There is no abstract available for this thesis. / Department of Anthropology

L’empreinte écologique de l’homme sur les milieux naturels forestiers d’Afrique centrale n’a cessé de s’accroître au cours des dernières décennies, et rares sont les écosystèmes qui ne sont pas exploités. Ainsi, même des milieux a priori hostiles comme les grottes constituent des ressources répondant aux besoins primaires des populations environnantes (chasse, pêche, lieu de culte), mais permettant également le développement d’activités économiques (exploitation minière et écotourisme). Cette anthropisation est susceptible d’augmenter l’exposition des populations humaines à une multitude d'agents infectieux circulant au sein de la faune cavernicole. La présence d'animaux sauvages ou domestiques dans l'environnement immédiat des grottes contribue également à augmenter un tel risque. Parmi ces agents infectieux, certains peuvent être transmis par contact direct avec le réservoir animal, d’autres peuvent nécessiter l’intervention d’insectes hématophages. Le rôle de ces insectes dans l'épidémiologie de nombreux pathogènes est bien connu en Afrique en milieux épigés, mais demeure largement sous-investigué dans les environnements cavernicoles. Dans ce travail de thèse, nous nous sommes proposés de réponde à cette problématique. Dans six grottes du Gabon nous avons entrepris une étude de la diversité des diptères hématophages, en réalisant un inventaire taxonomique et l'étude de la dynamique temporelle des assemblages d'espèces. Dans un second temps, nous avons entrepris un criblage moléculaire d'agents infectieux parasitaires, bactériens et viraux en ayant recours à des techniques de détection par PCR nichée et séquençage à haut débit.Les travaux menés nous ont permis de réaliser un inventaire taxonomique de la faune diptérienne hématophage colonisant les grottes explorées. Notre étude a permis de découvrir une part importante de sa diversité de diptères hématophages cavernicoles, représentant plus de 60% des espèces de diptères (tout milieux confondus) actuellement au Gabon. Nos données ont montré que la composition des communautés de diptères était différente d'une grotte à une autre, et que ces dernières présentaient des variations au cours du temps en lien avec les variations microclimatiques des grottes. Le criblage d'agents infectieux chez les diptères collectés a permis 1) d'explorer la diversité parasitaire, virale et bactérienne qu'ils hébergent et 2) d'évaluer leur implication dans la transmission / The man's ecological mark on natural forest environments of central Africa has been increasing in recent decades, and only few natural areas remain non exploited yet. Thus, even supposedly hostile environments such as caves meet the primary needs of surrounding populations (hunting, fishing, shamanic practices), or economical needs (mining and ecotourism). That anthropization is likely to increase the exposure of human populations to multiple infectious agents carried by cave fauna. The presence of wild or domestic animals in the surroundings of caves also increase that risk. Among these infectious agents, some can be transmitted by direct contact with animal reservoirs, whereas others may require the involvement of blood-sucking insects. The role of these insects in the epidemiology of many pathogens is well known in Africa, particularly in epigeic environments, but remains largely investigated in caves. In this thesis work, we proposed to address that issue. In six caves of Gabon we firstly explored the diversity of blood-sucking Diptera, and we studied temporal dynamics of species assemblages. Secondly, we undertook a molecular screening of haemosporidia, bacteria and viruses using nested PCR and high-throughput sequencing.The work carried out has enable to make a taxonomic inventory of the Diptera fauna of the investigated caves. Our study revealed a significant diversity of the blood-sucking Diptera fauna, accounting for more than 60 percent of blood-sucking Diptera species currently known in Gabon, in all types of areas. Our data showed that the composition of Diptera communities was different from one cave to another, and that Diptera assemblages varied over time according to micro-climate fluctuations within caves. The screening of infectious agents in Diptera collected helped 1) to explore the parasitic, viral and bacterial diversity they host, and 2) to assess their involvement in transmission.

Submitted by Izabel Franco (izabel-franco@ufscar.br) on 2016-09-12T13:55:20Z No. of bitstreams: 1 DissTZ.pdf: 3737067 bytes, checksum: 3b8fbeeaf9b22bee8d5df8d70aff841b (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-12T18:41:00Z (GMT) No. of bitstreams: 1 DissTZ.pdf: 3737067 bytes, checksum: 3b8fbeeaf9b22bee8d5df8d70aff841b (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-12T18:41:22Z (GMT) No. of bitstreams: 1 DissTZ.pdf: 3737067 bytes, checksum: 3b8fbeeaf9b22bee8d5df8d70aff841b (MD5) / Made available in DSpace on 2016-09-12T18:41:34Z (GMT). No. of bitstreams: 1 DissTZ.pdf: 3737067 bytes, checksum: 3b8fbeeaf9b22bee8d5df8d70aff841b (MD5) Previous issue date: 2015-04-06 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / There are several factors that may influence the richness and distribution in the subterranean fauna, just as resource avaiability and distribution, the local climate characteristics, the quality of the habitat and the vegetation surrounding it. Hypogean systems present high degree of endemism and their populations present as intrinsic characteristics a reduced number of individuals and are usually dependent on nutrients imported from the surface. These factors, among other results in an extremely fragile hypogean environment. This study aimed to verify the taxonomics groups that occur in Presidente Olegário caves, located at northwestern of Minas Gerais, Brazil. Along with that it aimed to verify through statistical tests as the biotics and abiotics variables influence the distribution and composition of subterranean fauna of this region. For these purposes, collections using combinated sampling methods occured in five different visiting occasions, contemplating both dry and rainy periods. The Presidente Olegário karst area presented high richness (386 species in seven caves sampled). Four new species and three new records besides four troglomorphic morphotypes were registrated. It was also verified how essential the execution of replics are, since the detection of rare species increases with the number of samplings. The caves presented high taxonomic distinctness and therefore, presented high faunistic singularity. The species distribution is positively associated to abiotics variables (temperature, relative humidity and precipitation), which can promote niche diversification when changed and consequently increase the local diversity. Therefore faunistic patterns can be changed for sazonality influence in the subterranean environment. High values of richness and abundance were registered at the entrance and twilight zones, where higher amounts of organic matter were found. The fauna stratification occurred with some taxa occurring preferentially in certain substrates types, which is probably related to food resources availability. Therefore, the terrestrials communities studied seem to be strutured based on energy resources and thus, a food web was built for these caves. Several impacts are present in Presidente Olegário, such as pasture, agriculture and future projects of gas extration and hidreletrics. Thus, this region with high richness and faunistic singularity and its area of influence should be considered as priority for conservation. / Há diversos fatores que influenciam a riqueza e a distribuição da fauna no ambiente subterrâneo, como a disponibilidade e distribuição dos recursos, as características climáticas locais, a qualidade do habitat e a cobertura vegetal do entorno. Sistemas hipógeos apresentam elevado grau de endemismo, e suas populações apresentam como características intrínsecas um número reduzido de indivíduos e, geralmente, são dependentes de nutrientes importados da superfície. Estes fatores, dentre outros, tornam o meio hipógeo extremamente frágil. Este estudo teve como objetivos verificar quais grupos taxonômicos ocorrem em cavernas de Presidente Olegário, noroeste de Minas Gerais, Brasil, além de verificar, por meio de testes estatísticos, como as variáveis bióticas e abióticas influenciam na distribuição e composição da fauna subterrânea dessa região. Para isso, foram realizadas coletas utilizando métodos combinados de amostragem ao longo de cinco ocasiões de visita, contemplando períodos secos e chuvosos. A área cárstica de Presidente Olegário apresentou elevada riqueza (386 espécies em sete cavernas amostradas). Foi registrada a ocorrência de quatro espécies novas, três registros novos, além de quatro morfotipos troglomórficos. Também se verificou a necessidade e importância da realização de réplicas, uma vez que a detecção de espécies raras aumenta com o número de amostragens. As cavernas apresentaram elevada distinção taxonômica e, portanto, possuem elevada singularidade faunística. A distribuição das espécies está associada de forma positiva às variáveis abióticas (temperatura, umidade relativa e precipitação), as quais podem promover a diversificação de nichos quando alteradas e, consequentemente, aumentar a diversidade local. Ainda, padrões faunísticos podem ser alterados por influência da sazonalidade no ambiente subterrâneo. Maiores valores de riqueza e abundância foram registrados nas zonas de entrada e penumbra, onde havia maior quantidade de matéria orgânica. Foi observada a estratificação da fauna subterrânea, com alguns táxons ocorrendo preferencialmente em determinados tipos de substratos, o que provavelmente está relacionado à disponibilidade de recursos alimentares. Portanto, as comunidades terrestres das cavernas estudadas parecem ser estruturadas com base em recursos energéticos e, assim, foi proposta uma teia alimentar para essas cavernas. Diversos impactos e ameaças estão presentes em Presidente Olegário, como atividades agropecuárias, projetos futuros de extração de gás e construção de pequenas centrais hidrelétricas. Assim, essa região com elevada riqueza e singularidade faunística e toda sua área de influência deve ser considerada como prioritária para conservação.

nÃo hà / In CearÃ, plus the famous Grotto of Ubajara, there are many other caves in this way, it is essential to know the current situation to achieve this speleologically protect it. Speleology, which is the study of caves has revealed to mankind the great importance of these environments. In addition to having served as a shelter for man in prehistoric times, the caves are as natural and cultural storehouses of valuable scientific records, paleontological, archaeological, among others. The cave environments also stand out due to its beautiful scenery of rock formations, ornamented by speleothems (stalactites, stalagmites, etc.) and their subterranean ecosystems, peculiar and fragile, with endemic and rare species, like the troglodyte. Natural underground cavities, popularly known like caves, grottos, caves, burrows, limpets, pits or holes, are considered by the Federal Constitution as "property of the Union" in the country and there is a specific, relevant to the protection of the Brazilian speleologically legislation. Cavers in Brazil estimated that only about 5% of the existing caverns have been identified. In CearÃ, many of the known caves are not officially registered in the National Speleological entries. For this reason, this dissertation aims to present the current landscape of speleologically in CearÃ. For this are worked in research knowledge and concepts related to caving, as its importance, use, weaknesses and impacts; relevant legislation for the protection, licensing and environmental conservation speleologically; and the current survey information on the known caves in the territory of CearÃ, with recommendations for their use and conservation. It is intended this way, based on this overview, base public policies on environmental protection and management of natural underground cavities and areas of potential occurrence. / No CearÃ, alÃm da famosa Gruta de Ubajara, existem muitas outras cavernas, desta forma, à essencial conhecer o panorama atual deste patrimÃnio espeleolÃgico para conseguir protegÃ-lo. A espeleologia, que à o estudo das cavernas, tem revelado para a humanidade a grande importÃncia desses ambientes. AlÃm de ter servido de abrigo para o homem na prÃ-histÃria, as cavernas sÃo como celeiros naturais e culturais de valiosos registros cientÃficos, paleontolÃgicos, arqueolÃgicos, dentre outros. Os ambientes cavernÃcolas tambÃm se destacam devido aos seus belos cenÃrios de formaÃÃes rochosas, ornamentados por espeleotemas (estalactites, estalagmites, etc.) e seus ecossistemas subterrÃneos, peculiares e frÃgeis, com espÃcies endÃmicas e raras, como os troglÃbios. As cavidades naturais subterrÃneas, conhecidas popularmente como cavernas, grutas, furnas, tocas, lapas, abismos ou buracos, sÃo consideradas pela ConstituiÃÃo Federal como âbens da UniÃoâ e existe no paÃs uma legislaÃÃo especÃfica, pertinente à proteÃÃo do patrimÃnio espeleolÃgico brasileiro. EspeleÃlogos estimam que no Brasil, apenas cerca de 5% das cavernas existentes tenham sido identificadas. No CearÃ, muitas das cavernas conhecidas nÃo estÃo oficialmente registradas nos cadastros espeleolÃgicos nacionais. Por essa razÃo, esta dissertaÃÃo tem como objetivo principal apresentar o panorama atual do patrimÃnio espeleolÃgico no Estado do CearÃ. Para isso sÃo trabalhados na pesquisa os conhecimentos e conceitos relativos à espeleologia, como a sua importÃncia, utilizaÃÃo, as fragilidades e os impactos; a legislaÃÃo pertinente à proteÃÃo, ao licenciamento e à conservaÃÃo ambiental do patrimÃnio espeleolÃgico; e o atual levantamento de informaÃÃes sobre as cavernas conhecidas no territÃrio cearense, com recomendaÃÃes de uso e conservaÃÃo. Pretende-se desta forma, com base neste panorama, fundamentar polÃticas pÃblicas de proteÃÃo e gestÃo ambiental das cavidades naturais subterrÃneas e suas Ãreas de potencial ocorrÃncia.

O presente projeto estudou aspectos da ecologia populacional de duas novas espécies troglomórficas de Siluriformes dos gêneros Rhamdia e Ancistrus, sintópicas em um riacho subterrâneo da área cárstica da Serra da Bodoquena, Mato Grosso do Sul. Foram investigados os tamanhos e as densidades populacionais com base em censo visual e marcação e recaptura, as taxas de sobrevivência, a taxa de crescimento individual, a frequência de comprimento-padrão, de peso e de fator de condição, e os deslocamentos. Adicionalmente, foi estudado o comportamento de Rhamdia sp. n., com foco na ritmicidade locomotora e na reação à luz. Foram realizados seis eventos de coleta entre 2010 e 2011 para tomada de dados populacionais, além de prospecções por novas localidades com ocorrência dessas espécies. O tamanho populacional estimado para Rhamdia sp. n. foi de 391 indivíduos na Gruta das Fadas e 104, na Gruta Cinco de Ouros. Com base nos resultados de densidade, a população de Ancistrus parece ser menor do que a de Rhamdia sp. n., com tamanho populacional na ordem de 100 indivíduos. A densidade populacional média estimada através do censo visual para Rhamdia sp. n. foi de 0,09 ind/ m² na Gruta das Fadas e 0,1 ind./ m² na Gruta Cinco de Ouros, valores inferiores ao calculado com base nos resultados de marcação e recaptura, 0,76 ind./ m² e 1,48 ind./m², respectivamente. Em Ancistrus sp. n., a densidade populacional média foi de 0,018 ind/ m². Foi observado que Rhamdia sp. n. se concentra mais em poções, enquanto que Ancistrus sp. n., em corredeira. A pequena variação ao longo do ano nas densidades, no peso, e no fator de condição de ambas as espécies na Gruta das Fadas, indica maior estabilidade ambiental nessa caverna em comparação com a Gruta Cinco de Ouros. Em Rhamdia sp. n., indivíduos sem olhos externamente visíveis (anoftálmicos) apresentaram maior taxa de sobrevivência quando comparados com aqueles com olhos assimétricos ou dois olhos normais. O crescimento individual de Rhamdia sp. n. foi heterogêneo, sem relação com o tamanho do indivíduos e apresentou, pelo modelo de von Bertalanffy, comprimento máximo médio de 170 mm CP e constante de crescimento (K) de 0,241 A longevidade máxima média foi de aproximadamente 15 anos. Com a maior parte das recapturas ocorridas no mesmo setor da captura anterior, indivíduos de Rhamdia sp. n. apresentam filopatria, enquanto que Ancistrus sp. n. se deslocou mais, com somente um registro de recaptura no mesmo setor da captura anterior. Quanto ao comportamento de Rhamdia sp n., os exemplares apresentaram ritmicidade circadiana significante, com diferenças intra-específicas nos valores de potência espectral. No estudo de reação à luz, observou-se variação intra-específica no grau de fotofobia relacionado com a morfologia dos olhos. Prospecções realizadas em 24 cavernas do Assentamento Campina revelam que Rhamdia sp. n. ocorre até o momento somente nas cavernas Fadas, Cinco de Ouros, Manoel Cardoso e Dona Benedita, enquanto que ncistrus sp. n. somente na Gruta das Fadas. O mosaico de variações morfológicas observado em Rhamdia sp. n. e em Ancistrus sp. n., a forte ritmicidade circadiana da atividade locomotora e o elevado grau de fotofobia observado em Rhamdia sp. n., sugere que estas espécies estão em estágio inicial de fixação de caracteres troglomórficos, indicando um isolamento recente no hábitat subterrâneo / This project studied aspects of the population ecology of two troglomorphic Siluriformes of genera Rhamdia and Ancistrus, which are syntopics in a subterranean stream of Serra da Bodoquena karst area, Mato Grosso do Sul. The research comprised the investigation of the population sizes and densities, survival rates, individual growth rate, frequency of standard length, weight and condition factor, and displacements. Adicionally, the behavior of Rhamdia sp. n. was investigated with focus on locomotor rhythmicity and reaction to light. Six collections were made between 2010 and 2011 to gather population data, based on visual census and mark-recapture, as well as search for other localities to investigate the distribution range of these species. The population size estimated to Rhamdia sp. n. was 391 individuals in Fadas Cave and 104 individuals in the Cinco de Ouros Cave. The population densities of Ancistrus sp. n. suggests a lower population size compared to Rhamdia sp. n., possibly with less than 100 individuals in the studied area. The average population density estimated through visual census to Rhamdia sp. n. was 0.09 ind / m² in the Fadas Cave and 0.1 ind. / m² in the Cinco de Ouros Cave, lower than the results estimated by mark-recapture, 0. 76 ind. / m² and 1.48 ind. / m², for each cave, respectively. To Ancistrus sp. n., the average population density was 0.018 ind / m². The low variability throughout the year in population densities, weight, and in condition factor for both species in Fadas Cave, indicate and higher environmental stability in this cave compared to Cinco de Ouros Cave. In Rhamdia sp. n., individuals without externally visible eyes (anophthalmics) showed higher survival rate compared to those with asymmetric or two normal eyes. The individual growth of Rhamdia sp. n. was heterogeneous with no relation to individuals\' size and through the von Bertalanffy model estimate the maximum length (L ∞) of 170 mm and growth constant (K) of 0.241. The median maximum longevity was 15 years. With little movement between sectors, individuals of Rhamdia sp. n. exhibited philopatry, while Ancistrus sp. n. moved around, with only one individual recaptured in the same cave sector. In relation do behavior Rhamdia sp n. showed significant circadian rhythmicity, with intra-specific differences in the spectral power values. In the study of light reduction, the intra-specific variation was observed in the degree of photophobia related to eyes morphology. Surveys conducted in 24 caves in the Campina settlement revealed that Rhamdia sp. n. occurs in the Fadas, Cinco de Ouros, Manoel Cardoso and Dona Benedita caves, while Ancistrus sp. n. occurs only in the Fadas Cave. The mosaic of morphological variations observed in Rhamdia sp. n. and Ancistrus sp. n., the strong circadian locomotor activity and the high degree of photophobia observed in Rhamdia sp. n. suggests that these species are in early stages of setting troglomorphic characters, indicating a recent isolation in subterranean environment

Aspergillus is a speciose genus encompassing nearly 400 species that has significant economic impacts on human health, the food industry, biotechnology and pharmacology. The research included in this thesis focuses on current issues related to the generic concept, subgeneric classification and species delimitation in Aspergillus. It addresses the need for revisions of several sections or species complexes. It provides novel information regarding etiology of aspergillosis as well as the antifungal susceptibilities of several less common opportunistic pathogens. The taxonomic section of the thesis contributes to the taxonomic stability and the new concept of the genus Aspergillus, which changed in response to the discontinuation of dual nomenclature in fungi. Sufficient arguments were collected (e.g., verification of monophyly, unifying phenotypic characters) for maintaining a broad concept of the genus and avoiding splitting it into several genera. All genera typified by sexual morphs and having Aspergillus asexual states were synonymized with Aspergillus and the appropriate names adopted; new combinations were made for teleomorphic species that lacked Aspergillus names. This thesis also contributed to infrageneric taxonomy of the genus via the proposal of four new sections in the subg. Circumdati,...

10 Abstract Actinobacteria are important bacterial group participating in various ecosystem processes particularly in the decomposition of complex organic compounds. Their abilities enable them to surviving in harsh conditions of oligotrophic habitats like lakes, deserts, cave walls or recalcitrant and resistant litter in soil, where Actinobacteria often dominate. Although certain biotic and abiotic factors were recognized to modulate Actinobacteria incidence in such habitats, the influence of anthropogenic pressure on their communities is scarcely known. The main objective of this thesis is therefore to determine differences of Actinobacteria communities under the direct (the human visitors changing microenvironment of caves, part 1) and indirect (climate change factors like altered precipitation or plant litter quality, part 2) anthropogenic influence in two habitats, plant litter in soil and cave walls, where Actinobacteria play important roles and dominate. In a first part of the thesis we monitored Actinobacteria communities in French limestone caves walls differently affected by humans (pristine versus anthropized caves). For identification of important species like potential pathogens or pigments producing Actinobacteria using amplicon sequencing of environmental DNA (Illumina MiSeq), we firstly used...

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Flank margin caves of the Bahamas are formed by mixing dissolution in a fresh-water lens. As they evolve, the probability of intersecting neighboring voids increases, and they enlarge in a nonlinear fashion. Large flank margin caves become constrained by surface topography and their morphology is influenced by the shape of the enclosing land mass as a result. High phreatic ceilings can be dissolved if the fresh-water lens is distorted by lithological heterogeneities or hydrologic loading due to storm events. Early diagenesis of the host rock causes the reorganization of porosity and permeability through dissolution and cementation processes. Meteoric overprinting occurs but cannot be used as a tool in determining the age of eolianites or the climatic conditions at the time of deposition. Current evidence indicates an OIS 5e speleogenesis of large flank margin caves. An OIS 11 origin can be advanced only with compelling evidence of a pre-OIS 5e highstand.