Mutualism is an understudied phenomenon across taxa, but is important to the persistence and structure of communities. The role of positive interactions in supporting threatened species is critically important given that freshwater fish are extremely vulnerable due to the combined effects of climate change and habitat degradation. To disentangle complex positive multi-species interactions, I applied both Eltonian and Hutchinsonian niche approaches to the reproductive mutualism of leuciscids known as nest association, a form of alloparental care characterized by an adult of one species guarding the offspring of another. I conducted this study with the leuciscid community of Toms Creek in which Bluehead Chub Nocomis leptocephalus is the primary nest builder and nest associate species include Rosyside Dace Clinostomus funduloides, Rosefin Shiner Lythrurus ardens, Mountain Redbelly Dace Chrosomus oreas, Crescent Shiner Luxilus cerasinus, White Shiner Luxilus albeolus, Central Stoneroller Campostoma anomalum, Creek Chub Semotilus atromaculatus, and Blacknose Dace Rhinycthys atratulus. I applied Hutchinsonian niche theory with respect to hydrology and water temperature to define the reproductive phenology of each species involved in the reproductive mutualism, then used Eltonian niche theory to define the role of each species in parental and alloparental care. My dual niche theory approach elucidates the reproductive requirements of each species and quantifies the contribution of nest associates to alloparental care, which historically have not been included in definitions of nest association. My results show that Blacknose Dace Rhinichthys atratulus and Creek Chub Semotilus atromaculatus are not true nest associates of Bluehead Chub Nocomis leptocephalus based on their reproductive phenology and observed nesting behaviors. In contrast to previous work on nest association, most associate species did contribute to parental care through nest defense and vigilance behaviors, and their specific behaviors were influenced by morphology. By clearly defining the reproductive niches of these species, this study lays the groundwork for future investigation of how various climate scenarios may impact multi-species reproductive mutualisms. / Master of Science / Positive interactions are understudied throughout ecology, but are important to the persistence and structure of communities. The role of positive interactions in supporting threatened species is critically important given that freshwater fish are at high risk of extinction due to the combined effects of climate change and habitat degradation. To understand the complex positive interactions in freshwater fish, I applied both niche theory approaches to a mutualistic reproductive interaction known as nest association, where an adult of one species builds a nest on which it guards the offspring of other species (formally: a type of alloparental care). I conducted this study with the leuciscid (commonly known as minnow) community of Toms Creek in which Bluehead Chub Nocomis leptocephalus is the primary nest builder and nest associate species include Rosyside Dace Clinostomus funduloides, Rosefin Shiner Lythrurus ardens, Mountain Redbelly Dace Chrosomus oreas, Crescent Shiner Luxilus cerasinus, White Shiner Luxilus albeolus, Central Stoneroller Campostoma anomalum, Creek Chub Semotilus atromaculatus, and Blacknose Dace Rhinycthys atratulus. For each species involved in the reproductive mutualism, I defined the seasonal timing of reproduction with respect to hydrology and water temperature, then defined their role in parental and alloparental care. My approach clarifies the reproductive requirements of each species and establishes the contributions of associate species to alloparental care, which historically have not been included in definitions of nest association. My results show that Blacknose Dace Rhinichthys atratulus and Creek Chub Semotilus atromaculatus are not true nest associates of Bluehead Chub Nocomis leptocephalus based on their reproductive requirements and observed nesting behaviors. In contrast to historic descriptions of nest association, most associate species did contribute to parental care through nest defense and vigilance behaviors, and their specific behaviors were influenced by their size and physical adaptations. By clearly defining the reproductive needs and roles of these species, this study lays the groundwork for future investigation of how various climate scenarios may impact positive relationships among species.

<p dir="ltr">The Dorothy and Ray Garman Preserve is a 35.4 hectare tract of hydro-mesophytic forest that includes ephemeral pools and scrub-shrub wetlands with <i>Cephalanthus occidentalis</i> as the dominant species component, a previously farmed agricultural field (now planted with native trees), and areas within that field which have reverted into wetlands. Garman is located within the Cedar Creek Conservation Area of Allen County, a region of important biodiversity in northeast Indiana. To document the structure and composition of the plant communities at this property, I utilized random and systematic plot samping, as well as a meandering floristic survey. The focus of my efforts was to explore the forested portion of the property and its immediate margins. I counted 150 species, representing 53 genera and 50 families. Using the Floristic Quality Assessment (FQA) method, eleven species had coefficient of conservatism values of 8-10, ten of which were herbaceous and one arboreal species (<i>Populus heterophylla</i>). This indicates that Garman is a relatively high-quality site with some quality remnant components. The site has an FQA value of 46.4, and the mean coefficient of conservatism was 3.8. Furthermore, 95.3 percent of the total species documented were native, a relatively high mark for a fragment within a larger suburban area. Species potentially indicative of bog habitats such as <i>Sphagnum fimbriatum </i>(a non-vascular species of interest), <i>Ilex verticillata</i>, and <i>Viola nephrophylla</i>, as well as historical occurrences of other peatland communities in the area, indicate that Garman may have historically been a true bog that has since senesced into buttonbush wetland type due to anthropogenic impact. Overall, the vascular plant flora of Garman demonstrates that this site is of unique importance to the broader Cedar Creek Conservation Area, since it contains several plant species not present at other sites within this region, as well as intact natural plant communities.</p>

No description available.

A number of emerging vector-borne diseases have the potential to be transmitted in the UK by native mosquitoes. Human infection by some of these diseases requires the presence of communities of multiple vector mosquito species. Mitigating the risk posed by these diseases requires an understanding of the spatial distributions of the UK mosquito fauna. Little empirical data is available from which to determine the distributions of mosquito species in the UK. Identifying areas at risk from mosquito-borne disease therefore requires statistical modelling to investigate and predict mosquito distributions. This thesis investigates the distributions of potential vector mosquitoes in the UK at landscape to national scales. A number of new methodological approaches for species distri- bution modelling are developed. These methods are then used to map and understand the distributions of mosquito communities with the potential to transmit diseases to humans. Chapter 2 reports the establishment of substantial populations of the West Nile virus (WNV) vector mosquito Culex modestus in wetlands in southern England. This represents a drastic shift in the species’ known range and an increase in the risk of WNV transmission where Cx. modestus is present. Chapter 3 develops and applies a new species interaction distribution model which identifies fish and ditch shrimp of the genus Palaemonetes as predators which may restrict the distribution of the potential WNV vector community in these wetlands. Chapter 4 develops a number of methods to make robust predictions of the probability of presence of a species from presence-only data, by eliciting and applying estimates of the species’ prevalence. Chapter 5 introduces a new Bayesian species distribution modelling approach which outperforms existing methods and has number of useful features for dealing with poor- quality data. Chapter 6 applies methods developed in the previous two chapters to produce the first high-resolution distribution maps of potential vector mosquitoes in the UK. These maps identify several wetland areas where vector communities exist which could maintain WNV transmission in birds and transmit it to humans. This thesis makes significant contributions to our understanding of the distributions of UK mosquito species. It also provides methods for species distribution modelling which could be widely applied in ecology and epidemiology.

Community ecology from the perspective of classic and Bayesian statistics Ekologie společenstev z hlediska klasické a Bayesovské statistiky Řešitel: Adam Klimeš Vedoucí práce: Mgr. Petr Keil, Ph.D. Abstract Quantitative evaluation of evidence through statistics is a central part of present-day science. Bayesian approach represents an emerging but rapidly developing enrichment of statistical analysis. The approach differs in its foundations from the classic methods. These differences, such as the different interpretation of probability, are often seen as obstacles for acceptance of Bayesian approach. In this thesis I outline ways to deal with the assumptions of Bayesian approach, and I address the main objections against it. I present Bayesian approach as a new way to handle data to answer scientific questions. I do this from a standpoint of community ecology: I illustrate the novelty that Bayesian approach brings to data analysis of typical community ecology data, specifically, the analysis of multivariate datasets. I focus on principal component analysis, one of the typical and frequently used analytical techniques. I execute Bayesian analyses that are analogical to the classic principal components analysis, I report the advantages of the Bayesian version, such as the possibility of working with...

Les interactions entre organismes ont des conséquences majeures sur la composition des communautés et le fonctionnement des écosystèmes. En écologie l'étude des interactions négatives, telles que la prédation et la compétition, a largement dominé la littérature. Des travaux récents ont souligné l’importance des interactions positives dans la nature, telles que la facilitation, mais ces interactions restent malgré tout peu intégrées dans les théories contemporaines en écologie. Cette thèse s’inscrit dans cette démarche et aborde deux questions centrales : (i) Comment la facilitation indirecte (via la protection contre le pâturage) affecte-t-elle la structure fonctionnelle (caractéristiques des distributions de traits) des communautés de plantes ? (ii) L'effet net des interactions facilitatrice-bénéficiaire identifiées à l’échelle d’une paire d’espèces restent-elles valides en présence d’une communauté entière d'espèces bénéficiaires potentielles ? Deux expérimentations in situ dans des environnements contrastés ont été mises en place : l’exclusion du pâturage dans des tourbières tropicales alpines et une transplantation de communautés de plantules sous des plantes adultes en milieu méditerranéen semi-aride. Nous avons montré que la facilitation indirecte affectait les caractéristiques du filtre environnemental, la dominance des espèces et la différenciation de niche au sein de la communauté. Nos travaux suggèrent également que la composition des communautés de plantules modifie les interactions adultes-plantules, remettant ainsi en cause la possibilité d’extrapolation des résultats entre paires d'individus à l’échelle de la communauté. / Interactions between organisms are key drivers of community composition and ecosystem functioning. Ecology has a long history of studies on negative interactions, such as predation and competition. Recent studies have highlighted the importance of positive interactions, such as facilitation in nature. The integration of these interactions into modern ecological theory has nonetheless lagged behind. This thesis aims at contributing to this research effort and addresses two core questions : (i) How does indirect facilitation (through protection against grazing) affect the functional structure (characteristics of trait distributions) of plant communities? (ii) Does the net effect of the interactions between a species pair (benefactor-beneficiary) remain valid in the presence of several beneficiary species at community level? We set up two insitu experiments in contrasted environments: a grazing exclusion experiment in tropical alpine peatlands and a transplantation experiment of sapling communities beneath adult plants in a mediterranean environment. Our results showed that indirect facilitation affects the characteristics of the environmental filter, species dominance and niche differentiation in the community. Our results also suggested that the composition of sapling communities modifies adult-sapling interactions, thereby questioning the possibility of extrapolating results from pairs of individuals to the community scale.

Le massif forestier guyanais présente à la fois une grande originalité en termes de biodiversité, un bon état de conservation, une forte contribution au stock de carbone amazonien et une dynamique socio-économique très rapide. Les connaissances sur la diversité des écosystèmes forestiers de Guyane française restent cependant insuffisantes pour asseoir une gestion optimale des différents services écosystémiques à l’échelle du territoire. Les travaux réalisés dans le cadre de cette thèse, visent prioritairement à étudier la diversité des écosystèmes forestiers de Guyane, les facteurs déterminant leur variabilité et les conséquences de cette variabilité en termes de services écosystémiques et de gestion.La première partie de la thèse met en évidence les différentes échelles de structuration spatiale de la diversité forestière et les patrons de composition qui en résultent à l’échelle régionale. Elle s’appuie sur une récente campagne d’inventaires forestiers (2006-2013) couvrant l’ensemble du département et rassemblant 3 132 placettes de 0.2ha implantées selon un plan d’échantillonnage emboîté et pluristratifié. Les résultats obtenus vérifient l’hypothèse d’une forte influence de la géomorphologie, à l’échelle des paysages, sur la bêta et l’alpha-diversité des forêts guyanaises en termes d’espèces dominantes (métrique de Simpson). Cette première étape a nécessité plusieurs développements méthodologiques préalables notamment l’évaluation de l’incertitude taxonomique des inventaires forestiers et sa propagation dans les analyses de diversité, ainsi que l’élaboration de modèles cartographiques permettant de caractériser précisément l’environnement géomorphologique à diverses échelles d’études.La deuxième partie de la thèse vise à expliquer l’influence exercée par les paysages géomorphologiques sur la végétation forestière à travers l’étude des relations entre géomorphologie et sols. Elle s’appuie sur l’analyse de près de 450 sondages pédologiques couplés à la campagne d’inventaire forestier. Les résultats obtenus démontrent une forte dépendance de la nature et des propriétés des sols vis-à-vis des paysages géomorphologiques et du dénivelé régional. Ils suggèrent l’existence d’un effet de filtre édaphique sous-jacent au déterminisme géomorphologique sur la diversité forestière. Une part importante de l’influence géomorphologique reste cependant indépendante du filtre édaphique et est interprétée comme un effet conjugué de deux autres mécanismes sur deux échelles de temps distinctes : le contrôle du turn-over forestier par la dynamique géomorphologique au cours du quaternaire récent et l’intégration des effets biogéographiques sous l’influence des changements globaux plus anciens.La troisième partie de la thèse s’intéresse aux conséquences de la diversité biotique et abiotique décrite sur la gestion forestière et sur la variabilité des services écosystémiques rendus par la forêt, notamment en termes de stockage du carbone dans la biomasse et dans les sols. La quantité de carbone stockée, très variable à l’échelle locale, se révèle significativement influencée par la diversité écosystémique à l’échelle régionale. Ce service de régulation est mis en relation avec la richesse spécifique locale (service de support) et la quantité de bois exploitable (service d’approvisionnement). Des relations complexes de corrélation et de compromis sont mises en évidence entre ces différents services. Elles illustrent la variabilité des réponses des services écosystémiques à la diversité des écosystèmes forestières.La mise en perspective de ces différents volets permet de proposer une typologie précise des habitats forestiers de Guyane et de fournir des pistes de prise en compte de cette diversité écosystémique pour l’aménagement du territoire et la gestion forestière. / French Guiana forest presents a high originality in terms of biodiversity, a good state of preservation, a strong contribution to the overall Amazonian carbon stocks and a very fast socio-economic dynamic. However, our knowledge about forest ecosystems diversity remains insufficient to ensure an optimal management of the various ecosystems and of the services they may provide across the territory. This thesis aims to answer this central issue by studying the diversity of forest ecosystems at the scale of the entire forested area of French Guiana. Specifically we targeted highlighting the factors that determine ecosystems variability and evaluating the consequences of this variability in terms of ecosystem services and management.Firstly, we bring out complex patterns of diversity at different scales including strong floristic variation at the regional scale, using a recent forest inventories campaign (2006-2013) that has been conducted according to a stratified sampling design which includes 3,132 0.2ha-plots covering the whole territory. Our results verify the hypothesis of a strong control of forest beta and alpha diversity by geomorphology, especially at the landscape scale and for dominant species (Simpson metric). This first step required several preliminary methodological developments including an assessment of the taxonomic uncertainty in forest inventories, and spatial models to accurately characterize the geomorphological context at various scales.Secondly, we aimed at interpreting the influence of geomorphological landscapes on the composition of forest vegetation by exploring the relationship between geomorphology and soils. Using about 450 soil sampling locations coupled with the forest inventory plots, we demonstrated that nature and properties of soils are dependent on geomorphological landscapes and locally distributed along regional elevation gradients. A significant soil filtering effect was found underlying the geomorphological influence on forest composition and diversity. However, a major part of this influence proved to be independent of soil filtering and is interpreted as a combination of two mechanisms at two different time-scales: (i) the control of forest turn-over by the geomorphological dynamics during the Late Quaternary and (ii) the integration of biogeographic effects under the influence of tectonic evolution and ancient climate changes.Last of all, we addressed the consequences of the analysed biotic and abiotic variations, which combine into habitats diversity on forest management and on the variability of ecosystem services provided by forests, particularly for carbon storage in biomass and soils. The amount of carbon stored is highly variable at local scale but proves to be significantly influenced by habitats diversity at the landscape level. This regulation service is related with the local species richness (pertaining to the category of support services) and the amount of usable wood (pertaining to the category of supply services). Complex relationships, including correlations and compromises, are evidenced between these different services. This illustrates the variability of the responses of ecosystem services to the habitats diversity.Finally our work allowed us to provide a new typology of natural habitats present in French Guiana forest and to propose suggestions in order to improve land uses and multifunctional forest management in French Guiana.

O conjunto de alterações causadas pela poluição atmosférica é considerado uma fonte importante de estresse ambiental. A poluição é hoje uma das maiores preocupações ambientais do mundo, pois afeta todas as fontes de recursos naturais que as populações humanas utilizam para a sobrevivência. Agravando esse quadro, somam-se as modificações na paisagem, que intensificam ainda mais os efeitos da poluição. As comunidades de liquens, entre as mais sensíveis em nível de ecossistema, são capazes de demonstrar sinais precoces como resposta às mudanças ambientais e ser úteis como biondicadoras e biomonitoras dessas mudanças. Avaliações em nível de indivíduos e de comunidades de liquens podem ser ferramentas de monitoramento ambiental, assim como uma abordagem com base na estrutura funcional dessas comunidades. Ainda, o uso de atributos funcionais pode permitir compreender como os liquens são capazes de se adaptar funcionalmente à forte pressão ambiental da poluição, além de servir como nova ferramenta para o biomonitoramento da qualidade do ar. Assim sendo, o objetivo geral desta tese foi avaliar os efeitos da poluição atmosférica e da paisagem (como descritora de poluição) na estrutura e na resposta funcional das comunidades de liquens. A partir dos resultados obtidos demonstramos que os liquens de áreas urbanas têm clara influência da poluição atmosférica e das mudanças na paisagem como estresse ambiental, tanto em nível estrutural quanto funcional. No primeiro artigo, avaliamos a qualidade do ar em cada um dos municípios amostrados, contribuindo para a gestão destas áreas com informações relevantes em nível de saúde pública e ambiental. No segundo, demonstramos que tanto a riqueza, cobertura e composição de espécies, além da vitalidade dos liquens, são afetadas pela poluição atmosférica e pelas mudanças da paisagem, sendo a vitalidade e a composição de espécies os melhores indicadores para avaliar os efeitos de múltiplos distúrbios ambientais neste tipo de áreas urbanas. No terceiro artigo, verificamos que alguns atributos funcionais de liquens podem ser bons indicadores da qualidade do ar, relacionados ao tipo de alga, tipo de crescimento, estratégia reprodutiva e à presença de proteção no talo. Fechamos a tese com a descrição de uma nova espécie encontrada, até o momento, somente em áreas pouco urbanizadas. Portanto, novas formas de se utilizar os liquens como bioindicadores e biomonitores de qualidade do ar foram propostas, ampliando ainda mais a aplicação prática desses organismos. / The set of changes caused by air pollution is an important source of environmental stress. Pollution is one of the greatest environmental concerns worldwide in the present days, since it affects all natural resources that people need to survive. Worsening this panorama, there are serious changes in land cover intensifying the effects of pollution. Lichens, which are among the most sensitive organisms in the ecosystem, are able to show early signs as responses to environmental changes. Besides, they can also be useful as bioindicators and biomonitors of such changes. Evaluations using single lichen species and/or lichen communities can be tools of environmental monitoring, as well as an approach based on the functional structure of these communities. The use of functional traits may allow the understanding of how lichens are able to functionally adapt to the strong pressure of pollution. Furthermore, this is also a promising method to be used as a new tool for air quality biomonitoring. Therefore, the main objective of this thesis was to evaluate the effects of air pollution and land cover changes (as surrogates of this pollution) on lichen communities structure and functional response. From the results found, we could demonstrate that lichens from urban areas have clear influence of atmospheric pollution and land cover changes as environmental stresses. The effects are both in structure and function of these communities. In the first paper, we evaluated the air quality in each of the studied cities, contributing to the environmental management of these areas with relevant information for public and environmental health. In the second, we demonstrated that lichen species richness, cover and composition, besides thallus vitality, are affected by air pollution and land cover changes. Among these parameters, we showed that vitality and species composition are the best indicators to evaluate multiple disturbances in this type of urban environment. In the third paper, we verified that some functional traits can be good indicators of air quality, namely the ones related to the type of lichen algae, growing form, reproduction strategy and the presence of any protection (physical or chemical) in the thallus. We ended the thesis with the description of a new species which is so far only found in low urbanized areas. Thus, new means of using lichens as bioindicators and biomonitors of air quality were proposed, helping to expand the application of these organisms in environmental studies and actions.

Radiações evolutivas estão entre os eventos mais fascinantes da evolução. Grande parte da diversidade da vida, tanto de espécies como ecológica, surgiu nos breves intervalos temporais de rápida especiação que configuram as radiações. As causas ecológicas e não-ecológicas do surgimento da diversidade em radiações evolutivas, em especial nas radiações adaptativas, são tema de pesquisa há muito tempo, pelo menos desde que Darwin observou a imensa diversidade de um grupo de pássaros nas ilhas Galápagos. Desde então, as ilhas têm sido os ambientes ideais para o estudo desse fenômeno, e foi a partir das observações e experimentos em ilhas que toda a teoria ecológica das radiações evolutivas surgiu. Contudo, as causas ecológicas das radiações explosivas ocorridas em amplas escalas continentais permanecem tema de constante debate. Nesta tese, foram investigados os determinantes ecológicos e não-ecológicos (e.g., geografia, contingências históricas, efeitos filogenéticos) da evolução morfológica dos roedores sigmodontíneos durante sua radiação na região Neotropical, em especial no continente sul-americano. Para isso, foi quantificada a morfologia do crânio e mandíbula de mais de dois mil exemplares do grupo, e foram investigadas variações ecomorfológicas nos níveis interespecífico (I), intraespecífico (II), e entre assembleias de sigmodontíneos (III). Na Parte I da tese, foram investigadas duas predições da teoria da radiação adaptativa, a correlação-fenótipo ambiente (capítulo 1) e a funcionalidade do fenótipo através da força da mordida (capítulo 2), permitindo determinar o papel da divergência ecológica na evolução morfológica das espécies. Na Parte II (capítulo 3), foram investigadas as contribuições relativas de processos determinísticos e neutros sobre a variação morfológica entre populações de uma espécie de roedor sigmodontíneo amplamente distribuída, Akodon cursor. Na Parte III, a influência da variação ambiental e da distribuição espacial das linhagens filogenéticas de sigmodontíneos sobre o tamanho corporal (capítulo 4) e forma do crânio e mandíbula (capítulo 5), foram investigados no contexto biogeográfico da variação no tamanho e forma média entre assembleias de sigmodontíneos. As contribuições originais desta tese foram: (i) mostrar que a radiação evolutiva dos roedores sigmodontíneos foi guiada principalmente por fatores históricos e geográficos ao invés de fatores ecológicos; (ii) sugerir que radiações evolutivas ocorridas em escalas continentais, especialmente de roedores, têm um componente geográfico e histórico mais determinante do que o componente ecológico; (iii) revelar que a força da mordida varia pouco entre roedores sigmodontíneos herbívoros e granívoros, o que provavelmente é resultado do fenótipo generalista desses roedores; (iv) apontar que sigmodontíneos com dieta insetívora têm uma taxa de evolução mais rápida, e parecem estar evoluindo sua forma do crânio/mandíbula e sua força da mordida em uma direção diferente das demais espécies; (v) demonstrar que, dentro de uma espécie de sigmodontíneo (Akodon cursor), fluxo gênico e deriva genética explicam melhor a forma do crânio entre populações, enquanto a variação ambiental explica melhor o tamanho do crânio, indicando que o tamanho é uma característica mais lábil e mais sujeita a pressões ambientais do que a forma do crânio; (vi) mostrar que a variação biogeográfica, tanto do tamanho quanto da forma média do crânio/mandíbula entre assembleias de sigmodontíneos, está sob influência da distribuição diferencial das linhagens filogenéticas ao longo do espaço geográfico, bem como de variáveis ambientais; o que indica conservação filogenética de nicho à nível de metacomunidades. De modo geral, ao investigar as contribuições relativas dos componentes adaptativo e não-adaptativo da evolução morfológica, foram obtidas informações importantes para conhecer as causas da diversificação morfológica em Sigmodontinae, aumentando nosso conhecimento sobre as origens de toda a diversidade biológica. / Evolutionary radiations are among the most fascinating phenomena of evolution. Most of the biological diversity on the planet, both in terms of species and ecological diversity, appeared during these brief intervals of rapid speciation. The ecological and non-ecological causes of the emergence of diversity in evolutionary radiations, especially in adaptive radiations, have long been the subject of research, beginning with Darwin and his notice of the astonishing diversity of bird forms in the Galapagos Islands. Islands have since been ideal environments in which to study evolutionary and adaptive radiations, and indeed it was from observations and experiments on islands that all ecological theory of evolutionary radiations arose. However, the ecological causes of explosive radiations occurring on large continental scales are still a matter of debate. In this dissertation, I investigated the ecological and non-ecological (e.g., geography, historical contingencies, phylogenetic effects) determinants of morphological evolution in sigmodontine rodents during their radiation in the Neotropical region, particularly on the South-American continent. The skull and mandible morphology of more than two thousand specimens was quantified, and ecomorphological variation was investigated on three levels: interspecific (I), intraspecific (II), and among sigmodontine assemblages (III). In part I, two predictions from the ecological theory of adaptive radiation were investigated: the phenotype-environment correlation (chapter 1), and the trait utility through the bite force (chapter 2). This approach enabled determination of the role of ecological divergence in species morphological evolution. In part II (chapter 3), I investigated the relative contributions of deterministic and neutral processes to morphological variation among populations of one widely distributed sigmodontine species, Akodon cursor. In part III, I investigated the influence of environmental variation and spatial distribution of phylogenetic lineages on body size (chapter 4) and on shape of the skull and mandible (chapter 5), in the context of biogeographical variation of mean size and shape in sigmodontine assemblages. The original contributions of this dissertation are as follows: (i) to demonstrate that the evolutionary radiation of sigmodontines was driven mainly by historical and geographical factors instead of ecological factors; (ii) to suggest that evolutionary radiations on continental scales, especially rodent radiations, have a more determinant historical and geographical component than an ecological one; (iii) to show small variation in bite force between sigmodontine herbivores and granivores, which is likely a consequence of the generalist phenotype of these rodents; (iv) to highlight that insectivorous sigmodontines have a faster rate of morphological evolution than other diet groups, and that skull and mandible morphology and bite force are evolving in different directions than in other species; (v) to demonstrate that within a sigmodontine species (Akodon cursor), gene flow and genetic drift better explain variation in skull shape among populations, while environmental variation better explains variation in skull size, which suggests that size is more labile feature than shape and thus more prone to change with environmental pressures; and (vi) to show that biogeographical variation in mean body size, mean skull shape, and mean mandible shape across sigmodontine assemblages is influenced by the different distributions of phylogenetic lineages over geographical space, as well by environmental variables, which indicates phylogenetic niche conservatism at the metacommunity level. These results shed light on some of the factors driving morphological diversification in Sigmodontinae. Further, the analytical approach(es) utilized may be useful for general investigations of the relative contributions of adaptive and non-adaptive components of morphological evolution, thereby potentially increasing our knowledge of the origins of all biological diversity.

L'étude de l'écologie des micro-organismes est récente malgré son importance pratique et théorique intrinsèque mais également son rôle central dans la niche des macro-organismes. Les interactions plantes-champignons, de par leur importance socio-écologique et de leur diversité -- du mutualisme au parasitisme en passant par le commensalisme --, offrent un modèle judicieux pour étudier l'écologie des communautés de micro-organismes en interaction avec des macro-organismes. À l'aide de techniques de séquençage à haut débit (NGS) et d'analyse des réseaux, nous explorons certains déterminants de la structure des champignons des forêts corses à travers trois guildes : les champignons ectomycorhiziens, endophytiques et saprotrophes. Ce travail considère les processus de dispersion, les perturbations (feux et chablis), les facteurs environnementaux (par ex. la profondeur du sol) et les contraintes dérivées de l'interaction avec les hôtes (par ex. taxinomie). Les assemblages des communautés des différentes guildes présentent des patrons communs qui pourraient être issus de mécanismes identiques. Ainsi, l'ensemble des guildes étudiées présentent des variations fortes à l’échelle des micro-régions de Corse et entre forêts ayant des histoires de feux différentes. En revanche, l'importance des différents processus d'assemblage et les échelles spatiales auxquelles ils s'appliquent varient selon les guildes. Nous discutons des implications que suscitent ce travail pour les écologues des communautés et pour les gestionnaires d'espaces naturels. / Study of micro-organisms ecology arose recently despite its intrinsic importance -- both practical and theoretical --, but also despite its overriding role in the niches of macro-organisms. Plant-fungi interactions offer a relevant model to study the ecology of micro-organisms interacting with macro-organisms because of their considerable ecological and economical values in addition to their high taxonomic and ecological diversity. Using next-generation sequencing (NGS) and network analysis, we explore some drivers of fungal community composition in Corsica, at various scales and through three guilds: ectomycorrhizal, endophytic and saprotrophic fungi. We investigate the effect of disturbance (e.g. fire and treefall), environmental variables (e.g. soil depth), constraints due to the interacting plants (e.g. taxonomy) and dispersion on fungal communities. Some community assembly rules are similar across guilds. For instance, forests in different micro-regions of Corsica harbor dissimilar fungal communities. However relative importance of processes and the scales at which they occur vary across guilds. In Corsican pine forests, fifteen years after fire occurrence, soil fungal diversity is close to the level of diversity in unburnt stand. Despite the absence of effect on diversity, fire induces marked shifts in soil fungal community composition, in particular for soil saprobic fungi. We discuss the implication of this work for ecologists -- both plant and fungal ecologist -- and stakeholders.