Biodiversity is a complex concept encapsulating the variation that occurs within and among levels of biological organization. It is positively linked to ecosystem persistence, adaptability, and function. Biodiversity loss, driven by global change and human activities, is one of the most prominent threats to ecosystems. Characterizing the variation of and processes driving biodiversity is a critical step in understanding the causes, consequences, and magnitude of biodiversity loss. However, characterizing biodiversity comprehensively requires understanding multiple dimensions, or types, of diversity, such as genetic, taxonomic, phylogenetic, and life history diversity, that encompass both ecological and evolutionary processes varying across space and time. In this dissertation, I investigate spatial and temporal variation in frog and toad (order Anura) biodiversity to understand the effects of how diversity is measured on biodiversity characterization and the underlying processes driving biodiversity. In my first chapter, I examined the spatial and temporal variation of genetic diversity and other population genetic metrics to understand the effects of multi-year sampling on population genetic inference in an anuran metapopulation (Arizona treefrog, Hyla (Dryophytes) wrightorum). I found that a single sample year captures global, but not local, population genetic dynamics, as there is considerable temporal variation in genetic metrics within individual populations. In my second chapter, I developed a tool to improve the characterization of anuran life history diversity using species traits. Traits are the measurable attributes of species, and a suite of species traits is used to distinguish ecological strategies found among species. I collated trait data from 411 primary and secondary sources for 106 anuran species found in the United States to develop an anuran traits database for use in conservation, management, and research. In my third chapter, I investigated spatial variation within and among taxonomic, phylogenetic, and life history anuran diversity in the United States and examined the abiotic relationships behind observed patterns. To do this, I developed species distribution models at a 1 km2 resolution for the majority of the native US anurans. I identified relationships among diversity metrics for improved, comprehensive biodiversity characterization and potential ecological and evolutionary processes underlying biodiversity. Spatial variation in multidimensional relationships highlights regional needs for multiple metrics of diversity to comprehensively characterize biodiversity. This spatial variation is driven by temperature, elevation, and water availability, likely related to the biological limits for anurans. Collectively, these chapters highlight the considerable variation that exists within and among species of a broad and diverse biological. Furthermore, these chapters call attention to the importance of measuring multiple biodiversity dimensions for effective conservation in a rapidly changing world. / Doctor of Philosophy / Biodiversity loss, from global change and human activities, is one of the biggest threats to the Earth's ecosystems. Biodiversity is the similarities and differences in organismal characteristics, such as their genetics, evolutionary history, and ecology. Biodiversity is often linked to how well an ecosystem will persist and adapt to global change. To understand the causes and consequences of biodiversity loss, it is important to first measure diversity and what shapes it. However, there are many types of diversity and ways to measure them, such as the number of species in a system, or species richness, the span of evolutionary lineages in a system, or phylogenetic diversity, the number of roles species fill in a system, or life history diversity, and the genetic relationships within individuals and populations, or genetic diversity. In this dissertation, I investigate how our understanding of biodiversity is affected by the ways it can be measured and the relationship among those metrics. To do this, I studied diversity in three ways for frogs and toads of the United States. First, I investigated whether sampling across multiple years is necessary to adequately characterize genetic diversity in a frog species (Arizona treefrog: Hyla (Dryophytes) wrightorum) with populations that fluctuate in size over time. Here, I found that multiple sample years are necessary to capture the genetic variation within individual populations over time, but unnecessary to capture the average genetic variation among all populations over space and time. Second, I developed a tool to improve our ability to measure anuran life history diversity using traits. Traits are measurable attributes of species, and multiple species traits can be used to define the role of a species in an ecosystem. I collected trait data from 411 sources for 106 frog and toad species found in the United States to develop a traits database for use in conservation, management, and research. Third, I investigated the similarities in multiple diversity metrics across the United States using species richness, phylogenetic diversity, and life history diversity. Species richness is highest in the eastern US, phylogenetic diversity is highest in the western US, and life history diversity is clustered around eastern US mountains. These regional relationships among metrics coincided with regional water availability, temperature, and elevation. These results collectively call attention to changes over space and time in frog and toad diversity and how the relationships within and among diversity types relate to our understanding of frog and toad biodiversity. Considering how, where, and when to measure biodiversity can lead to more effect biodiversity conservation in a rapidly changing world.

Understanding mechanisms regulating the assembly of ecological communities is a major goal of community ecology. I combined experimental and theoretical approaches to investigate the influences of various ecological factors on the assembly of protist communities. My research included three experimental studies and one theoretical study. Two experimental studies used freshwater heterotrophic ciliated protists as model organisms to examine how species dispersal across local communities and functional and phylogenetic diversity of the species pool influence historical contingency of the assembled communities, respectively. The results of the first experiment showed that the differences in species colonization history led to alternative community states that substantially differed in species composition and abundances, regardless of the level of species dispersal. The results of the second experiment showed that historical contingency, measured by beta diversity and the strength of inhibitive priority effects decreased as phylogenetic and functional diversity of the species pool increased. In the third experimental study, I used the same model system and observed positive relationships between phylogenetic diversity and temporal stability of community biomass. These positive relationships are likely due to the reduced competition among species and increased asynchronous species responses to environmental changes under higher phylogenetic diversity. The theoretical study explored how phytoplankton and zooplankton coevolution drives species diversity patterns along productivity gradients in a mathematical model system. I explored the conditions for evolutionary divergence in phytoplankton and zooplankton and the consequent productivity-diversity relationships (PDR) using the theory of adaptive dynamics and numerical simulations. The results of numerical simulations showed that the coevolutionary dynamics of phytoplankton and zooplankton can generate transient unimodal or positive PDRs, and positive PDRs when the systems reach steady states. The findings of my research suggest an important role of traits and species ecological difference in understanding causes and consequences of biodiversity in community ecology.

Biodiversity conservation requires a framework for prioritising limited resources to the many endangered species. One such framework that has seen much attention and is considered extensively in this thesis, is the Noah's Ark Problem (NAP). The NAP combines a biodiversity measure (Phylogenetic Diversity; PD) with species survival probabilities and conservation costs. The aim of the NAP is to allocate the limited conservation resources such that the future expected PD is maximised. Obtaining optimal solutions to the NAP is a computationally complex problem to which several efficient algorithms are provided here. An extension to the NAP is also developed which allows uncertainty about the survival probability estimates to be included. Using this extension we show that the NAP is robust to uncertainty in these parameters and that even very poor estimates are beneficial. To justify using or promoting PD, it must produce a significant increase in the amount of biodiversity that is preserved. We show that the increase attainable from the NAP is typically around 20% but may be as high as 150%. An alternative approach to PD and the NAP is to prioritise species using simple species specific indices. The benefit of these indices is that they are easy to calculate, explain and integrate into existing management frameworks. Here we investigate the use of such indices and show that they provide between 60% and 80% of the gains obtainable using PD. To explore the expected behaviours of conservation methods (such as the NAP) a distribution of phylogenetics trees is required. Evolutionary models describe the diversification process by which a single species gives rise to multiple species. Such models induce a probability distribution on trees and can therefore be used to investigate the expected behaviour of conservation methods. Even simple and widely used models, such as the Yule model, remain poorly understood. In this thesis we present some new analytic results and methods for sampling trees from a broad range of evolutionary models. Lastly we introduce a new model that provides a simple biological explanation for a long standing discrepancy between models and trees derived from real data -- the tree balance distribution.

Les milliers d’espèces de microorganismes présentes dans les océans sont essentiellement connus pour être planctoniques ou benthiques. Moins décrits, de nombreux micro-organismes colonisent également la surface et le tube digestif des macro-organismes marins, formant des communautés appelées microbiomes. Ces microbiomes ont des conséquences cruciales sur la fitness de leur hôte. Les récents progrès en biologie moléculaire ont ouvert la voie à une caractérisation des différentes facettes de sa biodiversité, à la fois taxonomique, phylogénétique, et fonctionnelle. L’objectif de cette thèse est donc de caractériser la biodiversité des microbiomes cutanés des organismes marins, d’identifier ses échelles de variabilité, ses déterminants, et son importance à l’échelle de l’écosystème. Dans un premier temps j’ai mesuré l’efficacité d’indices de biodiversité à détecter des signaux écologiques dans le cas spécifique de communautés microbiennes. Puis, j’ai décrit le microbiome cutané des principaux grands clades d’animaux marins (poissons téléostéens, cétacés et invertébrés de plusieurs classes). J’ai démontré que le microbiome cutané était très différent des communautés présentes dans l’eau environnante. J’ai aussi montré qu’il était variable, à la fois entre individus et entre espèces, mais ne présentait pas de patron de phylosymbiose. Enfin, j’ai évalué la contribution de la diversité des microbiomes cutanés à la diversité de la communauté microbienne globale d’un écosystème corallien. J’ai ainsi démontré que les animaux marins hébergent collectivement une richesse microbienne presque vingt fois supérieure à celle de l’eau les environnant, et 75% de la richesse phylogénétique à l’échelle de l’écosystème. Dans un contexte d’érosion massive de la diversité des macro-organismes marins, ces résultats soulignent la nécessité d’évaluer plus exhaustivement la biodiversité microbienne marine et sa vulnérabilité face aux pressions anthropiques. / Oceans contain thousands of microbial species playing crucial roles for the functioning of the marine ecosystem. These microorganisms are present everywhere in the water column. Some microorganisms also colonize the surface and the digestive tract of marine macro-organisms, forming communities called microbiomes. These microbiomes have positive effects for their host’s fitness. The diversity of these marine animal surface microbiome is still largely understudied, despite recent progress in molecular biology that now permits to fully assess its different facets of biodiversity, i.e. taxonomic, phylogenetic and functional. The goal of this thesis is therefore to describe the diversity of the surface microbiome of marine animals, to assess its variability at different levels, as well as its determinants, and the significance of such diversity at the ecosystem’s scale. Firstly, I have assessed the efficiency of various diversity indices to detect ecological signals in the specific case of microbial communities. Secondly, I have described the surface microbiome of major marine animal clades (teleostean fishes, cetaceans and several classes of invertebrates). I found that these microbiomes are highly distinct from the surrounding planktonic communities. I demonstrated that these microbiomes are variable both between individuals from the same species and between species, but do not show a phylosymbiosis pattern. Last, I assessed the contribution of surface microbiomes to the global microbial community at the scale of a coral reef ecosystem. I demonstrated that marine animal surfaces host almost twenty times more microbial species than the water column, and 75% of the phylogenetic richness present in the ecosystem. In a context of massive erosion of marine macroscopic organisms, it is therefore urgent to exhaustively assess marine microbial biodiversity and its vulnerability facing anthropic pressures.

This thesis focuses on phylogenetic, taxonomic, ecological, and conservation aspects of the crustose lichen genus Lecania (Ramalinaceae, lichenized Ascomycota). Lecania has previously been defined on basis of relatively few morphological characters, and the genus had never been treated in molecular phylogenies. The molecular phylogeny of the genus is inferred from DNA sequences. Twenty-five species traditionally placed in Lecania are included in the study along with 21 species from closely related genera. Lecania is a polyphyletic genus. A well-supported monophyletic group containing 16 Lecania species, including the type species L. fuscella is discovered, i.e. Lecania s. str. Nine species formerly included in Lecania do not belong in the genus. A new species, L. belgica, is described. The relationships of a group of morphologically similar Lecania species, i.e. the L. cyrtella group are investigated using morphological and molecular methods. Haplotype network and phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic. Two new species, L. leprosa and L. madida, are described, L. proteiformis is resurrected from synonymy, and the known range of L. prasinoides is greatly expanded. The type species Lecania fuscella has become endangered in many countries. Twelve localities in Sweden where the species had been found historically are investigated, but L. fuscella is only recovered in one locality. The species composition in these 12 localities, 58 old and 5 new collections with L. fuscella is determined and analyzed. The vegetation community differs between the old and the new collections, and between the locality where the species is recovered and those where it is not. Lecania fuscella has not been able to adapt to environmental changes and now only appears in a specific type of vegetation community. The phylogenetic diversity of the species is calculated, but does not reflect the species’ evolutionary potential.

Biodiversity conservation requires a framework for prioritising limited resources to the many endangered species. One such framework that has seen much attention and is considered extensively in this thesis, is the Noah's Ark Problem (NAP). The NAP combines a biodiversity measure (Phylogenetic Diversity; PD) with species survival probabilities and conservation costs. The aim of the NAP is to allocate the limited conservation resources such that the future expected PD is maximised. Obtaining optimal solutions to the NAP is a computationally complex problem to which several efficient algorithms are provided here. An extension to the NAP is also developed which allows uncertainty about the survival probability estimates to be included. Using this extension we show that the NAP is robust to uncertainty in these parameters and that even very poor estimates are beneficial. To justify using or promoting PD, it must produce a significant increase in the amount of biodiversity that is preserved. We show that the increase attainable from the NAP is typically around 20% but may be as high as 150%. An alternative approach to PD and the NAP is to prioritise species using simple species specific indices. The benefit of these indices is that they are easy to calculate, explain and integrate into existing management frameworks. Here we investigate the use of such indices and show that they provide between 60% and 80% of the gains obtainable using PD. To explore the expected behaviours of conservation methods (such as the NAP) a distribution of phylogenetics trees is required. Evolutionary models describe the diversification process by which a single species gives rise to multiple species. Such models induce a probability distribution on trees and can therefore be used to investigate the expected behaviour of conservation methods. Even simple and widely used models, such as the Yule model, remain poorly understood. In this thesis we present some new analytic results and methods for sampling trees from a broad range of evolutionary models. Lastly we introduce a new model that provides a simple biological explanation for a long standing discrepancy between models and trees derived from real data -- the tree balance distribution.

Made available in DSpace on 2014-07-29T16:21:18Z (GMT). No. of bitstreams: 1 Dissertacao Rosana Talita Braga.pdf: 1419131 bytes, checksum: 905d2678cb30fa1bbfc3760839d5cc86 (MD5) Previous issue date: 2012-03-02 / Changes of natural landscape caused by antropic activities are currently the main threats for biodiversity. Thus, the identification of priority areas has become a challenge for conservation biology. The scarcity of financial resources for conservation involves studies for emergency actions, considering important biological aspects, and different components of diversity in order to better allocate the available resources. Furthermore, the costs incorporation of potentially priority areas can display a favorable balance for minimize possible conflicts of interest. Hence, our objectives in this study were to identify priority areas for Carnivore species conservation in Brazil, considering social-economic variables as cost measure for conservation. We also investigate how the taxonomical, functional and phylogenetic diversities of the Carnivore are distributed in the Brazilian territory, in order to identify the set of regions that best represent this three diversity measures. In both cases, we investigate the efficiency of currently established conservation units (CUs), examining whether the current distribution in space of these is better than if they were randomly distributed in Brazil. Our results showed that regions of interest for conservation of species are also important in the social-economical development. Thus, other regions that were not at first priority will be considered important in order to minimize conflicts of conservation. We also found that taxonomic diversity was not the better predictor of functional and phylogenetic diversity. It is necessary the combination of a set of areas to represent these three diversity measures. The UC s are not efficient for all species to represent phylogenetic diversity. In the latter case even the UC s were distributed randomly in Brazilian territory, representing the largest indices of phylogenetic diversity. Thus, it is necessary the addition of new protected areas that complement the previous one. We concluded that it is important to include socio-economic analysis in prioritization, and that studies considering different measures of diversity are important since the species richness may not well represent the other measures of diversity. In conservation plans that incorporate such analysis, the results are more satisfactory for the long-term species protection. / As mudanças da paisagem natural provocadas por atividades antrópicas são atualmente importantes ameaças à biodiversidade. Diante disto, a identificação de áreas prioritárias tem se tornado um desafio para a biologia da conservação. A escassez de recursos financeiros para ações conservacionistas implica em estudos direcionados às ações emergenciais de conservação, que considerem aspectos biológicos importantes e diferentes componentes de diversidade, a fim de estabelecer a melhor possibilidade de alocação dos recursos existentes. Além disto, a incorporação de custos das áreas potencialmente prioritárias pode exibir um balanço favorável para minimizar possíveis conflitos de interesse. Assim, nossos objetivos nesta dissertação foi, indicar áreas prioritárias para conservação de espécies de Carnívoros no Brasil, considerando uma série de variáveis sócio-econômicas (e.g. índice de desenvolvimento humano, demografia urbana, cabeças de gado, dentre outras) como medida de custo para conservação. Também averiguamos como estão distribuídas no território brasileiro, a diversidade taxonômica, funcional e filogenética das espécies deste grupo, a fim de identificar o conjunto de regiões que melhor representam estas três medidas de diversidade. Em ambos os casos, averiguamos a eficiência das Unidades de conservação atualmente instituídas (UC s), analisando se a distribuição atual destas no espaço é melhor do que se tivessem distribuídas ao acaso no Brasil. Nossos resultados mostram que algumas regiões de interesse para conservação de espécies também são importantes no contexto sócioeconômico. Assim, outras regiões que a princípio não eram prioritárias passaram a ser consideradas importantes no intuito de minimizar conflitos de conservação. Encontramos também que a diversidade taxonômica não é um bom preditor de diversidade funcional e filogenética. Assim, é necessária uma combinação de conjunto de áreas para representar estas todas as espécies e as demais medidas de diversidade. As UC s não são eficientes para todas as espécies nem para representar diversidade filogenética. Neste último caso, nem mesmo se as UC s estivessem distribuídas ao acaso no território brasileiro, representariam maiores índices de diversidade filogenética. Sendo assim, é necessário o acréscimo de novas áreas protegidas que complementam as existentes. Concluímos que é importante inserir fatores sócio-economicos nas análises de priorização, e que estudos considerando diferentes medidas de diversidade são importantes pois, a riqueza de espécies pode não representar bem as outras medidas de diversidade. A medida em que os planejamentos de conservação incorporarem análises como estas, os resultados serão mais satisfatórios no que diz respeito a proteção das espécies em longo prazo.

Les changements globaux, du fait de l’empreinte humaine, sont associés à de nombreux déclins de populations et de disparitions d'espèces, et ce, notamment au sein des systèmes insulaires. L'importante biodiversité abritée par de tels écosystèmes est particulièrement vulnérable aux pressions anthropiques en raison de diverses caractéristiques (p. ex. syndrome d’insularité, faible redondance fonctionnelle, isolement géographique des îles). En dépit de cette vulnérabilité accrue, peu d’études se sont jusqu'à lors intéressées à ces systèmes comme modèle d’étude pour évaluer les patrons de menaces sur les différentes facettes de la diversité (taxonomique, fonctionnelle, et phylogénétique). Pourtant, un tel travail permettrait d’améliorer notre compréhension des menaces qui pèsent au sein des îles. Dans ce sens, l’objectif de cette thèse est de décrire les patrons de diversité endémique insulaire dans le contexte actuel des changements globaux et dans un contexte futur de changements climatiques, en explorant les différentes facettes de la diversité. Une finalité de ce travail est de mettre en évidence des priorités éventuelles de conservation pour ces écosystèmes particulièrement vulnérables. Nous avons abordé l'ensemble de ce travail de thèse à une grande échelle à l’aide de deux bases données recensant les îles mondiales et les espèces qui y sont endémiques. Dans une première partie, nous avons caractérisé les menaces pesant sur les écosystèmes insulaires à l'échelle globale, et prospecté également leurs distributions au sein de différents groupes taxonomiques et régions insulaires. Dans une deuxième partie, nous avons analysé l'incidence des menaces sur la biodiversité endémique insulaire et en particulier sur la composante fonctionnelle. Dans une troisième partie, nous avons identifié les régions insulaires à forte représentativité de la biodiversité endémique menacée au travers de différentes facettes et prospecté leurs niveaux de protection via les aires protégées et les menaces les affectant. Dans une dernière partie, nous avons étudié la vulnérabilité future des îles et de la biodiversité endémique face au changement climatique à l’échéance 2050. À la lumière de nos résultats (identification de menaces majeures dont l'importance varie suivant les groupes taxonomiques, les régions insulaires et également les dimensions de biodiversité considérées), nous avons discuté de l’implication des changements globaux pour la biodiversité endémique insulaire dans un contexte de conservation. Cette thèse révèle l’importance d’intégrer de multiples menaces (et leurs associations) et dimensions de diversité pour les approches de changements globaux et de conservation. / Global changes, because of human activities, are associated with numerous population declines and species extinctions, which are especially pronounced in island systems. The important biodiversity of such ecosystems is particularly vulnerable to anthropogenic pressures because of several characteristics (e.g. island syndrome, low functional redundancy, island geographical isolation). Despite this increased vulnerability, few studies have so far looked at these systems as a study model for assessing patterns of threats to the different facets of diversity (taxonomic, functional, and phylogenetic). However, such work would improve our understanding of islands threats. In this sense, the aim of this PhD thesis is to describe patterns of insular endemic diversity in the current context of global changes and in a future climate change context, by exploring different facets of diversity. The purpose of this work is to highlight potential conservation priorities for these particularly vulnerable ecosystems. We have addressed all of this thesis work on a large scale using two databases of worldwide islands and endemic species. In a first part, we characterized threats to island ecosystems at a global scale and also explored their distributions within different taxonomic groups and island regions. In a second part, we analyzed the impact of threats on the functional component of island endemic biodiversity. In a third part, we have identified priority areas for insular endemic biodiversity representativeness and conservation across different dimensions of biodiversity and explored their levels of protection through protected areas and threats affecting them. In a last part, we studied the future vulnerability of islands and endemic biodiversity to climate change by 2050 based on endemic mammals. In the light of our results (identification of major threats whose importance varies according to the taxonomic groups, the island regions and also the dimensions of biodiversity considered), we discussed the implications of global changes for island endemic biodiversity in a conservation context. This PhD thesis reveals the importance of integrating multiple threats and diversity dimensions for global changes and conservation approaches.

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No. of bitstreams: 2 Peixoto, Franciele Parreira-Dissertação-2013.pdf: 995120 bytes, checksum: 365969ffce47a58af2a011eb0370ed04 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-03-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Aim: To investigate global patterns of phylobetadiversity (PBD) in bats, with the purpose to better understand the mechanisms underlying current biodiversity patterns. We also aimed to use a metric that allows partitioning PBD into two components to distinguish the relative roles of local (e.g. lineage filtering) and regional processes (e.g. speciation) in shaping broad-scale patterns of PBD. Furthermore, we analyzed the distance-decay relationship of phylogenetic beta diversity to provide more information about factors that act in the PBD patterns. Location: global, delimited by biogeographic regions. Methods: Using the global distribution of bats and a supertree available for most species, we calculated PBD using the complement of phylosor index. We used a null model to test if two assemblages were more or less phylogenetically dissimilar than expected by chance. In addition, we decoupled PBD into turnover and nestednessresultant components, providing information about two factors that produce differences in assemblage phylogenetic composition. We also performed a Mantel analysis to analyze the distance-decay patterns of PBD and its two components. Results: The most striking difference in PBD was found between the Old and New World “phylogenetic composition”. We found the lowest values of PBD between adjacent regions (i.e., Neotropical/Neartic; Indo-Malay/Paleartic), revealing a strong geographical structure in PBD. These values were even lower when the turnover component was analyzed, demonstrating the differences in the role of regional processes in shaping regional diversity. On the other hand, we found out that for some adjacent regions (e.g., Afrotropical/Paleartic), the observed PBD was higher than expected by chance and comparatively different from expected by the distance decay relationship. This value remained high, even when we analyzed just the PBD turnover component. This demonstrates that although these regions are relatively close in space, there are other factors driving phylogenetic differences between them (e.g. an environmental barrier). Main conclusions: Our analyses revealed differences in the expected patterns of bat PBD among regions, suggesting that at broad scales, besides the effects of distance and geographic barriers, we also have to consider the importance of environmental gradients when studying the phylogenetic origin of bat assemblages. / A abordagem mais comum no uso de PD (diversidade filogenética) para conservação é selecionar locais com maior diversidade evolutiva. Essa estratégia parte do pressuposto de que locais com maior quantidade de PD indicam maior potencial para respostas evolutivas a mudanças ambientais futuras. No entanto, há um crescente debate sobre se as prioridades de conservação deveriam também ser voltadas para locais com baixo valor de PD, que podem representar centros de diversificação de espécies ou “berçários de diversidade”. Alguns trabalhos têm testado se os hotspots globais de biodiversidade, baseados em riqueza, também representam locais de desproporcional concentração de história evolutiva. Nós testamos aqui se os hotspots contêm mais, menos ou igual diversidade filogenética (PD) que o esperado por uma amostragem ao acaso de espécies em qualquer posição na filogenia, para a ordem Chiroptera. Buscamos responder qual a real contribuição de cada hotspot para a conservação de padrões e processos relacionados à diversidade filogenética. Nós utilizamos uma supertree disponível para a maioria das espécies da ordem, e dados de distribuição das espécies. Nós calculamos o PD para cada hotspot separadamente e utilizamos um modelo nulo para obter os valores esperados dado a riqueza. De 34 hotspots, apenas um apresentou maior PD do que o esperado, treze apresentaram valores menores e o restante valores iguais ao esperado. Nós demonstramos que a relação entre PD e riqueza varia entre regiões biogeográficas, de modo que não há como fazer generalizações acerca da contribuição dos hotspots para a conservação de diversidade evolutiva. De modo geral nossos resultados demonstram que devido ao fato da história evolutiva variar regionalmente, também devem ser estabelecidas as prioridades de conservação nessa escala.

Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-06-23T21:24:53Z No. of bitstreams: 1 AntonioCarvalho.pdf: 2731250 bytes, checksum: 35369a74be0aec3dd6b29a792c37fc35 (MD5) / Made available in DSpace on 2017-06-23T21:24:53Z (GMT). No. of bitstreams: 1 AntonioCarvalho.pdf: 2731250 bytes, checksum: 35369a74be0aec3dd6b29a792c37fc35 (MD5) Previous issue date: 2016-10-10 / Lung cancer has been identi ed as the leading cause of death among cancer patients worldwide. The high rates of deaths and instances of records of this type of cancer worldwide demonstrate the importance of the development and research in order to produce resources for the detection and early diagnosis of this disease. Because of the exhaustive analysis process, alternatives such as computational tools that use image processing techniques and pattern recognition have been widely explored. Therefore, to assist the expert in the identi cation and diagnosis of nodules, systems are developed Computer-Aided Detection (CAD) and Computer-Aided Diagnostic (CADx). This thesis proposes the development of methods that reduce false positives, and the diagnosis of volumes of interest in computed tomography. The proposed methods are based on image processing techniques and pattern recognition. For this, biology concepts have been adapted and applied to the study of the branch of the diversity of species; such concepts are the phylogenetic diversity indexes used in this thesis as texture descriptors. In another aspect, techniques that measure the properties of the shape of radiological ndings have been developed and adapted. Subsequently, an evolutionary methodology is used for the selection of the best models for training. Finally, a support vector machine is applied to perform the classi cation. Promising results were found in the 833 tests that we performed; these tests were divided into 80% for training and 20% for testing. In general, for the best results, we have false positive reduction methods, an accuracy of 99.57%, sensitivity of 99.45%, speci city of 99.61%, and an ROC curve of 0.992. The results obtained for the classi cation of the degree of malignancy and benignity are: accuracy of 93.46%, sensitivity of 92.95%, speci city of 93.49%, and an ROC curve of 0.931. / O câncer de pulmão é apontado como a principal causa de morte entre os pacientes com câncer. As altas taxas de mortes e registros de ocorrências desse câncer em todo o mundo demonstram a importância do desenvolvimento e investigação, a fi m de produzir meios para a detecção e o diagnóstico precoce dessa doença. Devido ao exaustivo processo de análise, alternativas como ferramentas de cunho computacional que utilizam técnicas de processamento de imagens e do reconhecimento de padrões têm sido amplamente exploradas. Assim, para auxiliar o especialista na identifi cação e diagnóstico de nódulos, são desenvolvidos sistemas Computer-Aided Detection (CAD) e Computer-Aided Diagnostic (CADx). Esta tese propõe o desenvolvimento de métodos para redução de falsos positivos em um sistema CAD e diagnóstico de nódulos em tomografi a computadorizada. Os métodos propostas baseiam-se em técnicas de processamento de imagens e reconhecimento de padrões. Para tanto, foram adaptados e aplicados os conceitos da biologia no ramo do estudo da diversidade entre espécies, sendo esses os índices de diversidade logenética, usados nesta tese como descritores de textura. Em outro aspecto, foram desenvolvidas e adaptadas técnicas capazes de mensurar propriedades de forma dos achados radiológicos. Seguindo, usou-se uma metodologia evolutiva genética para seleção dos melhores modelos de treinamento. E por fi m, foi aplicada a máquina de vetor de suporte para realizar a classificação . Resultados promissores foram encontrados em teste com 833 exames divididos em 80% para treino e 20% para testes. Em linhas gerais, para os melhores resultados tem-se, nos métodos de redução de falsos positivos: uma acurácia de 99,57%, sensibilidade de 99,45%, especificidade de 99.61% e uma curva ROC de 0,992. Já nos resultados para a classificação quanto a taxa de malignidade e benignidade, obtiveram-se os seguintes valores: acurácia de 93,46%, sensibilidade de 92,95%, especificidade de 93,49% e uma curva ROC de 0,931.