LiDAR (Light Detection and Ranging) is currently being used to extract the biophysical characteristics of forests. LiDAR can provide extensive information about tree canopies; pulses reflected back to the sensor can represent understory vegetation as well as partial tree canopies below the dominant trees. Canopy structure can yield valuable clues about the biodiversity, and processes affecting the ecology of forest stands. In addition, structural information can provide insight into other processes such as fire behaviour and the distribution of fuels. This thesis focuses in developing tools to better understand the forest structure. The tools are computer-based algorithms that use LiDAR data as input and provide output with detailed information about the different layers of vegetation in a forested area. Three main modules are used in this study: (1) treetop identification, (2) delineation of canopies for the dominant layer of vegetation, and (3) delineation of partial canopies underneath this dominant layer. The study area was located in the Greater Victoria Water District, west of Victoria, British Columbia, Canada. Nine plots were chosen to represent the study area. A complete census was conducted in the summer of 2005 to provide information about tree, diameter at breast height (DBH), and tree dominance (based on the criteria: suppressed, intermediate, codominant and dominant). Results show that the algorithm is able to properly identify and delineate the majority of trees in the study areas. The third module, partial canopy delineation, also presents promising results with the dataset used. Newer LiDAR systems, with higher number of returns, will definitely provide better datasets with more information of the different layers within the forest, increasing the identification and delineation of these partial trees. Need of new field data is a must for future work and for further tests with the algorithm.

Thesis (M.A.)--University of Hawaii at Manoa, 2005. / Includes bibliographical references (leaves 71-78). / x, 78 leaves, bound ill. (some col.), maps (some col.) 29 cm

Thesis (M.S.)--Mississippi State University. Department of Forestry. / Title from title screen. Includes bibliographical references.

Submitted by Viviane Lima da Cunha (viviane@biblioteca.ufpb.br) on 2017-07-18T13:48:04Z No. of bitstreams: 1 arquivototal.pdf: 15523479 bytes, checksum: a517df9669d4dc98ed45fa5ad61f7e53 (MD5) / Made available in DSpace on 2017-07-18T13:48:04Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 15523479 bytes, checksum: a517df9669d4dc98ed45fa5ad61f7e53 (MD5) Previous issue date: 2014-09-30 / Several factors influence the availability of daylighting such as the obstruction caused by the buildings or natural environment surroundings. Natural elements as arboreous vegetation can cause considerable obstruction resulting in changes in the amount of daylighting available at indoor environments. On the hand, vegetation can cast shadows and improve the quality of the light passing through the openings, reducing the intensity of the direct sunlight and glare from the sky. However, the vegetation is a difficult element to be incorporated in daylighting design. Regarding computer simulation, for example, all the elements involved in the reproduction of the light should be modeled in three dimensions. Ideally, variables such as height, canopy geometry, quantity, size and spacing of leaves, size of the trunk, branches and twigs, reflectance index, opacity index, among others, should be reproduced in a threedimensional model. However, the modeling is unfeasible, not only because of the complexity of all the variables involved in the process, but also because it overloads the model. Taking these aspects into considerations and based on previous studies on the subject, this research takes the daylighting intercepted by arboreous vegetation as its object of study. Accordingly, the overall goal is to characterize a method for representation and modeling of arboreous vegetation in computer simulation for daylighting. To reach this aim, the hemispherical photography method was used to determine the tree canopies gap fraction. These data helped to develop three different configurations of 3D virtual models of canopies, which were used to simulate the effect of the daylight interception by the tree. Using graphical and statistical methods, we assessed the degree of adjustment of these models with real trees. The results obtained with the MBE and RMSE statistical indicators and considering the variability of light and the scatter levels represented by the median showed that all three models tested in this study may be representative appropriate for real trees. However, it is noteworthy that, possibly, the type of representative model of each tree species is intrinsically linked to the characteristics of each tree. / São diversos os fatores que influenciam a disponibilidade da luz natural, dentre eles destacase a obstrução causada pelo entorno edificado ou natural. Elementos naturais, como a vegetação arbórea, podem provocar uma obstrução considerável, que se traduz na alteração da quantidade de luz natural disponível no interior dos ambientes. Por outro lado, a vegetação pode proporcionar sombras e melhorar a qualidade da luz que incide através das aberturas, reduzindo a intensidade da componente direta do sol, bem como o brilho vindo do céu. Contudo, a vegetação é um elemento de difícil inserção no projeto da iluminação natural. Considerando por exemplo, a prática da simulação computacional, todos os elementos intervenientes na reprodução da luz devem ser modelados tridimensionalmente. Idealmente, variáveis como a altura, a geometria da copa, a quantidade, dimensão e espaçamento das folhas, dimensão do tronco, ramos e galhos, índice de refletância, índice de opacidade, entre outras, devem ser reproduzidos no modelo tridimensional. Entretanto, essa modelagem é impraticável, não somente devido à complexidade de todas as variáveis envolvidas no processo, como também, na sobrecarga do modelo. A partir destas considerações e com base em estudos anteriores sobre o tema, esta pesquisa toma como objeto de estudo a iluminação natural interceptada pela vegetação arbórea. Neste sentido, o objetivo geral é caracterizar um método para a representação e modelagem da vegetação arbórea na simulação computacional da luz natural. Para tanto, através do método de fotografia hemisférica, foi possível obter dados de fração de lacuna de copas arbóreas. Estes dados ajudaram a desenvolver três diferentes configurações de modelos tridimensionais virtuais de copas, os quais foram usados para simular o efeito da intercepção da árvore na luz do dia. Por meio de métodos gráficos e estatísticos, avaliou-se o grau de ajuste desses modelos com as árvores reais. Os resultados obtidos com os indicadores estatísticos MBE e RMSE e considerando ainda a variabilidade da luz e os níveis de dispersão, representado pela mediana, demonstraram que todos os três modelos testados nesta pesquisa podem ser representantes adequados das árvores reais. Contudo, ressalta-se que, possivelmente, o tipo de modelo representante de cada espécie arbórea esteja intrinsicamente ligado às características próprias de cada árvore.

Orientador: Ricardo Ribeiro Rodrigues / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T23:57:55Z (GMT). No. of bitstreams: 1 Zanelli_CarolinaBrandao_M.pdf: 11021724 bytes, checksum: 074f594a75e3131636ec29a9f0cdbc07 (MD5) Previous issue date: 2013 / Resumo: A regeneração consiste no processo de reconstrução e reorganização da composição e estrutura de uma comunidade vegetal, e vem sendo bem estudada em florestas ombrofilas e estacionais sob a ótica da dinâmica de clareiras e da sucessão ecológica. No entanto, a regeneração de espécies lenhosas no cerrado ainda e pouco compreendida, e são poucos os estudos que avaliam conjuntamente o dossel e o sub-bosque em áreas de cerrado. O objetivo deste trabalho foi avaliar a floristica e a fitossociologia da comunidade lenhosa do dossel e do sub-bosque de um cerradão em Assis, SP. O trabalho foi realizado na Estação Ecológica de Assis, em uma parcela permanente de 10,4 ha, parte do "Projeto Parcelas Permanentes" do Programa BIOTA/FAPESP. Essa parcela permanente e subdividida em 256 subparcelas contiguas de 20 m x 20 m, das quais 100 foram sorteadas para amostragem. Para avaliar o dossel, foram considerados os dados já coletados no Projeto Parcelas Permanentes, referentes aos indivíduos lenhosos com perímetro na altura do peito (PAP) ? 15 cm, para as 100 subparcelas sorteadas. Para analisar o sub-bosque, foi delimitado um setor de avaliação de 2 m x 2 m em cada subparcela sorteada, onde foram medidos e identificados todos os indivíduos de espécies lenhosas com altura > 20 cm e PAP < 15 cm. Todas as espécies do dossel e do sub-bosque foram classificadas de acordo com o habitat, com base em estudos regionais de fitossociologia, em categorias não excludentes: floresta (F), quando ha registro da espécie em formações florestais não pertencentes ao cerrado sensu lato; cerradão (C), quando ha registro da espécie em cerradão; e cerrado sensu lato (c), quando ha registro da espécie nas demais fisionomias de cerrado sensu lato. Alem disso, foram calculados os parâmetros fitossociologicos usuais para todas as espécies no dossel e no sub-bosque. Tanto o dossel quanto o sub-bosque do cerradão em Assis foram compostos por espécies intermediarias entre diferentes habitats, a maior parte (46% das espécies no dossel e 36% no sub-bosque) constituída de espécies de cerrado/cerradão, incluindo espécies de ampla distribuição no domínio (como Bowdichia virgilioides, Machaerium acutifolium, Plathymenia reticulata, Pouteria ramiflora, Qualea grandiflora, Roupala montana e Xylopia aromática) e comuns em cerrados da província Meridional (como Eriotheca gracilipes, Eugenia pluriflora, Gochnatia polymorpha, Machaerium brasiliense, Myrcia venulosa e Ocotea corymbosa). Regenerantes das espécies do dossel constituíram a maior parte do sub-bosque do cerradão, tanto em numero de espécies (81% do total, n=60) quanto em valor de importância (221 do total de 300). O cerradão apresentou um conjunto de espécies de sub-bosque composto por arvores de pequeno porte e arbustos heliofitos que também ocorrem nas fisionomias mais abertas de cerrado, incluindo: Lacistema hasslerianum, Miconia albicans, Miconia langsdorffii, Miconia stenostachya, Palicourea marcgravii, Piptocarpha rotundifolia, Psychotria hoffmannseggiana e Psychotria vellosiana. Esse resultado e consistente com as características estruturais do dossel do cerradão, que possibilitam maior entrada de luz ao sub-bosque; e contrasta com o relatado para outras fisionomias florestais, onde as espécies de sub-bosque são tipicamente tolerantes a sombra / Abstract: Regeneration consists on the process of reconstruction and reorganization of the structure and composition of a plant community, and has been intensively studied in ombrophilous and seasonal forests according to the paradigm of gap dynamics and ecological succession. However, regeneration of woody plant species in the cerrado is still poorly understood, and few studies evaluate both the overstory and the understory in cerrado areas. The aim of this study was to investigate the floristics and phytosociology of the woody community of the overstory and understory in a cerradao fragment at Assis, Sao Paulo State, southeastern Brazil. Field work was conducted at Assis Ecological Station, in a 10,4 ha permanent plot, part of the Permanent Plots Project from the BIOTA/FAPESP Program. This plot is divided in 256 contiguous subplots of 20 m x 20 m, of which 100 subplots were randomly selected and analyzed. To study the overstory, we used data collected at the Permanent Plots Project, regarding all woody individuals with perimeter at breast height (PBH) ? 15 cm, for these 100 subplots. To study of the understory, we delimited a sector of 2 m x 2 m within each selected subplot, in which all woody individuals with height > 20 cm and PBH < 15 cm were measured and identified. All overstory and understory species were categorized according to their habitat, based in regional phytosociological studies, into non excluding groups: forest (F), when there is record of the species in forest formations that do not belong to cerrado sensu lato; cerradao (C), when there is record of the species in cerradao; and cerrado sensu lato (c), when there is record of the species in the remaining cerrado sensu lato physiognomies. We also calculated the usual phytosociological parameters for all overstory and understory species. Both the overstory and the understory in the study site were composed of species of intermediate distribution between habitats, the majority (46% of overstory species and 36% of understory species) occurring in cerrado/cerradão, including widely distributed Cerrado species (such as Bowdichia virgilioides, Machaerium acutifolium, Plathymenia reticulata, Pouteria ramiflora, Qualea grandiflora, Roupala montana e Xylopia aromatica) and common southern Cerrado species (such as Eriotheca gracilipes, Eugenia pluriflora, Gochnatia polymorpha, Machaerium brasiliense, Myrcia venulosa e Ocotea corymbosa). Regenerating individuals belonging to overstory species accounted for most of the cerradão understory, both in number of species (81%, n=60) and importance value (221 of the total of 300). At the cerradão, we observed a group of understory species composed of heliophyte and small sized trees and shrubs that also occur in the open cerrado physiognomies, such as: Lacistema hasslerianum, Miconia albicans, Miconia langsdorffii, Miconia stenostachya, Palicourea marcgravii, Piptocarpha rotundifolia, Psychotria hoffmannseggiana e Psychotria vellosiana. This result is consistent with the structural characteristics of the cerradão overstory, which enable light penetration to the understory; and differs from data reported in other forest formations, where understory species are typically shade tolerant / Mestrado / Biologia Vegetal / Mestre em Biologia Vegetal

Measurements of the energy balances and net photosynthesis rates of two low productivity coniferous forest canopies (12 and 22 years old), were made successfully during both wet and dry growing seasons, using a modified Bowen Ratio method. Canopy conductances (gc) were calculated from canopy evaporation rates (E) using the Penman-Monteith equation. A model was developed to predict canopy growth and evaporation rates from basic soil and weather data, and compared with the measured data. The photosynthesis model was physiologically based, derived from recent work of Farquhar and coworkers. The canopy conductance model used an empirical approach, based on simple relationships with recorded environmental variables, while canopy E was predicted from the Penman-Monteith equation. Findings were: (1) Daytime E and canopy net photosynthesis rates (Fc) were generally lower in the younger canopy. (2) In the old canopy, E was more strongly decoupled from net irradiance (Rn) and more dependent on the atmospheric vapour pressure deficit (D) in accordance with the predictions of McNaughton and Jarvis (1983). (3) In the old canopy, Fc was significantly reduced by low soil water potential (Ψs) within the range of soil water storages at which measurements were made, while gc was less dependent on Ψs. From consideration of changes in intercellular C0₂ concentration, gc was not found normally limiting to Fc. (4) No simple relationship was apparent between solar irradiance (S) and F at the canopy level. However highest Fc and canopy water use efficiency ratios occurred on cloudy days with low air temperature and low D. (5) Night-time Fc measurements indicated that canopy respiration rates are generally very high and hence air temperature was a major factor limiting overall forest productivity. (6) The computer model could predict gc from four variables (D, S, root-zone soil water storage, W and time since dawn, t) with reasonable 2 success (r² 0.75). However, on days when gc was low, due to high D, E was occasionally significantly in error, because the Penman-Monteith equation is more sensitive to gc when the latter is low. Best agreement between measured and modelled E occurred on cloudy days when D was low and gc consequently high. (7) Values for the maximum rates of carboxylation, as limited by foliar carboxylase activity and electron transport rate, were set at one third of those reported by Farquhar and coworkers, in order to obtain best overall agreement between measured and modelled data. This requirement indicated that poor nutrition was also limiting to stand productivity. (8) Model prediction of canopy net photosynthesis was not satisfactory (r² 0.50), attributed mainly to using too simple an approach to estimating irradiance at the individual leaf level, and partly to unexplained variation in the measurements of Fc. In spite of its limitations, the model was found to respond realistically to changes in weather and Ψs, suggesting the approach was valid, and might be more successful with further development. / Forestry, Faculty of / Graduate

Tree canopies form the most important interface between the earth and the atmosphere, but their role as a potential habitat for eukaryotic microorganisms has been severely understudied. This thesis addresses the hitherto insufficient characterisation of protist diversity and community composition in forest soils and the canopy region, while in particular focusing on the prominent and mostly plant pathogenic Oomycota. Accordingly, several microhabitat compartments were sampled on the ground and in the canopy with the Leipzig Canopy Crane in two seasons over two years, and additionally in a palaeotropical rainforest in Papua New Guinea. Taxon-specific primers were applied to characterise the oomycete diversity in a high-throughput metabarcoding approach. In four chapters, I assess the initial description of oomycete communities in the canopy, their distribution in the forest ecosystem via air dispersal, their seasonality and functional diversity including the quantification of plant pathogens, and their diversity in tropical canopies. These results contribute to a more comprehensive understanding of oomycetes and their pathogenic lineages, their diversity, ecology, distribution, and ecosystem functioning.

The objective of this study was to determine the effect of increasing leaf area index on the photosynthetic temperature response of a wheat canopy. Hard red spring wheat (Triticum aestivum L. cv. Veery-10) was grown hydroponically in a growth chamber, which also served as the gas-exchange chamber. Gas-exchange parameters were measured on single leaves and on wheat canopies at various leaf area indices. The temperature response curves of the canopy shifted from being steeper with a high temperature optimum to being flatter with a lower temperature optimum as leaf area index increased from 0 to 20.0 m2m-2. Single-leaf and canopy measurements show that this shift was primarily a result of increasing respiration from accumulating stems and reproductive structures and, to a lesser extent, from lower temperature optimums associated with lower light levels within the canopy.

Recent decades have seen remarkable increase in the fidelity of computational fluid dynamics (CFD) models for the simulation of exchange processes between plant canopies and the atmosphere. However, no matter how accurate the selected CFD solver is, model results are found to be affected by an irreducible level of uncertainty that originates from the inability of exactly measuring vegetation (leaf orientation, foliage density, plant reconfiguration) and flow features (incoming wind direction, solar radiation, stratification effects). Motivated by this consideration, the present PhD thesis proposes a Bayesian uncertainty quantification (UQ) framework for evaluating uncertainty on model parameters and its impact on model results, in the context of CFD for idealized and realistic plant canopy flow. Two problems are considered. First, for the one-dimensional flow within and above the Duke forest near Durham, NC, a one-dimensional Reynolds-averaged Navier--Stokes model is employed. In-situ measurements of turbulence statistics are used to inform the UQ framework in order to evaluate uncertainty on plant geometry and its impact on turbulence statistics and aerodynamic coefficients. The second problem is characterized by a more realistic setup, with three-dimensional simulations aiming at replicating the flow over a walnut block in Dixon, CA. Due to the substantial computational cost associated with large-eddy simulation (LES), a surrogate model is used for flow simulations. The surrogate is built on top of an exiguous number of LESs over realistic plant canopy, with plant area density derived from LiDAR measurements. Here, the goal is to investigate uncertainty on incoming wind direction and potential repercussions on turbulence statistics. Synthetic data are used to inform the framework. In both cases, uncertainty on model parameters is characterized via a Markov chain Monte Carlo procedure (inverse problem) and propagated to model results through Monte Carlo sampling (forward problem). In the validation phase, profiles of turbulence statistics with associated uncertainty are compared with the measurements used to inform the framework. By providing an enriched solution for simulation of flow over idealized and realistic plant canopy, this PhD thesis highlights the potential of UQ to enhance prediction of micro-scale exchange processes between vegetation and atmosphere.

Oomycetes (Stramenopiles, protists) are among the most severe plant pathogens, comprising species with a high economic and ecologic impact on forest ecosystems. Their diversity and community structures are well studied in terrestrial habitats, but tree canopies as huge and diverse habitats have been widely neglected. A recent study highlighted distinct oomycete communities in the canopy stratum compared to the ground region of three temperate deciduous trees (Quercus robur, Tilia cordata, Fraxinus excelsior). While the communities from the two strata were distinct when taking oomycete abundances into account, they were rather similar when only OTU presence/absence was considered. It remains, however, unknown if this homogeneity in the OTU presence also leads to a functional homogenisation among microhabitats within the two strata ground and canopy. In this study, we supplemented functional traits to oomycete communities in the tree microhabitats, which were determined over a time period of 2 years with a metabarcoding approach. Our results showed that even though most oomycetes occurred in all microhabitats, a strong discrepancy between the strata and correspondingly the distribution of oomycete lifestyles could be observed. This pattern was constant over several seasons. Obligate biotrophic species, exclusively feeding on living host tissue, dominated the canopy region, implying tree canopies to be a hitherto neglected reservoir for parasitic protists. OTUs assigned to the genus Hyaloperonospora—parasites highly specialised on hosts that were not sampled—could be determined in high abundances in the canopy and the surrounding air, challenging the strict host dependencies ruled for some oomycetes. Our findings further contribute to the understanding of oomycete ecosystem functioning in forest ecosystems