Orientador: Fernando Roberto Martins / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T13:06:00Z (GMT). No. of bitstreams: 1 Sfair_JuliaCaram_D.pdf: 3461984 bytes, checksum: cf19d74d1427ea20dbb84668bc5de435 (MD5) Previous issue date: 2011 / Resumo: A interação entre lianas (trepadeiras lenhosas) e forófitos (árvore-suporte) é caracterizada como antagonística, uma vez que as lianas diminuem a produção e a taxa de crescimento de árvores, aumentando a sua taxa de mortalidade. Esses estudos focam na interação entre pares de espécies, não dando ênfase na estrutura de interação sob uma perspectiva da comunidade. Essa tese teve como objetivo a compreensão dos padrões de interação entre lianas e forófitos utilizando a análise de redes, bem como a compreensão dos processos e implicações que surgem desse padrão. Mostramos que, para três áreas no sudeste brasileiro (cerradão, floresta estacional semidecídua e floresta ombrófila densa) o padrão foi o mesmo: aninhado. O aninhamento implica em um gradiente no número de interações, que pode ser explicado por caracteres e sua combinação (tamanho de lianas e de forófitos, mecanismos e morfologias de árvores que evitam lianas e modos de ascensão de lianas) e neutros (abundância). Apresentamos uma nova métrica (contribuição da espécie para o aninhamento) e mostramos que variáveis relacionadas aos caracteres e neutras explicam o aninhamento. A partir das análises de redes foi possível propor um novo método de manejo de lianas, que privilegia o corte de espécies com mais interações. Dessa maneira, espera-se que haja a manutenção da riqueza de lianas na comunidade / Abstract: The interaction between lianas (woody climbers) and phorophytes (host-tree) is characterized as antagonistic, since lianas decrease the fruit production and the rate of tree growth, which increases their mortality rate. These studies focus on the interaction of liana and phorophyte pairs, not emphasizing the community perspective as a whole. This thesis aimed at the understanding of interaction patterns between lianas and phorophytes using complex network analysis, as well the understanding of process and implications that arise from this pattern. We showed that three vegetation formations in southeastern Brazil (savanna woodland, seasonal dry tropical forest and tropical wet forest) have the same pattern: nestedness. Nestedness presupposes a gradient of number of interactions (from least to most linked species), that are explained by traits (liana and tree size, mechanisms and morphologies to avoid lianas, and liana climbing mode) and neutral (abundance) factors. We developed a new metric (species contribution to nestedness), which also varied according to traits and neutral factors. Using this knowledge, we proposed a new liana management method, which focuses on the most linked species. This method was designed to maintain the liana richness in a forest / Doutorado / Ecologia / Doutor em Ecologia

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / The open savanna areas of the Cerrado region in Central Brazil have been considered as marginal or complementary habitats to hummingbirds, even with a relatively small number of truly ornithophillous plant species. The structural and climatic conditions would explain the low number of ornithophilous species, which are better represented in forest environments, being the Atlantic forest the Brazilian biome with the greatest number of hummingbird pollinated species. The mutualistic interactions between plants and pollinators seem to be important for the evolution and maintenance of biodiversity, in such a way that modern methods and metrics for the analysis of these networks have been used to understand the organization of species in such communities. The objective of the present study was to describe the interaction between hummingbirds and plants in three cerrado areas, the Panga Ecological Station and the Clube de Caça e Pesca Itororó de Uberlândia, in Uberlândia, MG, and the Serra de Caldas Novas State Park, in Caldas Novas, GO. In each area there were used two transects of one hectare each, which were followed every other week to identify the plant species used by hummingbirds. The number of individuals and flowers were recorded and the distribution pattern along the transects were analyzed. The nectar was analyzed in order to estimate the amount of energy available for the hummingbirds during the study. Hummingbird species were identified and their visiting behavior was observed. Based on field data and literature records, the interaction networks between hummingbirds and plants for each area were built and analyzed. The number of plant species offering nectar for the hummingbirds (26) was higher than observed for other studies in the same areas but was lower than the ones recorded for tropical forest habits. Only nine species presented ornithophilous syndrome. The Vochysiaceae was the most representative family as a whole, and the Bromeliaceae and Rubiaceae were the most important among the truly ornithophilous. Most families were represented by a few genera and species, as in most hummingbird flora studies to date, supporting the idea of diffuse coevolution between these birds and plants. Among the non-ornithophilous plants, most have yellow flowers with gullet or flag corolla while among the ornithophilous, the tubular, red or yellow flowers predominate. Most ornithophilous plants were herbs while the non-ornithophilous were mostly trees. There were 13 hummingbird species among the three areas, most of the subfamily Trochilinae, a number of species greater than observed in study of pollination in most environments, including Tropical Forest areas. The relatively small number of truly ornithophilous species in the Brazilian savanna may cause the hummingbirds to visit many flowers with morphology adapted to other pollinators. Despite the morphological differences, the nectar features of ornithophilous and non-ornithophilous flowers were not significantly different. Although the Cerrado flora has been characterized by its high β-diversity, the transects and areas were very similar both for the plants used by hummingbirds and for the resource availability pattern. The interaction networks showed asymmetry and nestedness patterns similar to the described for other mutualistic networks, with average of connectance of 38%, even greater than observed for other plant/pollinator networks. Palicourea rigida was the most important plant species for the hummingbirds in most areas and Amazilia fimbriata was the hummingbird that visited the greatest number of plant species. / Os ambientes abertos de Cerrado têm sido considerados ambientes marginais ou complementares para beija-flores, inclusive com um número relativamente baixo de espécies de plantas tipicamente ornitófilas. As características estruturais e climáticas do Cerrado seriam a causa do baixo número de espécies ornitófilas, que estão mais bem representadas em ambientes florestais, sendo a Mata Atlântica o bioma com maior número de espécies polinizadas por beija-flores. As interações mutualísticas entre plantas e polinizadores parecem ser importantes para a evolução e manutenção da biodiversidade, de maneira que os métodos e métricas modernas de análise de redes de interações têm sido utilizados para entender como se organizam os grupos de espécies que interagem numa comunidade. O objetivo do presente trabalho foi descrever as interações entre beija-flores e plantas em três áreas de cerrado, a Estação Ecológica do Panga e o Clube de Caça e Pesca Itororó de Uberlândia, em Uberlândia, MG e o Parque Estadual da Serra de Caldas Novas, GO. Em cada área foram demarcados dois transectos de um hectare cada, em fisionomias de cerrado sentido restrito, que foram percorridos quinzenalmente para identificação das espécies utilizadas pelos beija-flores. Foram registrados o número de indivíduos e de flores e a distribuição destes no transecto. Características relativas ao néctar foram avaliadas para se estimar a quantidade de energia disponível aos beija-flores nas áreas, durante o período do estudo. As espécies de beija-flores foram identificadas e observadas. Com os dados obtidos, e com registros na literatura de interações ocorrentes nas mesmas áreas, foram construídas redes de interações entre beija-flores e plantas de cada comunidade estudada. O número de espécies de plantas registrado (26) foi maior que o encontrado em outros estudos nas mesmas áreas, porém foi menor que na maioria dos ambientes de florestas tropicais. Destas, apenas nove espécies apresentaram síndrome de ornitofilia. A família Vochysiaceae foi a mais representativa de modo geral, e entre as ornitófilas foram Bromeliaceae e Rubiaceae. A maior parte das famílias foi representada por poucos gêneros e espécies como ocorreu na maioria dos estudos de flora visitada por beijaflores, corroborando a descrição de uma coevolução difusa entre estes grupos de aves e plantas. Predominaram na flora flores não ornitófilas, amarelas, em forma de goela e estandarte. Entre as ornitófilas predominou o tipo tubo de coloração vermelha e amarela. O hábito herbáceo foi o mais representado entre as espécies ornitófilas e o arbóreo entre as demais. Foram registradas 13 espécies de beija-flores nas três áreas, sendo a maioria da subfamília Trochilinae, número maior que o registrado em estudos de polinização na maioria dos ambientes, inclusive em matas. O pequeno número de espécies tipicamente ornitófilas no cerrado talvez seja o motivo dos beija-flores visitarem um maior número de flores com características de outros sistemas de polinização. Apesar da diversidade morfológica, as características do néctar de espécies ornitófilas ou não, não foram significativamente diferentes. Apesar da grande diversidade beta descrita para as plantas do Cerrado, todas as áreas e transectos foram muito similares em relação às espécies de plantas e ao padrão de oferta de recursos. As redes de interações mostraram padrões de assimetria e aninhamento semelhantes aos descritos para outras redes mutualísticas, com média de conectância de 38 %, maior que o relatado para redes plantas/polinizadores. Palicourea rigida foi a espécie mais importante para os beija-flores na maioria das áreas, e entre os beija-flores, Amazilia fimbriata foi o beija-flor que visitou o maior número de espécies de plantas. / Doutor em Ecologia e Conservação de Recursos Naturais

La matrice extracellulaire est constituée d'un réseau tridimensionnel de protéines et de polysaccharides complexes, les glycosaminoglycanes. Elle apporte un support structural aux tissus et aux cellules dont elle est capable de moduler la prolifération, la migration et la différenciation. Nous avons créé une base de données d'interactions extracellulaires protéine-protéine et protéine-glycosaminoglycane, MatrixDB, qui est disponible sur le Web (http://matrixdb.ibcp.fr). Nous avons intégré des données expérimentales, des données issues de l’analyse de la littérature et des données issues de bases de données d'interactions publiquement disponibles. Nous avons respecté les standards de curation et d’échange de données du consortium IMEx dont fait partie MatrixDB. MatrixDB permet la construction et la visualisation de l'interactome extracellulaire entier et de plusieurs types de réseaux d'interactions, spécifiques d'une molécule, d'un tissu, d'une pathologie ou d'un processus biologique. Nous avons ainsi caractérisé le réseau d’interactions extracellulaire associé au vieillissement et mis en évidence le rôle important des glycosaminoglycanes et du calcium dans ce réseau. Nous avons construit le réseau d'interactions d'une matricryptine anti-angiogénique et anti-tumorale, l'endostatine, qui est issue du collagène XVIII. Les analyses structurales et fonctionnelles de ce réseau ont montré que les partenaires de l’endostatine sont majoritairement impliqués dans l’adhésion cellulaire et que les domaines EGF (Epidermal Growth Factor) sont surreprésentés. Cette propriété nous a permis d'identifier expérimentalement d'autres partenaires de l'endostatine possédant un ou plusieurs domaines EGF et de nouvelles fonctions de l’endostatine. Nous avons modélisé les complexes formés par l'endostatine avec deux de ses partenaires pour identifier les sites d'interactions. Ces prédictions, associées aux données expérimentales, ont permis de déterminer des interactions susceptibles d'être établies simultanément par l'endostatine. L'intégration de ces données et des paramètres cinétiques et d'affinité dans le réseau d'interactions de l'endostatine sera utilisée pour proposer un modèle de son mécanisme d'action qui reste mal connu / The extracellular matrix is composed of a tridimensional network of proteins and complex polysaccharides called glycosaminoglycans. It provides a structural support to tissues and modulates cell proliferation, migration and differenciation. We have created a database of protein-protein and proteinglycosaminoglycan extracellular interactions, MatrixDB (http://matrixdb.ibcp.fr). We have integrated experimental data, data issued of the literature curation and data from interaction databases publicly available. We have respected the curation and exchange standards of the IMEx consortium that includes MatrixDB. MatrixDB allows the construction and the visualization of the entire extracellular network and other types of interaction networks specific of a molecule, a tissue, a disease or a biological process. We have characterized the aging-related extracellular interaction network and underlined the important role of glycosaminoglycans and calcium in this network. We have constructed the interaction network of an antitumoral and anti-angiogenic matricryptin, endostatin, issued from collagen XVIII. Functional and structural analysis of their network showed that partners of endostatin are mostly involved in cell adhesion and that EGF domains are overrepresented. This has allowed us to to identify experimentally other partners of endostatin possessing one or more EGF domains and to propose new functions of endostatin. We have modelled complexes formed by endostatin with two of its partners to identify the binding sites.These predictions, associated with experimental data, allowed us to determine interactions able to be established simultaneously by endostatin. Integration of these data and of kinetics and affinity parameters in the interaction network of endostatin will be used to build a model of its mechanism of action that is not fully elucidated

Les interactions font partie intégrante des écosystèmes. Que ce soit aux niveaux les plus fins, comme les protéines, ou les plus larges, comme les méta-communautés, il est possible de les regrouper en réseaux et d’en étudier la structure. Cela a permis de mettre en évidence que certaines structures sont observables à différents niveaux, c’est le cas par exemple des réseaux emboîtés. De plus, les réseaux d’interaction ont la spécificité de ne pas être fixes dans le temps et l’espace, ce qui leur confère un avantage de taille pour l’étude de l’évolution. Ils peuvent ainsi servir de support à l’études des mécanismes intervenants dans les processus évolutifs. Cependant, il n’existe pas encore de méthodologie ayant fait consensus sur l’utilisation des réseaux et leur analyse à différentes échelles d’organisation. Cette thèse se base sur l’hypothèse que les réseaux, de par leurs propriétés, sont pertinents à considérer pour comprendre l’évolution et ce à différentes échelles d’organisation, et offrent la possibilité de faire des liens entre chacune d’entre elles. L’approche basée sur les réseaux, combinée à l’utilisation de modèles théorique serait donc un outil méthodologique puissant dans l’élargissement des connaissances concernant les processus sous-jacents à l’évolution. La thèse qui suit composée de six chapitres dont le contenu est le suivant. Elle commence par un chapitre d’introduction aux concepts d’intérêts, notamment sur l’évolution et la coévolution. Le deuxième chapitre est une introduction à l’utilisation des réseaux en écologie, suivit par le troisième chapitre qui effectue une revue non exhaustive des méthodologies développées autour des réseaux d’interactions. Les chapitres suivants sont en quelque sorte une mise en pratique de ces méthodes et ce à différents niveaux d’organisation. Le quatrième chapitre revient sur une étape avortée de ce doctorat qui servira tout de même à la construction du modèle du chapitre suivant. Le cinquième chapitre se concentre sur la coévolution et son suivit au travers des réseaux d’interaction entre les bactéries et leurs virus. Enfin, le sixième chapitre traque l’évolution des communautés grâce à la structure des arbres phylogénétiques et structure des réseaux d’interactions au cours du temps. / Interactions are an integral part of ecosystems. Whether at the finest levels, such as proteins, or the broadest, such as meta-communities, it is possible to group them into networks and study their structure. This made it possible to demonstrate that certain structures can be observed at different levels, such as nested networks, for example. In addition, interaction networks have the property of not being fixed in time and space, which gives them a major advantage for the study of evolution. They can thus serve as a support for the study of the mechanisms involved in the evolutionary processes. However, there is not yet a methodology that has achieved consensus on the use of networks and their analysis at different organizational scales. This thesis is based on the hypothesis that networks, by virtue of their properties, are relevant to consider in order to understand evolution at different organizational scales, and offer the possibility of making links between each of them. The network-based approach, combined with the use of theoretical models, would therefore be a powerful methodological tool in expanding knowledge about the processes underlying evolution. The thesis which follows consists of six chapters whose content is as follows. It begins with an introductory chapter to the concepts of interest, in particular on evolution and coevolution. The second chapter is an introduction to the use of networks in ecology, followed by the third chapter which performs a non-exhaustive review of the methodologies developed around interaction networks. The following chapters are in a way a practical application of these methods at different levels of organization. The fourth chapter returns to an aborted stage of this doctorate which will nevertheless be used to construct the model of the following chapter. The fifth chapter focuses on coevolution and its follow-up through the interaction networks between bacteria and their viruses. Finally, the sixth chapter tracks the evolution of communities thanks to the structure of phylogenetic trees and the structure of interaction networks over time.