It has been estimated that coral reefs shelter 830 000 species. Well-studied biodiversity patterns provide tools for better representation of species in marine protected areas. A cross-shelf gradient in biodiversity exists for fishes, corals, and macroalgae. Here, an inshore to offshore gradient in biodiversity on the Saudi Arabian coast of the Red Sea was sampled using Autonomous Reef Monitoring Structures (ARMS) with barcoding and metabarcoding techniques. It was hypothesized that differences in community structure would be driven by an increase in habitat area. The difference was attributed to the greater accumulation of sediments close to shore that increases the area habitable for sediment dwelling organisms and favors macroalgal cover. Macroalgae are inhabited by a greater number of species than live coral. Only 10% of the sequences of the barcoded fraction and <1% of the metabarcoded fraction had a BLAST hit on the NCBI database with a previously identified species sequence. In addition, the rarefaction curves for all fractions did not plateau. The ARMS community composition changed from inshore to offshore and was significantly correlated with the percentage of algal and bryozoan plate cover. The differences in community composition were related to changes in habitat but not to sediments retrieved from the ARMS.

A biodiversidade, as interações entre organismos e o meio físico são componentes do Sistema de Suporte da Vida no planeta, mantendo possível a vida do homem na Terra; entretanto, tem-se observado uma crescente e preocupante perda da biodiversidade, principalmente em função da perda de habitat e fragmentação, fogo, exploração excessiva dos recursos naturais e introdução de espécies exóticas e invasoras, entre outros. O Estado de São Paulo abriga dois grandes biomas brasileiros: a Mata Atlântica e o Cerrado, ambos reconhecidos como hotspots de biodiversidade, devido a grande biodiversidade e elevado grau de ameaças a que esses estão submetidos. Neste sentido, esta pesquisa propôs-se verificar a relação entre dados de riqueza de espécies (aves) e preditoras ambientais e de paisagem em diferentes regiões e escalas. Embora o Estado já conte com mapas de áreas prioritárias frutos do Biota/FAPESP de 2008, até o momento o componente de paisagem foi explorado muito superficialmente, da mesma forma que os dados biológicos não foram explorados em sua totalidade. Neste sentido, este projeto busca ir de encontro com as linhas diagnosticadas como necessárias para um maior direcionamento da ciência à conservação da biodiversidade. Foram utilizados dados pré-existentes de registros de aves no Estado de São Paulo (Brasil) compilados do banco de dado do Biota/FAPESP e do Livro vermelho de espécies ameaçadas do Estado de São Paulo. Para a análise dos dados utilizou-se de modelos aditivos generalizados (GAM), AKAIKE e análise de sensibilidade (SRC). Como principais apontamentos conclusivos escala é um fator extremamente importante e deve ser considerado ao buscar a compreensão de padrões biológicos, uma vez que, se ignorado pode resultar em relações não reais, e em decorrência disso uma má prática de conservação. Características da região de estudo, como tipo de bioma, também podem gerar diferentes relações entre variáveis ambientais e biológicas, e não devem ser subestimados; barreiras políticas não respeitam barreiras biológicas, e deve-se entender como isso pode influenciar as respostas obtidas. De todas as preditoras apenas porcentagem de floresta, altitude, precipitação e temperatura pareceram explicar todas as variáveis biológicas analisadas. Por fim, ainda observamos uma má gestão e padronização dos dados que irá ocasionar problemas na utilização e aplicação desses dados. Aqui se percebe que este viés pode ter influenciado na ausência de algumas relações ou na observação de padrões fracos. Apesar de extremante importante trabalhos com agrupamento de informações para buscar entender padrões de biodiversidade estes devem ser padronizados. / Biodiversity, the interactions between organisms and the environment are components of the Life Support System on the planet, keeping possible the man\'s life on the Earth; however, we are witnessing a growth and alarming loss of biodiversity, mainly due to habitat loss and fragmentation, fire, over-exploitation of natural resources and the introduction of exotic and invasive species, among others. The State of São Paulo is home to two major Brazilian biomes, the Atlantic Forest and Cerrado, both recognized as biodiversity hotspots, due to its high biodiversity and high level of threat to which these are subject. In this sense, this research proposed to investigate the relationship between species richness data (birds) and environmental and landscape predictors at different regions and scales. Although the state already counts with priority areas maps product of the Biota/FAPESP project (2008), the landscape component has been explored very superficially in the same way that biological data has not been fully explored. Thus, this project seeks to meet with the lines diagnosed as necessary for further direction of science to the conservation of biodiversity. Preexisting bird records data of the São Paulo\'s State (Brazil) were compiled from the databases of Biota/FAPESP and of the Red Book of endangered species of the São Paulo\'s State. For data analysis we used generalized additive models (GAM), Akaike and sensitivity analysis (SRC). The main conclusive notes were that scale is an extremely important factor and should be considered when seeking to understand biological patterns, given that if ignored may result in misleading relationships, and as result a bad conservation practice. Characteristics of the study area, such as biome, can also generate different relationships between environmental and biological variables, and should not be underestimated; political barriers do not respect biological barriers, and we should understand how this can influence the findings. Of all the predictors only forest percentage, altitude, rainfall and temperature seemed to explain all biological variables. Finally, we also observed that poor management and standardization of data will lead to problems in the use and application of such data. This bias may have influenced the absence of some relationships or the observation of weak standards. Despite been extremely important the gathering of information to try understand biodiversity patterns, these information should always be standardized.

A biodiversidade, as interações entre organismos e o meio físico são componentes do Sistema de Suporte da Vida no planeta, mantendo possível a vida do homem na Terra; entretanto, tem-se observado uma crescente e preocupante perda da biodiversidade, principalmente em função da perda de habitat e fragmentação, fogo, exploração excessiva dos recursos naturais e introdução de espécies exóticas e invasoras, entre outros. O Estado de São Paulo abriga dois grandes biomas brasileiros: a Mata Atlântica e o Cerrado, ambos reconhecidos como hotspots de biodiversidade, devido a grande biodiversidade e elevado grau de ameaças a que esses estão submetidos. Neste sentido, esta pesquisa propôs-se verificar a relação entre dados de riqueza de espécies (aves) e preditoras ambientais e de paisagem em diferentes regiões e escalas. Embora o Estado já conte com mapas de áreas prioritárias frutos do Biota/FAPESP de 2008, até o momento o componente de paisagem foi explorado muito superficialmente, da mesma forma que os dados biológicos não foram explorados em sua totalidade. Neste sentido, este projeto busca ir de encontro com as linhas diagnosticadas como necessárias para um maior direcionamento da ciência à conservação da biodiversidade. Foram utilizados dados pré-existentes de registros de aves no Estado de São Paulo (Brasil) compilados do banco de dado do Biota/FAPESP e do Livro vermelho de espécies ameaçadas do Estado de São Paulo. Para a análise dos dados utilizou-se de modelos aditivos generalizados (GAM), AKAIKE e análise de sensibilidade (SRC). Como principais apontamentos conclusivos escala é um fator extremamente importante e deve ser considerado ao buscar a compreensão de padrões biológicos, uma vez que, se ignorado pode resultar em relações não reais, e em decorrência disso uma má prática de conservação. Características da região de estudo, como tipo de bioma, também podem gerar diferentes relações entre variáveis ambientais e biológicas, e não devem ser subestimados; barreiras políticas não respeitam barreiras biológicas, e deve-se entender como isso pode influenciar as respostas obtidas. De todas as preditoras apenas porcentagem de floresta, altitude, precipitação e temperatura pareceram explicar todas as variáveis biológicas analisadas. Por fim, ainda observamos uma má gestão e padronização dos dados que irá ocasionar problemas na utilização e aplicação desses dados. Aqui se percebe que este viés pode ter influenciado na ausência de algumas relações ou na observação de padrões fracos. Apesar de extremante importante trabalhos com agrupamento de informações para buscar entender padrões de biodiversidade estes devem ser padronizados. / Biodiversity, the interactions between organisms and the environment are components of the Life Support System on the planet, keeping possible the man\'s life on the Earth; however, we are witnessing a growth and alarming loss of biodiversity, mainly due to habitat loss and fragmentation, fire, over-exploitation of natural resources and the introduction of exotic and invasive species, among others. The State of São Paulo is home to two major Brazilian biomes, the Atlantic Forest and Cerrado, both recognized as biodiversity hotspots, due to its high biodiversity and high level of threat to which these are subject. In this sense, this research proposed to investigate the relationship between species richness data (birds) and environmental and landscape predictors at different regions and scales. Although the state already counts with priority areas maps product of the Biota/FAPESP project (2008), the landscape component has been explored very superficially in the same way that biological data has not been fully explored. Thus, this project seeks to meet with the lines diagnosed as necessary for further direction of science to the conservation of biodiversity. Preexisting bird records data of the São Paulo\'s State (Brazil) were compiled from the databases of Biota/FAPESP and of the Red Book of endangered species of the São Paulo\'s State. For data analysis we used generalized additive models (GAM), Akaike and sensitivity analysis (SRC). The main conclusive notes were that scale is an extremely important factor and should be considered when seeking to understand biological patterns, given that if ignored may result in misleading relationships, and as result a bad conservation practice. Characteristics of the study area, such as biome, can also generate different relationships between environmental and biological variables, and should not be underestimated; political barriers do not respect biological barriers, and we should understand how this can influence the findings. Of all the predictors only forest percentage, altitude, rainfall and temperature seemed to explain all biological variables. Finally, we also observed that poor management and standardization of data will lead to problems in the use and application of such data. This bias may have influenced the absence of some relationships or the observation of weak standards. Despite been extremely important the gathering of information to try understand biodiversity patterns, these information should always be standardized.

Un ensemble de disciplines tente de comprendre les causes de la distribution de la biodiversité à la surface de la terre. Cette thèse, à l'interface entre macro-écologie et phylogéographie, démêle le rôle relatif des différents facteurs environnementaux et des processus contrôlant la diversité des crustacés aquatiques souterrains en Europe. L'utilisation d'un modèle biologique souterrain permet d'écarter l'effet de la saisonnalité thermique, omniprésente dans les milieux de surface. L'action de multiples facteurs – plus particulièrement la disponibilité des ressources trophiques et l'hétérogénéité environnementale – et les variations régionales de leur importance relative fournissent l'explication la plus parcimonieuse des patrons de richesse. Ce résultat s'oppose au paradigme du rôle prépondérant du processus d'extinction causé par les fortes oscillations climatiques du Pléistocène en Europe du nord. Toutefois, ces oscillations ont très probablement sélectionné des organismes mobiles qui participent à l'augmentation de la taille moyenne des aires de répartition des espèces avec la latitude. La reconstruction de la dynamique des aires de distribution montre que la dispersion est un processus très hétérogène entre et au sein des espèces. Elle interviendrait lors de courtes fenêtres temporelles entre lesquelles l'adaptation locale tendrait au contraire, à contrecarrer les capacités de dispersion. Enfin, ce travail propose des pistes de réflexion afin d'expliquer plus précisément, à partir de données moléculaires supplémentaires et d'outils génomiques, les variations géographiques des taux de diversification et de substitution à l'échelle continentale / A set of disciplines attempt to understand causes of biodiversity patterns on the earth. This thesis, at the frontier between macroecology and phylogeography, disentangles the relative influence of environmental factors and processes shaping groundwater crustacean diversity in Europe. Groundwater habitats offer useful case studies for avoiding the effect of thermal seasonality, which is pervasive in surface ecosystems. The influence of multiple factors – especially productive energy and spatial heterogeneity – and regional variation in their relative importance provide the most parsimonious explanation of species richness patterns. This result undermines the prominent role attributed to the disproportionate extinction of species in northern European regions with high historical climate oscillations. However, these oscillations have probably selected vagile species which contribute to the increase in median range size of species with latitude. Reconstructing range dynamics shows that dispersal is a heterogeneous process within and among species. It may occur during short time windows between which local adaptation favors specialization. Finally, I suggest several research avenues using molecular data and genomic tools for understanding geographical variation in diversification and substitution rates at continental scale

La distribution de l'abondance des espèces en un site, et la similarité de la composition taxonomique d'un site à l'autre, sont deux mesures de la biodiversité ayant servi de longue date de base empirique aux écologues pour tenter d'établir les règles générales gouvernant l'assemblage des communautés d'organismes. Pour ce type de mesures intégratives, le séquençage haut-débit d'ADN prélevé dans l'environnement (" ADN environnemental ") représente une alternative récente et prometteuse aux observations naturalistes traditionnelles. Cette approche présente l'avantage d'être rapide et standardisée, et donne accès à un large éventail de taxons microbiens jusqu'alors indétectables. Toutefois, ces jeux de données de grande taille à la structure complexe sont difficiles à analyser, et le caractère indirect des observations complique leur interprétation. Le premier objectif de cette thèse est d'identifier les modèles statistiques permettant d'exploiter ce nouveau type de données afin de mieux comprendre l'assemblage des communautés. Le deuxième objectif est de tester les approches retenues sur des données de biodiversité du sol en forêt amazonienne, collectées en Guyane française. Deux grands types de processus sont invoqués pour expliquer l'assemblage des communautés d'organismes : les processus "neutres", indépendants de l'espèce considérée, que sont la naissance, la mort et la dispersion des organismes, et les processus liés à la niche écologique occupée par les organismes, c'est-à-dire les interactions avec l'environnement et entre organismes. Démêler l'importance relative de ces deux types de processus dans l'assemblage des communautés est une question fondamentale en écologie ayant de nombreuses implications, notamment pour l'estimation de la biodiversité et la conservation. Le premier chapitre aborde cette question à travers la comparaison d'échantillons d'ADN environnemental prélevés dans le sol de diverses parcelles forestières en Guyane française, via les outils classiques d'analyse statistique en écologie des communautés. Le deuxième chapitre se concentre sur les processus neutres d'assemblages des communautés.[...] / Integrative patterns of biodiversity, such as the distribution of taxa abundances and the spatial turnover of taxonomic composition, have been under scrutiny from ecologists for a long time, as they offer insight into the general rules governing the assembly of organisms into ecological communities. Thank to recent progress in high-throughput DNA sequencing, these patterns can now be measured in a fast and standardized fashion through the sequencing of DNA sampled from the environment (e.g. soil or water), instead of relying on tedious fieldwork and rare naturalist expertise. They can also be measured for the whole tree of life, including the vast and previously unexplored diversity of microorganisms. Taking full advantage of this new type of data is challenging however: DNA-based surveys are indirect, and suffer as such from many potential biases; they also produce large and complex datasets compared to classical censuses. The first goal of this thesis is to investigate how statistical tools and models classically used in ecology or coming from other fields can be adapted to DNA-based data so as to better understand the assembly of ecological communities. The second goal is to apply these approaches to soil DNA data from the Amazonian forest, the Earth's most diverse land ecosystem. Two broad types of mechanisms are classically invoked to explain the assembly of ecological communities: 'neutral' processes, i.e. the random birth, death and dispersal of organisms, and 'niche' processes, i.e. the interaction of the organisms with their environment and with each other according to their phenotype. Disentangling the relative importance of these two types of mechanisms in shaping taxonomic composition is a key ecological question, with many implications from estimating global diversity to conservation issues. In the first chapter, this question is addressed across the tree of life by applying the classical analytic tools of community ecology to soil DNA samples collected from various forest plots in French Guiana. The second chapter focuses on the neutral aspect of community assembly.[...]