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Semi-arid forests are in a period of rapid transition as a result of unprecedented landscape scale fires, insect outbreaks, drought, and anthropogenic land use practices. Understanding how historically episodic disturbances led to coherent forest structural and spatial patterns that promoted resilience and resistance is a critical part of addressing change. Here my coauthors and I apply metabolic scaling theory (MST) to examine scaling behavior and structural patterns of semi-arid conifer forests in Arizona and New Mexico. We conceptualize a linkage to mechanistic drivers of forest assembly that incorporates the effects of low-intensity disturbance, and physiologic and resource limitations as an extension of MST. We use both aerial LiDAR data and field observations to quantify changes in forest structure from the sub-meter to landscape scales. We found: (1) semi-arid forest structure exhibits MST-predicted behaviors regardless of disturbance and that MST can help to quantitatively measure the level of disturbance intensity in a forest, (2) the application of a power law to a forest overstory frequency distribution can help predict understory presence/absence, (3) local indicators of spatial association can help to define first order effects (e.g. topographic changes) and map where recent disturbances (e.g. logging and fire) have altered forest structure. Lastly, we produced a comprehensive set of above-ground biomass and carbon models for five distinct forest types and ten common species of the southwestern US that are meant for use in aerial LiDAR forest inventory projects. This dissertation presents both a conceptual framework and applications for investigating local scales (stands of trees) up to entire ecosystems for diagnosis of current carbon balances, levels of departure from historical norms, and ecological stability. These tools and models will become more important as we prepare our ecosystems for a future characterized by increased climatic variability with an associated increase in frequency and severity of ecological disturbances.

The development of regional flood-frequency equations is a key component of engineering infrastructure design and flood risk assessment at ungauged sites. These equations are constructed based on regression analysis techniques to study the connection between peak flow observations and different explanatory variables. However, many regions of the world remain poorly gauged or have experienced dramatic changes in land use or climate that make past observations less useful. To remedy this situation, we need to interpret and construct these regional equations based on physical principles of water movement and general knowledge of the geographic and geomorphologic setting of the upstream catchment at the location of interest. Several studies have examined these regional equations through the scaling theory of floods, making physical interpretations of the equation parameters (or scaling parameters) with respect to rainfall properties and geomorphologic variables. However, despite the advances of these previous works, the scaling theory of floods must be concerted with different, well-known problems in statistical hydrology for a proper engineering application in flood regionalization. These problems can vary from limitations in peak flow observations (sampling errors) to selection of an inadequate model structure of peak flows (epistemic errors). I present a series of studies based on hydrologic simulations and peak flow observations that illustrate several aspects related to the application and use of the scaling theory of floods, which include the following: (1) description of spatial patterns of scaling parameters; (2) inclusion of river network descriptors in flood frequency equations; and (3) evaluation of sampling errors and epistemic errors in the construction of flood frequency equations. The results presented in this dissertation contribute to the development of a more complete regional flood frequency analysis framework that leverages the physics of peak flow scaling and river network descriptors.

Advanced understanding of the global carbon budget requires large-scale and long-term information on forest carbon pools and fluxes. In situ and remote sensing measurements have greatly enhanced monitoring of forest carbon dynamics, but incomplete data coverage in space and time results in significant uncertainties in carbon accounting. Although theoretical and mechanistic models have enabled continental-scale and global mapping, robust predictions of forest carbon dynamics are difficult without initialization, adjustment, and parameterization using observations. Therefore, this dissertation is focused on a synergistic combination of lidar measurements and modeling that incorporates biophysical principles underlying forest growth. First, spaceborne lidar data from the Geoscience Laser Altimeter System (GLAS) were analyzed for monitoring and modeling of forest heights over the U.S. Mainland. Results showed the best GLAS metric representing the within-footprint heights to be dependent on topography. Insufficient data sampling by the GLAS sensor was problematic for spatially-complete carbon quantification. A modeling approach, called Allometric Scaling and Resource Limitations (ASRL), successfully alleviated this problem. The metabolic scaling theory and water-energy balance equations embedded within the model also provided a generalized mechanistic understanding of valid relationships between forest structure and geo-predictors including topographic and climatic variables. Second, the ASRL model was refined and applied to predict large-scale patterns of forest structure. This research successfully expanded model applicability by including eco-regional and forest-type variations, and disturbance history. Baseline maps (circa 2005; 1-km2 grids) of forest heights and aboveground biomass were generated over the U.S. Mainland. The Pacific Northwest/California forests were simulated as the most favorable region for hosting large trees, consistent with observations. Through sensitivity and uncertainty analyses, this research found that the refined ASRL model showed promise for prognostic applications, in contrast to conventional black-box approaches. The model predicted temporal evolution of forest carbon stocks during the 21st century. The results demonstrate the effects of CO2 fertilization and climate feedbacks across water- and energy-limited environments. This dissertation documents the complex mechanisms determining forest structure, given availability of local resources. These mechanisms can be used to monitor and forecast forest carbon pools in combination with satellite observations to advance our understanding of the global carbon cycle.

Orientador: André Victor Lucci Freitas / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T19:14:01Z (GMT). No. of bitstreams: 1 Ribeiro_DaniloBandini_D.pdf: 21049242 bytes, checksum: aa5d5c4cafb6f3c74669788c029701d9 (MD5) Previous issue date: 2011 / Resumo: A Amazônia representa mais da metade da área de todas as florestas tropicais do mundo, e vem sendo ameaçada por diversas atividades antrópicas, incluindo vários tipos de extração de madeira. O corte seletivo de impacto reduzido (em inglês "Reduced Impact Logging - RIL") é considerado um método menos destrutivo de exploração madeireira que promove uma menor alteração na estrutura da floresta comparado com métodos convencionais. No entanto, existem poucas informações sobre os efeitos do RIL em invertebrados, incluindo borboletas. Desta forma, investigamos o efeito do RIL na estrutura da vegetação florestal e sobre as borboletas frugívoras, comparando a fauna do dossel e do sub-bosque entre uma área explorada (RIL) e uma área não explorada (controle). Devido à pouca informação disponível sobre protocolos de amostragem para as borboletas tropicais, alguns aspectos metodológicos relativos à amostragem dos ninfalídeos frugívoros foram investigados. Analisamos como a detectabilidade varia entre diferentes espécies, habitats (Amazônia x Mata Atlântica), estratos da floresta e também qual o esforço adequado de amostragem para detectar uma certa quantidade espécies em uma determinada área, no prente estudo esta quantidade foi estabelecida como 25% do total de espécies estimado no local. Implicações biológicas Uma floresta não explorada apresenta árvores adultas e juvenis maiores do que as de uma floresta explorada (RIL). O número de plântulas e mudas é maior na floresta explorada (RIL) e a distribuição de freqüências de tamanhos (SDFslope) não foi diferente entre as áreas de RIL (-2,61) e não explorada (-2,31). A abertura do dossel foi maior na floresta não explorada, provavelmente devido a um aumento das plantas do sub-bosque na floresta RIL. A área basal e altura das árvores foram maiores na floresta não explorada. Em relação às borboletas frugívoras, a fauna do dossel é diferente e significativamente mais rica do que a fauna do sub-bosque, mostrando que amostrar apenas o estrato mais baixo pode subestimar a diversidade de borboletas. Os efeitos do RIL foram detectados principalmente na assembleia de borboletas do sub-bosque, onde foram observadas diferenças significativas na composição de espécies entre as áreas. Os impactos do RIL, que incluem o corte de árvores, a abertura de trilhas de arraste e de estradas, são mais intensos no sub-bosque do que no dossel. Estas diferentes intensidades de impacto no dossel e no sub-bosque podem explicar os diferentes efeitos do RIL nas borboletas presente nesses estratos. Considerando o grande potencial das borboletas frugívoras para prever as respostas de vários outros grupos taxonômicos à perturbação da floresta na Amazônia, esperamos que padrões semelhantes sejam encontrados em outros táxons. No entanto, apesar dos efeitos detectáveis do RIL em borboletas frugívoras, não pudemos perceber espécies que foram excluídas ou que invadiram a área de RIL, os nossos resultados mostram principalmente diferenças nas abundâncias das espécies entre as áreas. Este resultado é similar ao encontrado em estudos feitos com outros taxa mostra que o RIL em geral não altera a diversidade de espécies podendo ser uma alternativa para preservar uma parcela significativa da fauna em áreas com este tipo de exploração. A criação de áreas protegidas na Amazônia apesar de desejável é bastante complicada e nem sempre é efetiva na preservação da cobertura vegetal, assim sendo o corte seletivo de impacto reduzido pode ser considerado uma boa alternativa para preservar borboletas frugívoras na floresta amazônica e, certamente, muitos outros táxons. Além disso, devido ao alto valor da madeira produzida neste sistema, esta poderia ser uma alternativa econômica desejável para a região. Implicações metodológicas Quase todas as borboletas e mariposas amostrados no presente estudo foram mais facilmente amostradas em um estrato específico (dossel ou sub-bosque). No presente estudo, mesmo as espécies mais comuns do dossel raramente foram amostradas no subbosque. Assim, fazer uso de um protocolo de amostragem que não utiliza armadilhas em ambos os estratos irá aumentar os erros de detecção de muitas borboletas e pode conduzir a inferências incorretas sobre a riqueza e diversidade em uma determinada área. As diferenças na detectabilidade entre os meses no conjunto de dados da Amazônia mostraram que mesmo quando as borboletas são amostradas durante o período do ano com maior probabilidade de captura, existem diferenças importantes na detectabilidade entre os meses. A baixa detectabilidade e a grande variação entre os estratos e meses nos levam a propor que, para borboletas frugívoras, a amostragem deve ser feita na época correta e em florestas altas os diferentes estratos devem ser considerados de modo a reduzir os erros de detecção e possíveis vieses nos resultados. O esforço amostral mínimo para a detecção de 25% das espécies presentes nas florestas tropicais é de 130 armadilhas / dia para a Mata Atlântica e 510 dias para Amazônia Central. Além disso, a amostragem deve ser feita com réplicas temporais em um curto espaço de tempo para aumentar o poder de interpretação dos dados coletados / Abstract: The Amazon region represents more than half of the area of all tropical forests in the world, and has been threatened by many anthropogenic activities, including several kinds of timber harvesting. Reduced-Impact Logging (RIL) is considered a less destructive method of timber harvesting that promotes a smaller change in forest structure than conventional logging. However, there is a general lack of information about the effects of RIL on Amazonian invertebrates, including butterflies. We therefore investigated the effect of RIL on forest vegetation structure and on fruit-feeding butterflies by comparing their distribution on canopy and understory between an area under RIL and a control area without RIL. Because of the relative lack of information about sampling protocols for tropical butterflies, some methodological aspects of fruit-feeding Nymphalidae sampling were investigated. We analyzed the variation in detectability among species, habitats (Amazon x Atlantic Forest), layers and the adequate sampling effort need for detect an specific amount of species in a given area were analyzed in this thesis, in the present study this amount was established as 25% of the total estimated species richness. Biological implications An unlogged forest has bigger juveniles and adult trees, and less seedlings and saplings than a RIL forest, and the Size Frequency Distribution (SDF) slope was not different from those of logged (-2.61) and unlogged (-2.31) areas. The canopy openness was greater in the unlogged forest, probably due to an increase of understory plants in the RIL forest. The basal area was wider and the height was taller in unlogged forest trees. In relation to the fruit-feeding butterflies, the canopy fauna is different and significantly richer than the understory fauna, showing that sampling only the lower strata underestimates the diversity of fruit-feeding butterflies. The effects of RIL were mainly detected in the understory butterfly assemblage, as significant differences were observed in species composition within this stratum. Effects of the RIL regime, which include tree cutting, skid trails and road openings, are stronger in the understory than in the canopy, explaining the reported differences. Despite the detectable effects of RIL on the composition of fruit-feeding butterfly's assemblages the overall diversity was not affected, this pattern is very similar for many other taxa indicating that a noticeable part of the diversity of many taxa could be preserved in areas under RIL management. Given the problems of creating protected areas in the Amazon, RIL is a good alternatives to preserve fruit-feeding butterflies and surely many other taxa, and it might be a desirable economic alternative for the region. Methodological implications Almost all butterflies and moths sampled in the present study were more readily trapped in one specific stratum. Indeed, in the present study, even the most common canopy species were rarely sampled in the understory. Thus, using a sampling protocol that does not locate traps in both layers will increase the imperfect detection of many butterflies and could lead to incorrect inferences about the richness and diversity in a given area. The differences in detectability between months in the Amazon dataset showed that even with an experimental design planned for sampling butterflies during the period that enhances capture probability, there are important differences in butterfly detectability across months. The low detectability and great variation among strata and months in fruit-feeding butterflies lead us to assume that sampling designs must address sampling effort to the correct season and strata reducing imperfect detections and biases in the results. The minimal sampling effort for detecting 25% of the species present in tropical forests is 130 trap/days in Atlantic Forest and 510 days in Central Amazon. Additionally, such sampling should use temporal replication over a short period to improve the interpretability of the data collected / Doutorado / Doutor em Ecologia

The general aim of my dissertation was to investigate the role of plant interactions in driving population dynamics. Both theoretical and empirical approaches were employed. All my studies were conducted on the basis of metabolic scaling theory (MST), because the complex, spatially and temporally varying structures and dynamics of ecological systems are considered to be largely consequences of biological metabolism. However, MST did not consider the important role of plant interactions and was found to be invalid in some environmental conditions. Integrating the effects of plant interactions and environmental conditions into MST may be essential for reconciling MST with observed variations in nature. Such integration will improve the development of theory, and will help us to understand the relationship between individual level process and system level dynamics. As a first step, I derived a general ontogenetic growth model for plants which is based on energy conservation and physiological processes of individual plant. Taking the mechanistic growth model as basis, I developed three individual-based models (IBMs) to investigate different topics related to plant population dynamics: 1. I investigated the role of different modes of competition in altering the prediction of MST on plant self-thinning trajectories. A spatially-explicit individual-based zone-of-influence (ZOI) model was developed to investigate the hypothesis that MST may be compatible with the observed variation in plant self-thinning trajectories if different modes of competition and different resource availabilities are considered. The simulation results supported my hypothesis that (i) symmetric competition (e.g. belowground competition) will lead to significantly shallower self-thinning trajectories than asymmetric competition as predicted by MST; and (ii) individual-level metabolic processes can predict population-level patterns when surviving plants are barely affected by local competition, which is more likely to be in the case of asymmetric competition. 2. Recent studies implied that not only plant interactions but also the plastic biomass allocation to roots or shoots of plants may affect mass-density relationship. To investigate the relative roles of competition and plastic biomass allocation in altering the mass-density relationship of plant population, a two-layer ZOI model was used which considers allometric biomass allocation to shoots or roots and represents both above- and belowground competition simultaneously via independent ZOIs. In addition, I also performed greenhouse experiment to evaluate the model predictions. Both theoretical model and experiment demonstrated that: plants are able to adjust their biomass allocation in response to environmental factors, and such adaptive behaviours of individual plants, however, can alter the relative importance of above- or belowground competition, thereby affecting plant mass-density relationships at the population level. Invalid predictions of MST are likely to occur where competition occurs belowground (symmetric) rather than aboveground (asymmetric). 3. I introduced the new concept of modes of facilitation, i.e. symmetric versus asymmetric facilitation, and developed an individual-based model to explore how the interplay between different modes of competition and facilitation changes spatial pattern formation in plant populations. The study shows that facilitation by itself can play an important role in promoting plant aggregation independent of other ecological factors (e.g. seed dispersal, recruitment, and environmental heterogeneity). In the last part of my study, I went from population level to community level and explored the possibility of combining MST and unified neutral theory of biodiversity (UNT). The analysis of extensive data confirms that most plant populations examined are nearly neutral in the sense of demographic trade-offs, which can mostly be explained by a simple allometric scaling rule based on MST. This demographic equivalence regarding birth-death trade-offs between different species and functional groups is consistent with the assumptions of neutral theory but allows functional differences between species. My initial study reconciles the debate about whether niche or neutral mechanisms structure natural communities: the real question should be when and why one of these factors dominates. A synthesis of existing theories will strengthen future ecology in theory and application. All the studies presented in my dissertation showed that the approaches of individual-based and pattern-oriented modelling are promising to achieve the synthesis.

The general aim of my dissertation was to investigate the role of plant interactions in driving population dynamics. Both theoretical and empirical approaches were employed. All my studies were conducted on the basis of metabolic scaling theory (MST), because the complex, spatially and temporally varying structures and dynamics of ecological systems are considered to be largely consequences of biological metabolism. However, MST did not consider the important role of plant interactions and was found to be invalid in some environmental conditions. Integrating the effects of plant interactions and environmental conditions into MST may be essential for reconciling MST with observed variations in nature. Such integration will improve the development of theory, and will help us to understand the relationship between individual level process and system level dynamics. As a first step, I derived a general ontogenetic growth model for plants which is based on energy conservation and physiological processes of individual plant. Taking the mechanistic growth model as basis, I developed three individual-based models (IBMs) to investigate different topics related to plant population dynamics: 1. I investigated the role of different modes of competition in altering the prediction of MST on plant self-thinning trajectories. A spatially-explicit individual-based zone-of-influence (ZOI) model was developed to investigate the hypothesis that MST may be compatible with the observed variation in plant self-thinning trajectories if different modes of competition and different resource availabilities are considered. The simulation results supported my hypothesis that (i) symmetric competition (e.g. belowground competition) will lead to significantly shallower self-thinning trajectories than asymmetric competition as predicted by MST; and (ii) individual-level metabolic processes can predict population-level patterns when surviving plants are barely affected by local competition, which is more likely to be in the case of asymmetric competition. 2. Recent studies implied that not only plant interactions but also the plastic biomass allocation to roots or shoots of plants may affect mass-density relationship. To investigate the relative roles of competition and plastic biomass allocation in altering the mass-density relationship of plant population, a two-layer ZOI model was used which considers allometric biomass allocation to shoots or roots and represents both above- and belowground competition simultaneously via independent ZOIs. In addition, I also performed greenhouse experiment to evaluate the model predictions. Both theoretical model and experiment demonstrated that: plants are able to adjust their biomass allocation in response to environmental factors, and such adaptive behaviours of individual plants, however, can alter the relative importance of above- or belowground competition, thereby affecting plant mass-density relationships at the population level. Invalid predictions of MST are likely to occur where competition occurs belowground (symmetric) rather than aboveground (asymmetric). 3. I introduced the new concept of modes of facilitation, i.e. symmetric versus asymmetric facilitation, and developed an individual-based model to explore how the interplay between different modes of competition and facilitation changes spatial pattern formation in plant populations. The study shows that facilitation by itself can play an important role in promoting plant aggregation independent of other ecological factors (e.g. seed dispersal, recruitment, and environmental heterogeneity). In the last part of my study, I went from population level to community level and explored the possibility of combining MST and unified neutral theory of biodiversity (UNT). The analysis of extensive data confirms that most plant populations examined are nearly neutral in the sense of demographic trade-offs, which can mostly be explained by a simple allometric scaling rule based on MST. This demographic equivalence regarding birth-death trade-offs between different species and functional groups is consistent with the assumptions of neutral theory but allows functional differences between species. My initial study reconciles the debate about whether niche or neutral mechanisms structure natural communities: the real question should be when and why one of these factors dominates. A synthesis of existing theories will strengthen future ecology in theory and application. All the studies presented in my dissertation showed that the approaches of individual-based and pattern-oriented modelling are promising to achieve the synthesis.

Dans cette thèse, nous avons répondu à certaines questions ouverts dans le domaine de la dynamique hors équilibre des systèmes quantiques unidimensionnels fermés. Durant ces dernières années, les avancées dans les techniques expérimentales ont revitalisé la recherche théorique en physique de la matière condensée et dans l'optique quantique. Nous avons traité trois sujets différents et en utilisant des techniques à la fois numériques et analytiques. Dans le cadre des techniques numériques, nous avons utilisé des méthodes de diagonalisation exacte, l'algorithme du groupe de renormalisation de la matrice densité en fonction du temps (t-DMRG) et l'algorithme de Lanczos. Au début, nous avons étudié la dynamique quantique adiabatique d'un système quantique près d'un point critique. Nous avons démontré que la présence d'un potentiel de confinement modifie fortement les propriétés d'échelle de la dynamique des observables en proximité du point critique quantique. La densité d'excitations moyenne et l'excès d'énergie, après le croisement du point critique, suivent une loi algébrique en fonction de la vitesse de la trempe avec un exposant qui dépend des propriétés spatio-temporelles du potentiel. Ensuite, nous avons étudié le comportement de bosons ultra-froids dans un réseau optique incliné. En commençant par l'hamiltonien de Bose-Hubbard, dans la limite de Hard-Core bosons, nous avons développé une théorie hydrodynamique qui reproduit exactement l'évolution temporelle d'une partie des observables du système. En particulier, nous avons observé qu'une partie de bosons reste piégée, et oscille avec une fréquence qui dépend de la pente du potentiel, au contraire, une autre partie est expulsée hors de la rampe. Nous avons également analysé la dynamique du modèle de Bose-Hubbard en utilisant l'algorithme t-DMRG et l'algorithme de Lanczos. De cette façon, nous avons mis en évidence le rôle de la non-intégrabilité du modèle dans son comportement dynamique. Enfin, nous avons abordé le problème de la thermalisation dans un système quantique étendu. À partir de considérations générales, nous avons introduit la notion de profil de température hors équilibre dans une chaîne des bosons à coeur dure. Nous avons analysé la dynamique du profil de temperature et, notamment, ses propriétés d'échelle / In this thesis we have addressed some open questions on the out-of-equilibrium dynamics of closed one-dimensional quantum systems. In recent years, advances in experimental techniques have revitalized the theoretical research in condensed matter physics and quantum optics. We have treated three different subjects using both numerical and analytical techniques. As far as the numerical techniques are concerned, we have used essentially exact diagonalization methods, the adaptive time-dependent density-matrix renormalization-group algorithm (t-DMRG) and the Lanczos algorithm. At first, we studied the adiabatic quantum dynamics of a quantum system close to a critical point. We have demonstrated that the presence of a confining potential strongly affects the scaling properties of the dynamical observables near the quantum critical point. The mean excitation density and the energy excess, after the crossing of the critical point, follow an algebraic law as a function of the sweeping rate with an exponent that depends on the space-time properties of the potential. After that, we have studied the behavior of ultra-cold bosons in a tilted optical lattice. Starting with the Bose-Hubbard Hamiltonian, in the limit of Hard-Core bosons, we have developed a hydrodynamic theory that exactly reproduces the temporal evolution of some of the observables of the system. In particular, it was observed that part of the boson density remains trapped, and oscillates with a frequency that depends on the slope of the potential, whereas the remaining packet part is expelled out of the ramp. We have also analyzed the dynamics of the Bose-Hubbard model using the tDMRG algorithm and the Lanczos algorithm. In this way we have highlighted the role of the non-integrability of the model on its dynamical behavior. Finally, we have addressed the issue of thermalization in an extended quantum system. Starting from quite general considerations, we have introduced the notion of out-of-equilibrium temperature profile in a chain of Hard-Core bosons. We have analyzed the dynamics of the temperature profile and especially its scaling properties