abstract: This work investigates the effects of non-random sampling on our understanding of species distributions and their niches. In its most general form, bias is systematic error that can obscure interpretation of analytical results by skewing samples away from the average condition of the system they represent. Here I use species distribution modelling (SDM), virtual species, and multiscale geographically weighted regression (MGWR) to explore how sampling bias can alter our perception of broad patterns of biodiversity by distorting spatial predictions of habitat, a key characteristic in biogeographic studies. I use three separate case studies to explore: 1) How methods to account for sampling bias in species distribution modeling may alter estimates of species distributions and species-environment relationships, 2) How accounting for sampling bias in fossil data may change our understanding of paleo-distributions and interpretation of niche stability through time (i.e. niche conservation), and 3) How a novel use of MGWR can account for environmental sampling bias to reveal landscape patterns of local niche differences among proximal, but non-overlapping sister taxa. Broadly, my work shows that sampling bias present in commonly used federated global biodiversity observations is more than enough to degrade model performance of spatial predictions and niche characteristics. Measures commonly used to account for this bias can negate much loss, but only in certain conditions, and did not improve the ability to correctly identify explanatory variables or recreate species-environment relationships. Paleo-distributions calibrated on biased fossil records were improved with the use of a novel method to directly estimate the biased sampling distribution, which can be generalized to finer time slices for further paleontological studies. Finally, I show how a novel coupling of SDM and MGWR can illuminate local differences in niche separation that more closely match landscape genotypic variability in the two North American desert tortoise species than does their current taxonomic delineation. / Dissertation/Thesis / Doctoral Dissertation Geography 2018

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The variation on the richness species in regional scales has been debated a lot. Three of the hypotheses mot frequently discussed as determinants of regional variability in richness species are energy, contemporary climatic conditions and habitat heterogeneity. Studies at mesoscale are very important to discover different patterns that underlying the variability in richness species. As the bats are so common in whole world and ecologically diverse, these organisms are excellent environmental characterized. On this basis, the goals of this study were to link the bat species composition with the vegetation in forest-grassland transition area in the Southeastern of South America and to assess the space influence on the bat species richness by environmental variables. The study area includes the southeastern of South America. Species distribution data were obtained by museums, review and database on line .The distribution s estimate for each species was done on a map with 139 cells 1º latitude by 1º longitude. It was collected distribution data to 79 bat species. Rain Forest and Seasonal Forest had the largest species richness. The cluster analysis based on the cells revealed three major clusters: the Forest cluster (at north), the Araucaria cluster (at middle), and the Grassland cluster (at south). The Araucaria cluster was associated to the Grassland cluster. The cluster analysis based in the phytogeographic zones revealed four clusters, where the Araucaria Forest was associated with the forested regions. The contemporary climatic conditions hypothesis was the best explained the variability on the richness data, where the mean annual temperature the main predictor variable, followed by extent of relief and AET, respectively. With the whole variables, the OLS regression also indicated the mean annual temperature as the main predictor variable, followed by AET. These same variables also explained the variability in the species richness in Phyllostomidae, Molossidae and Vespertilionidae. The Araucaria Forest is a filter area to the dispersal of tropical species into subtropical and temperate areas of South America, because the hard winters in that area, what may be explained likely for the intolerance of some species in colder climates. / A variação da riqueza de espécies em escala regional tem sido intensivamente discutida. Três das principais hipóteses que buscam explicar esse padrão de variação são as hipóteses energética, climática e de heterogeneidade do habitat. Estudos em meso-escala são importantes para descobrir padrões diferentes que influenciam a variação na riqueza de espécies. Como os morcegos são muito abundantes globalmente e bem diversificados ecologicamente, esses organismos são ótimos caracterizadores ambientais. Com base nisso, os objetivos deste estudo foram relacionar a composição das espécies de morcegos com a vegetação em área de transição floresta-campo no sudeste da América do Sul e avaliar a influência do espaço sobre a riqueza de morcegos através de variáveis ambientais. A área de estudo compreende a porção sudeste da América do Sul. Os dados de distribuição das espécies foram coletados através de visita a museus, revisão bibliográfica e consulta a bancos de dados on line. Foi feita a estimativa de distribuição para cada espécie sobre um mapa contendo 139 quadrículas de 1º de latitude por 1º de longitude. Foram obtidos dados de distribuição para 79 espécies de morcegos. Áreas de Floresta Ombrófila Densa e de Floresta Estacional possuíram a maior riqueza de espécies. A análise de agrupamento com base nas quadrículas formou três grupos nítidos: grupo Florestal (ao norte), Araucária (intermediário) e Campestre (ao sul). O grupo Araucária ficou associado ao grupo Campestre. A análise de agrupamento com base nas regiões fitogeográficas formou quatro grupos nítidos, sendo que a Floresta de Araucária ficou associada às formações florestais. A hipótese climática foi a que melhor explicou a variação dos dados de riqueza, sendo a temperatura média anual a principal variável preditora, seguida pela amplitude da altitude e pela AET, respectivamente. Considerando todas as variáveis, a regressão OLS também apontou a temperatura média anual como a principal variável preditora, seguida pela AET. Essas variáveis também explicaram a variação na riqueza de espécies das famílias Phyllostomidae, Molossidae e Vespertilionidae. A Floresta de Araucária é uma área filtro para a dispersão de espécies tropicais para as regiões subtropicais e temperadas da América do Sul, devido aos invernos rigorosos presentes nessa área, o que pode ser explicado principalmente pela intolerância de algumas espécies a climas mais frios.

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.

Do thermal barriers limit biotic composition and community similarity, potentially helping to shape biodiversity patterns at continental scales? Are environmental variables responsible for broad-scale patterns of species endemism? Are these patterns predictable? And, how can patterns of endemism can inform global conservation strategies? These are some of the questions that I attempted to answer during my doctoral research. In the first chapter, I tested one of the most contentious hypotheses in ecology: Do thermal barriers, which grow stronger along elevational gradients across tropical mountains, create a dispersal barrier to organisms and consequently contribute to the isolation and divergence of species assemblages? If so, do patterns potentially generated by this mechanism detectably relate to dissimilarity of biotic assemblages along altitudinal gradients across the mountains in the Americas? We found that mountain passes are not only higher in tropical realms, as initially thought by Janzen (1967), and extensively popularized and assumed in further research, but they are also present in temperate regions along the western coast of North America. We also found that the stronger the thermal barrier, the higher the dissimilarity between communities. However, the variance explained was low, suggesting thermal barriers play a minor role in creating and maintaining patterns of biodiversity. The second chapter raises the question of why are there more small-ranged species in some places than in others. I tested four macroecological hypotheses (H1: climate velocity; H2: climate seasonality; H3: climate distinctiveness or rarity; and, H4: spatial heterogeneity in contemporary climate, topography or habitat) to predict broad-scale patterns of species endemism, using a cross-continental validation approach. We found that there is no empirical reason, from the standpoint of model fitting, parameter estimates, and model validation, to claim that any of these hypotheses creates and maintains broad-scale patterns of endemism. Although we found statistically significant relationships, they failed stronger tests of a causal relationship, namely accurate prediction. That is, the hypotheses did not survive the test of cross-continental validation, failing to predict observed patterns of endemism. Climate velocity was dropped from some models, suggesting that early correlations in some places probably reflect collinearity with topography. The effect of richness on endemism was in some cases negligible, suggesting that patterns of endemism are not driven by the same variables as total richness. Despite low explained variance, spatial heterogeneity in potential evapotranspiration was the most consistent predictor in all models. The third chapter is aimed to evaluate the extent to which global protected areas (PAs) have included endemic species (species with small range size relative to the median range size). We measure the relative coverage of endemic species by overlapping species geographic ranges for amphibians, mammals, and birds, with the world database of PAs (1990-2016). Then we measure the rate of expansion of the global PA network and the rate of change in endemic species coverage. We found that ~30% of amphibian, ~6% of bird and ~10% of mammal endemic species are completely outside PAs. Most endemic species’ ranges intersect the PA network (amphibian species = 58%; birds = 83%; mammals = 86%), but it usually covers less than 50% of their geographic range. Almost 50% of species outside the PA network are considered threatened (critically endangered, endangered and vulnerable). We identified that ecoregions in tropical Andes, Mesoamerica, Pacific Islands (e.g., New Guinea, Solomon), Dry Chaco, and Atlantic forests are major conservation priorities areas. The historic rates of new PAs added every year to the network is between ~6,000 to ~15,000. In contrast, we found that rates of including endemic species within the PA network have been fairly slow. Historic data shows that every year, the entire geographic range of 3 (amphibians) to 6 (birds and mammals) endemic species is 100% included inside the PA network (amphibians = from 162 to 233; mammals = 10 to 84; and, amphibians = 16 to 99). Based on these trends, it is very unlikely PAs will include all endemic species (14% total endemic species, that is ~1,508 out of 11,274) currently outside the PA network by 2020. It will require five times the effort made in the last two decades. However, projections also showed that is very likely that some portions of the geographic ranges for all endemic birds and mammals, but not for all endemic amphibians, will be covered by the future PA network. I sum, I found that none of the hypotheses tested here can explain broad-scale patterns of total species richness and total species endemism. My main contribution on this research area is clearly rejecting these hypotheses from potential candidates that may explain biodiversity patterns. By removing them, we advance in this field and open possibilities to test new hypotheses and evaluate their mechanisms. I proposed that other drivers and mechanisms (whether biotic and biotic) acting at local scales, and escaping the detection of macroecological approaches, might be responsible for these patterns. Finally, in terms of conservation planning, I proposed that the international community has an opportunity to protect a great number of endemic species and their habitats before 2020, if they strategically create new PAs.

Les prédateurs marins supérieurs, ici les cétacés et les oiseaux marins, doivent développer des stratégies optimales d’utilisation des ressources et des habitats. Notre objectif était d’explorer leurs habitats en fonction de leurs coûts de vie. Nous avons postulé que les prédateurs coûteux étaient contraints d’occuper les habitats de meilleure qualité alors que les prédateurs plus économes pouvaient occuper les habitats de qualité moindre. Nous nous sommes basés sur des guildes de cétacés et oiseaux définies selon leurs coûts de vie et les observations de survols aériens dans trois régions tropicales (l’Atlantique Ouest tropical, le Sud Ouest de l’Océan Indien et la Polynésie française). Nous avons construit des modèles additifs généralisés à partir de variables physiographiques (ex : profondeur), océanographiques (ex : activité tourbillonnaire) et biologiques (ex : chlorophylle et micronecton) pour décrire la qualité des habitats. Nous avons d’abord modélisé les habitats des cétacés et oiseaux à l’échelle régionale. Les cétacés coûteux occupaient les habitats de meilleure qualité alors que les cétacés plus économes occupaient aussi les habitats de qualité moindre. La distribution des oiseaux reflétait principalement celle des colonies et leur dépendance à la qualité de l’habitat semblait moins claire. Nous avons ensuite mis en évidence des propriétés génériques de distribution des cétacés et fourni des prédictions circumtropicales. Cette thèse a donné un nouvel aperçu des stratégies d’utilisation des habitats des prédateurs supérieurs à la lumière de leurs coûts de vie. Ces prédictions spatiales ont des implications majeures pour la gestion de ces espèces et de leurs écosystèmes. / Marine top predators, here cetaceans and seabirds, must develop optimal strategies of resource and habitat utilization. The main goal of this dissertation was to investigate cetacean and seabird strategies of habitat utilization in relation to their energetic costs of living. We hypothesized that predators with high costs of living should be constrained to high quality habitats, whereas less active predators could cope with habitats of lesser quality. We studied the habitats of cetacean and seabird guilds defined according to their likely costs of living. We relied on sightings collected from aerial surveys in three tropical regions (the western tropical Atlantic, the Southwest Indian Ocean and French Polynesia). We built generalized additive models based on a range of physiographic (e.g. depth), oceanographic (e.g. mesoscale activity) and biological variables (e.g. chlorophyll concentration and micronekton) to describe the quality of pelagic habitats. We first modeled cetacean and seabird habitats at the regional scale. Energetically costly cetaceans appeared to be constrained to the highest quality habitats, whereas less active cetaceans exploited habitats of lesser quality. Seabird distributions primarily reflected colony locations and their dependences on habitat quality were less clear. We then highlighted generic properties of cetacean distributions and provided predictions at the circumtropical scale. This dissertation gave new insights on top predator strategies of habitats utilization in light of their costs of living. These spatial predictions have significant implications for the management of these species and of their pelagic ecosystems.

Plant-pollinator interaction assembly can be represented as so called pollination network. Using these networks, assembly of plant-pollinator communities and geographic patterns in pollination networks can be studied. During last years, a great progress in describing patterns in structure of plant-pollinator interaction webs and in describing their spatial variability was made. However, these results are mostly based on data from previous studies, which are not seamlessly comparable due to their nonuniformity. My thesis aims at the methodological concepts of study on pollination networks. Based on meta- analysis of previously published data and on data from four years detailed study of plant-pollination system from one locality, I show several methodological problems caused by dissimilarities in sam- pling method of current pollination-network data. These dissimilarities could be responsible for some observed patterns in the assembly of pollination networks. Thus, I propose a uniform method for observing pollination networks suitable for macroecolo- gical meta-analyses (pollination network samples). I tested this method in the field and I described 49 pollination networks from the central and eastern Europe by using such method. In these ne- tworks, no nonrandom structure character such as...

Cette thèse cherche à déterminer l’influence de l’environnement abiotique sur la structure des assemblages de poissons dans les estuaires européens tidaux à partir d’une approche macroécologique. L’environnement abiotique de 135 estuaires, du Portugal à l’Ecosse, est caractérisé par une quinzaine de descripteurs en utilisant une approche écohydrologique. Les assemblages de poissons d’une centaine d’estuaires sont caractérisés par les données de pêche acquises au cours de campagnes scientifiques conduites dans le cadre de la Directive-Cadre européenne sur l’Eau (DCE). Néanmoins, ces données sont souvent hétérogènes du fait des différences entre les protocoles d’échantillonnage utilisés. Afin de limiter cette hétérogénéité, une sélection rigoureuse et une procédure de standardisation des données ont été effectuées. Les assemblages de poissons sont décrits à l’aide d’indices globaux ou fonctionnels relatifs à la richesse spécifique et à l’abondance. A l’aide de modèles linéaires généralisés, des relations sont établies entre des attributs de l’ichtyofaune et des gradients abiotiques à large échelle et au sein de l’estuaire. La richesse spécifique totale, et en particulier celle des espèces marines et migratrices amphihalines, augmente avec la taille de l’estuaire. De plus, elle apparaît plus élevée dans les estuaires associés à un large plateau continental. Les plus fortes densités totales et, en particulier, celles des espèces résidentes et marines, sont associées aux estuaires présentant une grande proportion en zones intertidales. Les assemblages de poissons estuariens apparaissent fortement structurés par le gradient de salinité à la fois en termes de richesse spécifique et de densité. En parallèle, cette thèse apporte des éléments témoignant d’un décalage vers le Nord de plusieurs espèces de poissons estuariens dans le contexte du réchauffement climatique global. Les résultats de cette thèse contribueront à l’amélioration des indicateurs biotiques basés sur l’ichtyofaune qui sont actuellement développés dans le contexte de la DCE. / Based on a macroecological approach, this thesis aims at determining the influence of the abiotic environment on the structure of fish assemblages among European tidal estuaries. The abiotic environment of 135 North-Eastern Atlantic estuaries from Portugal to Scotland was characterised by fifteen descriptors using an ecohydrological approach. The fish assemblages of about a hundred estuaries were characterised by fish data collected during scientific surveys conducted in the context of the European Water Framework Directive (WFD). Nonetheless, differences among sampling protocols resulted in highly heterogeneous datasets. To limit this heterogeneity, a rigorous selections and standardisation processes were carried out. Fish assemblages were described by total or functional indices related to species richness or abundance. Relationships were identified between large-scale and intra-estuarine abiotic gradients and fish attributes by fitting generalised linear models. Results showed that the total number of species, and more especially of marine and diadromous species, increased with the estuary size. Moreover, the total species richness appeared higher in estuaries associated to a wide continental shelf. The greatest total densities, and more particularly total densities of resident and marine species, were associated to estuaries with a great proportion of intertidal areas. Fish assemblages appeared also strongly structured by the salinity gradient in terms of both species richness and density. Furthermore, this thesis brought some evidence of northward migration of estuarine fish species in the context of the global warming. The results of this thesis will contribute to improve the fish indicators that are currently developed in the context of the European WFD.

L'étude de la biodiversité passée, de sa dynamique et des paramètres déterminant son évolution, est un préalable nécessaire à la compréhension de l’érosion de la biodiversité actuelle. En étudiant les conditions environnementales et historiques associées aux assemblages taxinomiques, il est possible d'inférer les liens dynamiques qui unissent les variations de l'environnement et de la biodiversité. Pour cela, un Système d'Information Géographique (SIG) a été développé à partir des compilations du registre fossile des mammifères terrestres cénozoïques d'Amérique du Nord publiées par Janis et al. (1998, 2008). Ce registre, s'étendant de la crise Crétacé/Paléogène (66 Ma) au Pléistocène inférieur (�1,8 Ma) et couvrant les territoires actuels des Etats-Unis, du Canada et du Mexique, est l'un des registres fossiles les mieux connus et les plus complets au monde. Sur la base de ces données d'occurrences géoréférencées, il devient possible de caractériser les patrons de distributions et d'observer les fluctuations temporelles et spatiales de plusieurs dimensions de la biodiversité (diversité taxinomique, disparité, diversité fonctionnelle, diversité phylogénétique.). L'observation de ces variations spatio-temporelles de biodiversité peut être réalisée à différentes échelles (locale à continentale) et pour différents types d'assemblages écologiques ou taxinomiques (communautés, métacommunautés, guildes trophiques, groupes de taille, espèces, genres, familles.), permettant en retour de tester différentes hypothèses à l'interface entre macroévolution et macroécologie. Ainsi, deux axes de recherche principaux ont pu être développés dans le cadre de ce travail. Le premier s'enracine dans une problématique centrale en macroévolution : l'impact de l'organisation chronologique des informations paléontologiques dans un système biozonal discret sur la reconstruction de séries temporelles de diversité et de taux d'évolution (apparitions et extinctions). A partir de simulations, l'effet de la discrétisation temporelle est estimé en fonction du registre fossile étudié ; un algorithme est développé afin d'en corriger les distorsions. Le second axe de recherche s'enracine dans une problématique centrale en macroécologie : comment caractériser a posteriori, sur la base de données d’occurrences taxinomiques échantillonnées au sein d'assemblages, la part relative des processus d'assemblage par la niche et par la dispersion dans la construction et le maintien de communautés et métacommunautés ? Afin de répondre à cette question, un nouvel outil analytique appelé « PER-SIMPER » est développé à partir de la méthode SIMPER (Clarke 1993). Dans un premier temps, la précision et la consistance de cette nouvelle méthode sont évaluées à l'aide de simulations basées sur des automates cellulaires. Dans un second temps, l'analyse PER-SIMPER de l'ensemble des biozones enregistrées au sein du SIG est réalisée ; les résultats obtenus sont discutés au regard des changements climatiques et environnementaux associés à l’histoire évolutive des mammifères cénozoïques nord-américains. Finalement, les résultats obtenus permettent d’identifier différentes perspectives de recherche à court, moyen et long termes, tant sur leplan analytique que méthodologique / The study of past biodiversity, its evolutionary dynamics and related control parameters is a fundamental prerequisite for understanding the ongoing global biodiversity loss. Considering the environmental and historical conditions related to taxonomical assemblages, the dynamic links associating environmental changes and biodiversity can be inferred. To achieve this, a Geographic Information System (GIS) has been developed based on Janis et al.'s (1998, 2008) compilations of the north-American Cenozoic mammal fos- sil record. Ranging from the Cretaceous/Paleogene crisis (66 Ma) to the early Pleistocene (�1.8 Ma), this fossil record covers extant United States, Canada, and Mexico territories; it is one of the best known and most complete fossil record in the World. Based on these georeferenced data of fossil occurrences, it be- comes possible to characterize distribution patterns and to observe spatial and temporal variations of sev- eral aspects of biodiversity (taxonomical diversity, disparity, functional diversity, phylogenetic diversity.). The observation of spatial and temporal variations of biodiversity can be achieved at various geographical scales (local to continental) and for different types of ecological or taxonomical assemblages (communi- ties, metacommunities, trophic guilds, size groups, species, genera, families.); in turn, these observations make possible testing various hypotheses at the interface between macroevolution and macroecology. In this way, two main research axes have been developed in this work. The first research axis roots into a central issue of macroevolutionary studies: the impact of the chronological organization of paleontologi- cal data within a discrete biozonation on the reconstruction of biodiversity and evolutionary rate (origina- tion and extinction) time series. Based on simulations, the effect of time discretization is investigated; an algorithm is developed in order to correct the distorting effect induced by the time discretization process. The second research axis developed in this work roots into a central macroecological question: based on taxonomical occurrence data sampled within assemblages, how to characterize the relative contribution of niche- and dispersal-assembly processes in the building and conservation of communities and meta- communities? Building on Clarke's (1993) SIMPER method, a new analytical tool called "PER-SIMPER" has been developed in order to answer this question. First, the accuracy and consistency of this new method is evaluated through cellular automaton-like simulations. Then, the PER-SIMPER analysis of all biozones recorded within the GIS is achieved, and results are discussed with respect to the climate and environmen- tal changes related to the evolutionary history of north-American Cenozoic mammals. Finally, the results obtained from both research axes allow the identification of several short, middle and long-term analytical as well as methodological research perspectives

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

Photoelectron Photoion Coincidence (PEPICO) spectroscopy is a robust tool for elucidating complex unimolecular dissociation mechanisms and for determining thermochemical and kinetic data of gas-phase ion dissociations with high accuracy. In this work, the dissociative photoionization of two sets of isomeric systems were analyzed with PEPICO: 1) C7H7+ ions of toluene (Tol) and 1,3,5-cycloheptatriene (CHT), and 2) two butyl alcohol isomers, 1-butanol and isobutanol. Threshold dissociative photoionization data on these four molecules of interest were collected on the imaging PEPICO apparatus at the VUV beamline of the Swiss Light Source. Data analysis was aided by ab initio calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) statistical rate theory was employed to model the complex dissociation pathways of each system. Finally, thermochemical, reaction mechanism, and dissociation kinetics data were extracted from the modeled data and are reported here. In the first project, the dissociation of energy-selected 1,3,5-cycloheptatriene (CHT) and toluene (Tol) cations was investigated by imaging photoelectron photoion coincidence spectroscopy. In the measured energy ranges of 10.30−11.75 eV for CHT and 11.45−12.55 eV for Tol, only the hydrogen atom loss channels open up, leading to C7H7+ from both molecular ions, which are both metastable at the H-loss threshold. Our quantum chemical calculations showed that these ions can interconvert below their dissociation thresholds. Therefore, we constructed a single statistical model to describe both systems simultaneously. We determined 0 K appearance energies (E0) for the tropylium and benzyl fragment ions from CHT to be 9.520 ± 0.060 eV and 9.738 ± 0.082 eV, and from Tol to be 10.978 ± 0.063 eV and 11.196 ± 0.080 eV, respectively. Using the experimentally determined benzyl ion appearance energy, its 0 K heat of formation was calculated to be 937.9 ± 7.7 kJ mol–1. On the basis of this value and the recently determined benzyl ionization energy, we point out discrepancies concerning the benzyl radical thermochemistry. For the second project, the fragmentation processes of two internal energy-selected C4H10O+• cations, 1-butanol and isobutanol, were investigated. For both isomers, the first dissociation channel leads to the formation of C4H8+• ions (m/z = 56) by a water loss. Using statistical energy distribution and rate models, which include isomerization of the molecular ions, the 0 K appearance energies (E0) were determined to be 10.347 ± 0.015 eV and 10.566 ± 0.050 eV, for 1-butanol and isobutanol, respectively. The second dissociation channel, the formation of CH3OH2+, quickly overtakes the water-loss channel in isobutanol, with an E0 of 10.612 ± 0.020 eV, but appears only as a minor channel in 1-butanol with an E0 of 10.738 ± 0.080 eV. The methanol-loss channel, forming propylene ion, opens up at E0 = 10.942 ± 0.040 eV and 10.723 ± 0.020 eV in 1-butanol and isobutanol, respectively. The next two fragmentation pathways correspond to a complementary pair of C3H7+ through the loss of CH2OH, and CH2OH+ through the loss of C3H7. From both isomers, C3H7+ is the isopropyl ion, which is readily formed in isobutanol via a simple bond cleavage at E0 = 10.970 ± 0.050 eV and its pair, CH2OH+, at E0 = 11.11 ± 0.20 eV. However, there is an internal hydrogen shift necessary in 1-butanol and, therefore, the complementary ions appear at the same E0 of 11.104 ± 0.030 eV, which most likely corresponds to their common transition state. Finally, C3H5+, a product of sequential dissociation from m/z = 56, appears above 11.6 eV as a minor channel for both isomers.