The Aristolochiaceae are one of the largest angiosperm families, the family has been divided into two subfamilies: Asaroideae, which include Asarum and Saruma, and Aristolochioideae, which includes Thottea sensu lato and Aristolochia sensu lato (Kelly and Gonzales, 2003). Aristolochia sensu lato comprise between 450 and 600 species, distributed throughout the world with centers of diversities in the tropical and subtropical regions (Neinhuis et al., 2005, Wanke et al., 2006a, 2007). However, the extended Mediterranean region including Turkey, the Caucasus and the Near East is likely to be the only diversity hotspot of the genus Aristolochia in the northern hemisphere were up to 60 species and subspecies could be observed (Wanke 2007). Most important contributions to the knowledge of these species were published by Nardi (1984, 1988, 1991, 1993) and Davis & Khan (1961, 1964, 1982), all of these studies were based on morphological characters only. In recent years, with the progress of molecular techniques and in light of the systematic chaos, a detailed study was needed to unravel the evolutionary history prior to a taxonomic revision of this group. The first chapter of my thesis should be regarded as the starting point for more detailed investigation on population level. Preliminary molecular phylogenitic analysis recovered the Mediterranean Aristolochia species as monophyletic (de Groot et al 2006). However, only very few members were included in that study. The latest phylogenetic study by Wanke (2007) dealed with west Mediterranean Aristolochia species and sampled also few members belonging to the east Mediterranean and Caucasian species (3 from Greece, 2 from Georgia and 1 from Turkey). This study reported the Mediterranean Aristolochia species as two molecular and morphologically well supported clades, which were sister to each other. Furthermore, the two closely related species A. sempervirens and A. baetica which have an east west vicariance and are known as Aristolochia sempervirens complex has been recovered as sister group to the remaining west Mediterranean species. A detailed investigation of the evolutionary history of this group is the topic of the second chapter of my thesis (Chapter 2). The Aristolochia sempervirens complex is characterized by an unusual growth form and has a circum Mediterranean distribution. The investigation of these species complex seem to be of great importance to understand speciation and colonization of the Mediterranean by the genus Aristolochia and might shade light in historical evolutionary processes of other plant lineages in the Mediterranean. Furthermore, I test applicability and phylogenetic power of a nuclear single copy gene (nSCG) region to reconstruct well resolved and highly supported gene genealogies as a prerequisite to study evolutionary biology questions in general. Furthermore, a comprehensive overview of leaf epicuticular waxes, hairs and trichomes of 54 species from the old and new world taxa of the genus Aristolochia were investigated using scanning electron microscopy (SEM) to clarify taxonomic status of theses species in contrast to their molecular position. Also this study which is the third chapter of this thesis (Chapter 3), has a strong focus on Mediterranean Aristolochia and tries to provide additional support for molecular findings based on epicuticular waxes and to test them as synapomorphies. Each chapter has its own introduction and abstract resulting in a short general introduction here.

The research presented in this dissertation integrates data and theory to examine three important topics in biology. In the first chapter, I investigate genetic variation at two loci involved in a genetic incompatibility in the genus Xiphophorus. In this genus, hybrids develop a fatal melanoma due to the interaction of an oncogene and its repressor. Using the genetic variation data from each locus, I fit evolutionary models to test for coevolution between the oncogene and the repressor. The results of this study suggest that the evolutionary trajectory of a microsatellite element in the proximal promoter of the repressor locus is affected by the presence of the oncogene. This study significantly advances our understanding of how loci involved in both a genetic incompatibility and a genetically determined cancer evolve. Chapter two addresses the role polyploidy, or whole genome duplication, has played in generating flowering plant diversity. The question of whether polyploidy events facilitate diversification has received considerable attention among plant and evolutionary biologists. To address this question, I estimated the speciation and genome duplication rates for 60 genera of flowering plants. The results suggest that diploids, as opposed to polyploids, generate more species diversity. This study represents the broadest comparative analysis to date of the effect of polyploidy on flowering plant diversity. In the final chapter, I develop a computational method for designing disease surveillance networks. The method is a data-driven, geographic optimization of surveillance sites. Networks constructed using this method are predicted to significantly outperform existing networks, in terms of information quality, efficiency, and robustness. This work involved the coordinated efforts of researchers in biology, epidemiology, and operations research with public health decision makers. Together, the results of this dissertation demonstrate the utility of applying quantitative theory and statistical methods to data in order to address complex, biological processes. / text

Major progress has been made during the last twenty years towards a better understanding of the evolution of angiosperms. Early molecular-phylogenetic analyses revealed three major groups, with eudicots as well as monocots being monophyletic, arisen from a paraphyletic group of dicotyledonous angiosperms (= basal angiosperms). Consistently, numerous phylogenetic studies based on sequence data have recovered the eudicot-clade and increased confidence in its existence. Furthermore this clade, which contains about 75% of angiosperm species diversity, is characterized by the possession of tricolpate and tricolpate-derived pollen and has thus also been called the tricolpate clade. Based on molecular-phylogenetic investigations several lineages, such as Ranunculales, Proteales (= Proteaceae, Nelumbonaceae, Platanaceae), Sabiaceae, Buxaceae plus Didymelaceae, and Trochodendraceae plus Tetracentraceae were shown as belonging to a early-diverging grade (early-diverging or “basal” eudicots), while larger groups like asterids, Caryophyllales, rosids, Santalales, and Saxifragales were identified as being members of a highly supported core clade, the so called “core eudicots”. Nevertheless, phylogenetic relationships among several lineages of the eudicots remained difficult to resolve. This thesis is mainly concentrated on fully resolving the branching order among the different clades of the early-diverging eudicots as well as on clarifying phylogenetic and systematic conditions within several lineages, based on phylogenetic reconstructions using sequence data of rapidly-evolving and non-coding molecular regions, such as spacers and introns. Commonly, fast-evolving and non-coding DNA was used to infer relationships among species and genera, as practised in chapter 3, due to the assumption of being inapplicable caused by putative high levels of homoplasy through multiple substitutions and frequent microstructural changes resulting in non-alignability. However, during the last few years numerous molecular-phylogenetic studies were able to present well resolved angiosperm trees on the basis of rapidly-evolving and non-coding regions from the large single copy region of the chloroplast genome comparable to multi-gene analyses concerning topology and statistical support. Mutational dynamics in spacers and introns was revealed to follow complex patterns related to structural constraints like the introns secondary structure. Therefore extreme sequence variability was always confirmed to mutational hotspots that could be excluded from calculations. Moreover it became clear that combining these non-coding regions with the fast-evolving matK gene can lead to further resolved and statistical supported trees. Chapter 1 deals with the placement of Sabiales inside the early-diverging eudicot grade, while investigating mutational dynamics as well as the utility of different kinds of non-coding and rapidly-evolving DNA within deep-level phylogenetics. It was done by analyzing a combination of nine regions from the large single copy region of the chloroplast genome, including spacers, the sole group I intron, three group II introns and the coding matK for a sampling of 56 taxa. The presented topology is in mainly congruence with the hypothesis on phylogenetic relationships among early-branching eudicots that was gained through the application of a reduced set of five non-coding and fast-evolving molecular markers, including the plastid petD (petB-petD spacer, petD group II intron) plus the trnL-F (trnL group I intron, trnL-F spacer) region and the matK gene. It showed a grade of Ranunculales, Sabiales, Proteales, Trochodendrales and Buxales. The current study differs in showing Sabiales as sister to Proteales in all phylogenetic analyses, in contrast to a second-branching inside early-diverging eudicots and a Bayesian tree displaying Sabiales branching after Proteales. All three hypotheses were tested concerning their likelihood. None of them was shown as being significantly declinable. Thus, albeit the number of characters and informative sites was doubled in comparision to the five-region investigation, the exact position of the Sabiales remained to be resolved with confidence. However, the advanced analyses of the phylogenetic structure of the three different non-coding partitions in comparison to coding genes resulted in the recognition of a significantly higher mean phylogenetic signal per informative character within spacers and introns than in the frequently applied slowly-evolving rbcL gene. The fast-evolving and well performing matK gene is shown to be nested within the non-coding partitions in this respect. Interestingly, the least constrained spacers displayed considerably less phylogenetic structure than both, the group I intron and the group II introns. Molecular evolution is again shown to follow certain patterns in angiosperms, as indicated by the occurrence of mutational hotspots and their connection to structural and functional constraints. This is especially shown for the group II introns studied where highly dynamic sequence parts were rather found in loops than stems. The aim of chapter 2 was to present a comprehensive reconstruction of the phylogenetic relationships inside the order of Ranunculales, the first-branching clade of the early-diverging eudicots, with an emphasis on the evolution of growth forms within the group. Currently, the order comprises seven families (Ranunculaceae, Berberidaceae, Menispermaceae, Lardizabalaceae, Circaeasteraceae – not included due to lacking plant material, Eupteleaceae, Papaveraceae) containing predominantly herbaceous groups as well as trees and lianescent/shrubby forms. A surprising result that emerged due to the increased use of molecular data within systematics during the last twenty years is the inclusion of the woody Eupteleaceae into Ranunculales. Because of its adaptation to wind pollination it was previously placed next to Hamamelididea. Although phylogenetic hypotheses agreed in the exclusion of Eupteleaceae and the predominantly herbaceous Papaveraceae from a core clade the branching order within early-diverging Ranunculales remained a question to be answered. Thus phylogenetic reconstructions based on molecular data of 50 taxa (including outgroup), applying the well-performing non-coding petD and trnL-F as well as the trnK/matK-psbA region including the coding matK, were carried out. The comprehensive sampling resulted in fully resolved and highly supported phylogenies in both, maximum parsimony and model based approaches, with family relations within the core clade being identical and Euptelea appearing as first branching lineage. However, the relationships among the early-diverging Ranunculales could not be resolved with confidence, a result in line with the finding made in chapter 1. The topology was further resolved as Lardizabalaceae being sister to the remaining members of the order, followed by Menispermaceae, Berberidaceae and Ranunculaceae, the latter sharing a sistergroup relationship. Inside the mainly lianescent Lardizabalaceae the shrubby Decaisnea was clearly depicted as first-branching. The systematic controversial Glaucidium and Hydrastis are shown to be early-diverging members of the Ranunculaceae. A central goal of chapter 3 was to test phylogenetic relationships among the members of the ranunculaceous tribe Anemoneae. Currently it consists of the subtribes Anemoninae including Anemone, Hepatica, Pulsatilla and Knowltonia, and Clematidinae, consisting of Archiclematis, Clematis and Naravelia. Furthermore the position and taxonomic rank of several lineages inside the subtribe Anemoninae were examined. Since recent comprehensive molecular-phylogenetic investigations have been carried out for the members of Clematidinae or Anemoninae, 63 species representing all major lineages of the two subtribes were included into analyses. Calculations were carried out on the basis of molecular data of the nuclear ribosomal ITS1&2 and the plastid atpB-rbcL intergenic spacer region. Phylogenetic reconstructions resulted in the recognition of two distinct clades within the tribe, thus corroborating the formation of the two subtribes. Within the subtribe Anemoninae the traditional genera Knowltonia, Pulsatilla and Hepatica are confidently shown to be nested within the genus Anemone. The preliminary classification of the genus, currently consisting of the two subgenera Anemone and Anemonidium, is complemented by the subgenus Hepatica.

A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

En raison de sa remarquable diversité végétale, de son taux d’endémisme, parmi les plus élevés au niveau mondial (79%) et de son extrême vulnérabilité, la Nouvelle-Calédonie est un des premiers hotspots de la biodiversité mondiale. L’une des remarquables originalités de la flore Calédonienne repose sur la présence de nombreux taxa reconnus, en raison de leurs positions phylogénétiques, comme appartenant aux lignées les plus anciennes des plantes à fleurs. Ces lignées d’Angiospermes « reliques » ont une valeur scientifique et patrimoniale importante, puisqu’elles sont de véritables fenêtres sur le passé. A travers l’étude des traits foliaires, de l’anatomie du bois (e.g. type d’éléments conducteurs, perforations, diamètre et longueur des vaisseaux), de l’architecture (e.g. sympoldialité vs monopodialité, phénomène de réitération, rythmicité de croissance) et de la biomécanique des axes, nous chercherons à caractériser les formes et fonctions de ces taxons. Ce projet de thèse vise à examiner les déterminants structurels et fonctionnels de la répartition spatiale actuelle des Angiospermes basales (grade ANITA + Magnoliidae) en Nouvelle-Calédonie. Dans cette perspective nous chercherons à comprendre quels sont les facteurs qui ont conduit au confinement de certains taxons à des habitats restreints ou au contraire à leur dispersion dans des milieux contrastés. Un premier volet du projet en cours, a pour objectif de caractériser la dynamique de croissance d’Amborella trichopoda et sa plasticité architecturale sous différents régimes lumineux. Certains traits écologiques de ces espèces d’Angiospermes de divergence précoce, s’ils n’ont pas contribué à la radiation des plantes à fleurs actuelles, ont pu permettre son enracinement écologique au sein de la flore du Mésozoïque et fournir un répertoire développemental pour l’explosion subséquente de leur diversité. L’identification et l’étude de ces caractères sont donc déterminantes pour la compréhension de l’évolution structurelle et fonctionnelle des plantes à fleurs. / New Caledonia (NC) is one of the main biodiversity hotspots (Myers 1988), this is because of its remarkable plant diversity, its endemism rates, among the highest in the world (79%), and because of the vulnerability of its flora. One of the main originalities of New Caledonia flora is based on the presence of a large number of taxa recognized, due to their phylogenetical positions, as the most ancient extant representatives of angiosperms. For a long time, New Caledonia has been considered as an early upset fragment of the Gondwana (Pelletier 2006) that suffered an interrupted history of isolation which conferred the evolutionary particularities that we observe today. However, recent evidences show that NC has derived from the Australian land during the late Mesozoic (~80 Mya), the island was then submerged during the first half of the Cenozoic (Pelletier 2006) and a reemergence of the island seems to have occurred ~37 Mya (Cluzel et al. 1998). After the reappearance of the island above the sea level, several events of recolonisation occurred and they wrought the biodiversity that we observe nowadays (Pillon 2012). NC presents humid forests which are unique relics; under the influence of climate changes, these forests have virtually disappeared from other regions of the globe (Morat et al. 1986). The lineages of “relictual” angiosperms, mainly subservient to these humid forests, have a great scientific and patrimony value, as they can be considered as genuine windows on the past. These taxa are susceptible to contain primitive characters which have either disappeared in most of the existing flowering plants, or that are still shared by a narrow number of them. The identification and the study of these characters are therefore determinants for the comprehension of angiosperms evolution. Some ecological features of these panchronic species, may have either contributed to the huge radiation of extant angiosperms, or they may have contributed to the ecological settling of angiosperms within the Mesozoic flora, providing them with a developmental repertoire for the subsequent explosion of their diversity. This PhD project aims to study the ecological, anatomical and functional diversity of basal angiosperms and it seeks to analyze the evolutionary patterns of these structural and functional features. We will consider here as “basal” angiosperms a great group of flowering plants that has diverged before the monocot and eudicot node. This group is conformed by the ANITA grade, formed by Amborella (a single species endemic to NC), Nymphaeales (waterlilies and other herbaceous aquatic plants) and Austrobaileyales (aromatic woody plants). The Magnoliid subclass, a clade of flowering of early divergence, which contains plants considered as paleodicots by Cronquist (1988), will be also included in the analysis of the « basal » taxa. More recently, the Magnoliids have been redefined as a clade comprising Chloranthales, Canellales, Laurales, Magnoliales, et Piperales (APG III, 2009). In a second part of the project, a fieldtrip to Mexico will be held in order to include speces belonging to the Chloranthaceae and Schisandraceae, as well as Cabombaceae et Nymphaeaceae, by this means, we will incorporate species belonging to all the orders of the “basal” angiosperms, reinforcing the comparative analysis. This research work will lean on the recent publications of the phylogenetic relations within basal angiosperms...

Submitted by Filipe Marcel Fernandes Gonçalves null (filipemfg@gmail.com) on 2016-10-13T22:19:26Z No. of bitstreams: 1 Dissertação_Mestrado_Filipe_Marcel_Fernandes_Gonçalves.pdf: 6479864 bytes, checksum: 4596171ab4ce8e8c1a6ce9723f335b36 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-10-19T18:04:08Z (GMT) No. of bitstreams: 1 goncalves_fmf_me_sjrp.pdf: 6479864 bytes, checksum: 4596171ab4ce8e8c1a6ce9723f335b36 (MD5) / Made available in DSpace on 2016-10-19T18:04:08Z (GMT). No. of bitstreams: 1 goncalves_fmf_me_sjrp.pdf: 6479864 bytes, checksum: 4596171ab4ce8e8c1a6ce9723f335b36 (MD5) Previous issue date: 2016-08-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O grande volume de imagens disponível na Web gerado em diferentes domínios requer um conhecimento especializado para sua a análise e identificação. Nesse sentido, recentes avanços ocorreram com desenvolvimento de técnicas de recuperação de imagens baseadas nas características visuais. Entretanto, o gap semântico entre as características de baixo-nível das imagens e aquilo que a imagem representa ainda é um grande desafio. Uma solução para diminuir o gap semântico consiste em combinar a informação de características visuais das imagens com o conhecimento do domínio de tais imagens. Nesse sentido, ontologias podem auxiliar, já que estruturam o conhecimento. Desse modo, o presente trabalho apresenta uma nova abordagem denominada Recuperação Interativa de Imagens Guiada por Semântica (Semantic Interactive Image Retrieval – SIIR) que combina técnicas de recuperação de imagens baseadas no conteúdo (Content Based Image Retrieval – CBIR) e aprendizado não supervisionado, com o conhecimento definido em ontologias. Desse modo, o trabalho em questão propõe uma nova abordagem a fim de simular o papel dos biólogos na classificação de famílias de Angiospermas a partir de uma imagem e seu conteúdo. Para tanto, foi desenvolvida uma ontologia de estruturas e propriedades de plantas com flor e fruto, de modo a conceitualizar e relacionar tais atributos visando a classificação de famílias de Angiospermas. Para análise das características visuais foram utilizados métodos de extração de características de baixo-nível das imagens. Com relação ao aprendizado não supervisionado foi utilizado o algoritmo RL-Sim a fim de melhorar a eficácia da recuperação das imagens. A abordagem combina técnicas CBIR com ontologias ao utilizar um grafo bipartido e um grafo discriminativo de atributos. O grafo discriminativo de atributos permite a análise semântica utilizada para selecionar o atributo que melhor classifica a planta da imagem de busca. Os atributos selecionados são utilizados para formular uma interação com um usuário, de modo a melhorar a eficácia da recuperação e diminuir os esforços necessários na identificação da planta. O método proposto foi avaliado nos conjuntos de dados públicos Oxford Flowers 17 e 102 Classes, de modo que os resultados demonstram alta eficácia para ambos os conjuntos de dados quando comparados com outras abordagens. / A large amount of images is currently generated in many domains, thus requiring specialized knowledge on the identification and analysis. From one standpoint, many advances have been accomplished in the development of image retrieval techniques based on visual image properties. However, the semantic gap between low-level features and high level concepts still represents a challenge scenario. One another standpoint, knowledge has also been structured in many fields by ontologies. A promising solution for bridging the semantic gap consists in combining the information from low-level features with semantic knowledge. This work proposes a new approach denominated Semantic Interactive Image Retrieval (SIIR) which combines Content Based Image Retrieval (CBIR) and unsupervised learning with ontology techniques. We present a novel approach aiming to simulate the biologists role in the classification of Angiosperm families from image sources and their content. In order to achieve this goal, we developed a domain ontology from plant properties and structures, hence relating features from the Angiosperm families. In regard to Unsupervised Learning, we used the RL-Sim algorithm to improve image classification. The proposed approach combines CBIR techniques with ontologies using a bipartite graph and a discriminative attribute graph. Such graph structures allow a semantic analysis used for the selection of the attribute that best classify the plant. The selected attributes are used for formulating the user interactions, improving the effectiveness and reducing the user efforts required. The proposed method was evaluated on the popular Oxford Flowers 17 and 102 Classes datasets, yielding very high effectiveness results in both datasets when compared to other approaches.

A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

Les travaux de cette thèse portent sur la caractérisation chimique des ambres provenant de plusieurs gisements d’âges et d’origines géographiques variés, dont certains sont inédits. Des protocoles identiques à tous les échantillons et combinant les analyses spectroscopiques (IR et RMN 13C) et chromatographiques (THM-CPG-SM) ont été appliqués, permettant d’identifier l’origine botanique des ambres et fournissant des indices pour la reconstitution des paléoenvironnements terrestres. La caractérisation chimique des gisements d’ambre du Jurassique supérieur (Kimméridgien) jusqu’au Crétacé supérieur (Santonien) du Liban, de Jordanie, du Congo, d’Equateur et de France, permet de proposer des biomarqueurs pour les résines de Cheirolepidiaceae, une famille exclusivement mésozoïque de Conifères. Une évolution des sources botaniques des résines produites durant le Mésozoïque et le Cénozoïque est alors discutée. Une production dominée par les familles de Conifères Araucariaceae et Cheirolepidiaceae est remarquée au Jurassique supérieur et Crétacé inférieur. La production au Crétacé supérieur est plutôt dominée par des Cupressaceae. Au Cénozoïque, les origines botaniques des ambres sont plus variées, et des familles d’Angiospermes sont à l’origine de nombreux gisements, dont l’ambre du Pérou produit par une Fabaceae. La production par des Conifères reste toutefois importante au Tertiaire, à l’exemple des ambres de Nouvelle-Zélande qui ont pour origine les Araucariaceae. Les données obtenues ont permis une ré-évaluation de la classification des ambres par Py-GC-MS. Ainsi, une nouvelle molécule dont la structure est inconnue encore, a été identifiée dans les chromatogrammes d’ambres de classe Ib et Ic, ajoutant un caractère discriminant entre ces deux sous-classes. Enfin, la relation âge / maturation des résines fossiles est discutée, qui dépend avant tout des conditions d’enfouissement des résines. Une large base de données moléculaires est ainsi établie pour un grand nombre de gisements d’âges et d’origines botaniques variés, qui permettra une comparaison globale dans les travaux futurs. / This work focuses on the chemical characterisation of amber from different outcrops from different localities, and varied ages. Some of these outcrops had never been studied. All the amber samples were analysed with the same analytical techniques. The combination of the data obtained from spectroscopic (IR and 13C NMR) and chromatographic (THM-GC-MS) analysis allows the identification of the botanical origin of the amber and provide some information, for the reconstruction of the palaeoenvironment. Biomarkers for the cheirolepidiaceous resins were proposed based on the chemical characterisation of different amber outcrops dating from the Upper Jurassic (Kimmeridgian) to the Upper Cretaceous (Santonian) from Lebanon, Jordan, Congo, Ecuador and France. The Cheirolepidiaceae familt was exclusively present in the Mesozoic era. Hence, the evolution of the botanical origins of the produced resins during the Mesozoic and Cenozoic eras was discussed. It seems that Araucariaceae and Cheirolepidiaceae were the dominant resin producing trees during the Upper Jurassic and the Lower Cretaceous. While, cupressaceous resiniferous plants were dominant during the Upper Cretaceous. Howerver, resins dating from the Cenozoic era, were produced by a wider variety of plants, as resiniferous families of Angiosperm intensively participated in the resin production, i.e. the Peruvian amber produced by Fabaceae. Conifer resins traces were also detected in the Tertiary, such as the amber from the Araucariaceae found in New Zealand. The obtained data allowed a re-evaluation of the classification of ambers by Py-GC-MS, leading to the discovery of a novel molecule. This molecule of an unknown structure brings a new discrimination factor between the classes Ib and Ic. Finally, the age / maturity relationship is showed to be dependent on the burial and the conservation conditions of the resins. A broad molecular database is established based a large group of amber outcrops from different ages, and having diverse botanical origins. This database could be used as a comparative platform for further work in the future.

Major progress has been made during the last twenty years towards a better understanding of the evolution of angiosperms. Early molecular-phylogenetic analyses revealed three major groups, with eudicots as well as monocots being monophyletic, arisen from a paraphyletic group of dicotyledonous angiosperms (= basal angiosperms). Consistently, numerous phylogenetic studies based on sequence data have recovered the eudicot-clade and increased confidence in its existence. Furthermore this clade, which contains about 75% of angiosperm species diversity, is characterized by the possession of tricolpate and tricolpate-derived pollen and has thus also been called the tricolpate clade. Based on molecular-phylogenetic investigations several lineages, such as Ranunculales, Proteales (= Proteaceae, Nelumbonaceae, Platanaceae), Sabiaceae, Buxaceae plus Didymelaceae, and Trochodendraceae plus Tetracentraceae were shown as belonging to a early-diverging grade (early-diverging or “basal” eudicots), while larger groups like asterids, Caryophyllales, rosids, Santalales, and Saxifragales were identified as being members of a highly supported core clade, the so called “core eudicots”. Nevertheless, phylogenetic relationships among several lineages of the eudicots remained difficult to resolve. This thesis is mainly concentrated on fully resolving the branching order among the different clades of the early-diverging eudicots as well as on clarifying phylogenetic and systematic conditions within several lineages, based on phylogenetic reconstructions using sequence data of rapidly-evolving and non-coding molecular regions, such as spacers and introns. Commonly, fast-evolving and non-coding DNA was used to infer relationships among species and genera, as practised in chapter 3, due to the assumption of being inapplicable caused by putative high levels of homoplasy through multiple substitutions and frequent microstructural changes resulting in non-alignability. However, during the last few years numerous molecular-phylogenetic studies were able to present well resolved angiosperm trees on the basis of rapidly-evolving and non-coding regions from the large single copy region of the chloroplast genome comparable to multi-gene analyses concerning topology and statistical support. Mutational dynamics in spacers and introns was revealed to follow complex patterns related to structural constraints like the introns secondary structure. Therefore extreme sequence variability was always confirmed to mutational hotspots that could be excluded from calculations. Moreover it became clear that combining these non-coding regions with the fast-evolving matK gene can lead to further resolved and statistical supported trees. Chapter 1 deals with the placement of Sabiales inside the early-diverging eudicot grade, while investigating mutational dynamics as well as the utility of different kinds of non-coding and rapidly-evolving DNA within deep-level phylogenetics. It was done by analyzing a combination of nine regions from the large single copy region of the chloroplast genome, including spacers, the sole group I intron, three group II introns and the coding matK for a sampling of 56 taxa. The presented topology is in mainly congruence with the hypothesis on phylogenetic relationships among early-branching eudicots that was gained through the application of a reduced set of five non-coding and fast-evolving molecular markers, including the plastid petD (petB-petD spacer, petD group II intron) plus the trnL-F (trnL group I intron, trnL-F spacer) region and the matK gene. It showed a grade of Ranunculales, Sabiales, Proteales, Trochodendrales and Buxales. The current study differs in showing Sabiales as sister to Proteales in all phylogenetic analyses, in contrast to a second-branching inside early-diverging eudicots and a Bayesian tree displaying Sabiales branching after Proteales. All three hypotheses were tested concerning their likelihood. None of them was shown as being significantly declinable. Thus, albeit the number of characters and informative sites was doubled in comparision to the five-region investigation, the exact position of the Sabiales remained to be resolved with confidence. However, the advanced analyses of the phylogenetic structure of the three different non-coding partitions in comparison to coding genes resulted in the recognition of a significantly higher mean phylogenetic signal per informative character within spacers and introns than in the frequently applied slowly-evolving rbcL gene. The fast-evolving and well performing matK gene is shown to be nested within the non-coding partitions in this respect. Interestingly, the least constrained spacers displayed considerably less phylogenetic structure than both, the group I intron and the group II introns. Molecular evolution is again shown to follow certain patterns in angiosperms, as indicated by the occurrence of mutational hotspots and their connection to structural and functional constraints. This is especially shown for the group II introns studied where highly dynamic sequence parts were rather found in loops than stems. The aim of chapter 2 was to present a comprehensive reconstruction of the phylogenetic relationships inside the order of Ranunculales, the first-branching clade of the early-diverging eudicots, with an emphasis on the evolution of growth forms within the group. Currently, the order comprises seven families (Ranunculaceae, Berberidaceae, Menispermaceae, Lardizabalaceae, Circaeasteraceae – not included due to lacking plant material, Eupteleaceae, Papaveraceae) containing predominantly herbaceous groups as well as trees and lianescent/shrubby forms. A surprising result that emerged due to the increased use of molecular data within systematics during the last twenty years is the inclusion of the woody Eupteleaceae into Ranunculales. Because of its adaptation to wind pollination it was previously placed next to Hamamelididea. Although phylogenetic hypotheses agreed in the exclusion of Eupteleaceae and the predominantly herbaceous Papaveraceae from a core clade the branching order within early-diverging Ranunculales remained a question to be answered. Thus phylogenetic reconstructions based on molecular data of 50 taxa (including outgroup), applying the well-performing non-coding petD and trnL-F as well as the trnK/matK-psbA region including the coding matK, were carried out. The comprehensive sampling resulted in fully resolved and highly supported phylogenies in both, maximum parsimony and model based approaches, with family relations within the core clade being identical and Euptelea appearing as first branching lineage. However, the relationships among the early-diverging Ranunculales could not be resolved with confidence, a result in line with the finding made in chapter 1. The topology was further resolved as Lardizabalaceae being sister to the remaining members of the order, followed by Menispermaceae, Berberidaceae and Ranunculaceae, the latter sharing a sistergroup relationship. Inside the mainly lianescent Lardizabalaceae the shrubby Decaisnea was clearly depicted as first-branching. The systematic controversial Glaucidium and Hydrastis are shown to be early-diverging members of the Ranunculaceae. A central goal of chapter 3 was to test phylogenetic relationships among the members of the ranunculaceous tribe Anemoneae. Currently it consists of the subtribes Anemoninae including Anemone, Hepatica, Pulsatilla and Knowltonia, and Clematidinae, consisting of Archiclematis, Clematis and Naravelia. Furthermore the position and taxonomic rank of several lineages inside the subtribe Anemoninae were examined. Since recent comprehensive molecular-phylogenetic investigations have been carried out for the members of Clematidinae or Anemoninae, 63 species representing all major lineages of the two subtribes were included into analyses. Calculations were carried out on the basis of molecular data of the nuclear ribosomal ITS1&2 and the plastid atpB-rbcL intergenic spacer region. Phylogenetic reconstructions resulted in the recognition of two distinct clades within the tribe, thus corroborating the formation of the two subtribes. Within the subtribe Anemoninae the traditional genera Knowltonia, Pulsatilla and Hepatica are confidently shown to be nested within the genus Anemone. The preliminary classification of the genus, currently consisting of the two subgenera Anemone and Anemonidium, is complemented by the subgenus Hepatica.