information from scarce data. In this thesis, I build upon some of the recent advances in the field. My first three studies focus on the consequences of sex differences in life history for population dynamics. Firstly, I test whether males matter for the dynamics of African lion (Panthera leo) populations via a previously unquantified mechanism: the inheritance of phenotype from father to offspring. Secondly, I develop a method to estimate age-specific mortality rates for both sexes in species where one of the sexes disperses around the age of maturity. Thirdly, I apply this method to study variation in mortality between the sexes and between two populations of African lions. After these three chapters, which make contributions to the field of sex-structured population dynamics, I focus on the integration of phenotype structured modelling and quantitative genetics. I illustrate how heritability of a quantitative character that develops with age depends on (i) viability selection, (ii) fertility selection, (iii) the development of the phenotype with age, and (iv) phenotype inheritance from parents to offspring. Our results question the adequacy of quantitative genetics methods to obtain unbiased estimates of heritability for wild populations. This thesis advances our understanding of population development over ecological time scales. This knowledge has applications in conservation and population management, but also contributes to untangling evolutionary processes in wild animals.

Serpentine areas in the Czech Republic form minor but important islands in the landscape with specific chemical properties such as high content of magnesium and other heavy metals. Due to this, serpentine is toxic for most plants. Increased demands on the survival and occurrence of plants lead to the emergence of serpentine specialists obligatorily specialized in these extreme habitats. Currently, serpentine areas are threatened by gradual overgrowth of sites, insufficient or poor site management and fragmentation or shrinkage of sites due to anthropogenic activities. Along with the disappearing localities, the serpentine specialists, are becoming highly endangered. Minuartia smejkalii is highly endangered serpentine specialist with an endemic occurrence in the Czech Republic with great need of its conservation. The aim of the work was to collect data on population dynamics of the species and identify habitat and climatic factors affecting population growth. We studied dynamics in all existing 7 populations during the period from 2006 to 2020 were collected. We linked these data to information on population dynamics, habitat and climatic factors and analysed them using Integral projection models (IPM). The study presents the importance of individual habitat and climatic conditions on the dynamics...

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.

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.

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.