Showing results 5641 to 5660 on 6583 in total
La co-occurrence dans un même individu de deux demi-génomes semblables mais différents (hétérozygotie) est une caractéristique générale des organismes diploïdes qui pose de gros problèmes techniques lors du séquençage : double pics, échec de l'assemblage des données,... En dépit de ces difficultés apparentes, les séquences d'organismes hétérozygotes apportent une mine d'informations très utiles à la délimitation des espèces et à l'analyse de leurs génomes. Après avoir montré comment reconstruire les allèles d'individus hétérozygotes par séquençage direct, sans cloner, j'introduirai une approche nouvelle pour la délimitation moléculaire des espèces basée sur l'analyse de l'hétérozygotie : cette approche, appelée "haplowebs", ne repose pas sur le critère de monophylie et surpasse pour cette raison les méthodes actuellement utilisées en barcoding (GMYC, ABGD,...). Dans la deuxième partie de mon exposé, je montrerai comment l'analyse récente de l'hétérozygotie d'un rotifère bdelloïde a permis de prouver son asexualité et de mettre en évidence l'importance des conversions géniques et des transferts horizontaux dans l'évolution de son génome.
While we often think of colour as synonymous with pigment, many of the most spectacular colours in nature are caused by differential interference of different wavelengths of light as they are scattered by nano structured surface features. There are many famous examples of such structural colour in animals, such as the iridescent scales on morpho butterflies and peacock feathers, but structural colour is also common throughout the plant kingdom, from algae to numerous groups of flowering plants. Structural colour in flowers is thought to aid in pollinator attraction, but it is also common in leaves, where its functional significance is not well understood. We are investigating the genetic basis and functional significance of structural colour in a variety of plant species with a range of approaches including genomics. We are working with genome-wide transcription data for two distinct lineages of iridescent plants: the living fossil Selaginella, which produces blue iridescence in the l eaves and the flowering plant Spiloxene which has iridescent flowers. We have obtained RNAseq data for four different tissues for each of four Selaginella species exhibiting a range of iridescence intensities and for Spiloxene capensis. For each species, de novo transcriptome assemblies were produced and used for differential gene expression analysis. Between 14,000 and 26,000 gene families were found for each species, with between 150 and 250 gene families exhibiting significant differences in gene expression across the four tissues examined. We have identified several genes that code for cell wall modifying enzymes that are differentially expressed only in iridescent species as candidates for the generation of cell wall layering responsible for iridescence in Selaginella. We are also investigating differentially expressed photosynthesis genes to test the hypotheses that iridescence may play a role in increasing photosynthetic efficiency or in photoprotection. We hope that t he use of functional genomics, coupled with detailed anatomical and developmental studies and optical modelling that are ongoing in our lab, will help to unravel the evolutionary origins and ecological roles of plant structural colour.
We study a poorly characterized bacterial gender of the Planctomycetes phylum, Gemmata obscuriglobus. Planctomycetes are major players in the global nitrogen and carbon cycles and are uniquely capable of anaerobic ammonium oxidation (a globally important nitrogen transformation). Within that phylum, the bacteria of the gender Gemmata are particularly interesting due to their complex intracellular membranous organization that is sustained by proteins showing similarity to the eukaryotic equivalent ones and their capability to internalize fully folded proteins in a process reminiscent of eukaryotic endocytosis (Lohnienne et al., 2010).We use a combination of computational, molecular biology, and electron-microscopy to first, decipher the peculiar biology of the Planctomycetes and second, to understand their contribution to eukaryotic origin. Computationally, we use structure to push the limits of sequence homology detection. Amongst other tools, we use protein architecture correlation to detect potential relationship between distantly related proteins (Santarella-Mellwig et al. PLoS Biol. 2010).
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The distribution of fitness effect of new mutations is central to many questions in evolutionary biology such as: what type of genetic variation enables sustained evolution, does adaptation to a given environment entails systematically a cost in different environments, what forces maintain phenotypic and molecular variation we observe in extant populations, etc. Fitness landscapes link the (phenotypic) effect of a new mutation and its fitness consequences. I will present recent work geared at inferring distribution of fitness effects and more broadly the properties of fitness landscapes underlying adaptation. I will consider empirical data bearing both on phenotypic evolution in experimental populations and patterns of molecular variation in natural populations.
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La répartition spatiale d'une espèce est une combinaison des effets de variables environnementales et des activités humaines. Selon leur position géographique, les groupes d'individus d'une espèce sont soumis à des conditions différentes qui influencent notamment leur probabilité de présence et leur biomasse. La répartition des différents groupes d'individus et la connectivité entre ces groupes peuvent avoir une influence primordiale sur la dynamique spatiale et temporelle de la population. La modélisation des habitats potentiels relie des biomasses observées avec les facteurs environnementaux par corrélation, grâce à des modèles linéaires généralisés (GLM) ou des modèles additifs généralisés (GAM). La modélisation permet de s'affranchir de l'observation complète d'une zone d'étude en prédisant la répartition des espèces sur les zones non observées si les facteurs environnementaux sont disponibles. La répartition spatiale des biomasses peut ensuite être couplée à un modèle de cycle de vie pour estimer la dynamique de population. La carte de répartition des laminaires en mer d'Iroise sera utilisée comme exemple de modélisation des habitats potentiels en statistiques fréquentistes. Ces cartes seront utilisées pour la gestion des stocks de laminaires, espèce récoltée pour ses alginates très utilisés en cosmétique. Un point important de cette étude est de faciliter l'interprétation des résultats par les gestionnaires tout en intégrant les effets de l'incertitude de prédiction sur cette interprétation. Le modèle de cycle de vie de la sole commune en Manche Est illustrera l'intégration (1) d'un modèle de dispersion larvaire pour la distribution des larves entre les nourriceries, (2) d'un modèle d'habitat potentiel pour la répartition des juvéniles dans ces nourriceries, et (3) d'un modèle de population (non spatialisé) pour les adultes soumis à la pression de pêche, dans le cadre d'un modèle hiérarchique bayésien. Ce modèle vise notamment à comparer l'importance relative des mortalités naturelles par rapport aux mortalités d'origine anthropique (dégradation des habitats juvéniles, pêche). Il pourrait aussi être utilisé pour l'évaluation du stock.
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It has long been argued that single species laboratory tests do not necessary predict the ecological effects of chemicals in the field. By ecological effects is used to mean effects on populations, communities and ecosystems. However ecotoxicologists have continued to use single species laboratory tests. My short research career has involved a number of change in direction - or backflips - in my attitude to these tests and I will illustrate this with examples of the effect of increased salinity on stream invertebrates, insecticides and fungicides on stream invertebrates and herbicides on benthic diatoms. I will discuss how such simple test systems combined with more complicated test systems can potential serve as models to test hypothesises as to how chemical stressors effect ecological systems.
Conflicts between wolves and livestock have continued to escalate since wolf re-introduction in the Northern Rockies, USA. We will provide an overview wolf re-introduction, including trends in populations and predation rates. We will also review how wolves have (or have not) affected livestock management practices and ranch profitability. We will then review the legal framework for wolf control in Wyoming, including predation compensation policies. Compensation policies have attempted to reduce the impact of wolf-livestock conflicts by compensating producers for lost livestock. Compensation schemes, however, focus only on direct predation (i.e., confirmed losses) despite a growing body of evidence that predation pressure also have indirect effects on prey, particularly domesticated livestock (e.g., slower weight gain, higher disease rates, or lower reproduction rates). We will then discuss our research, which uses an economic model of livestock production to estimate the economic impact of both direct and indirect effects of wolf predation. Our results suggest that short-run (i.e., year-to-year) financial impacts of wolf indirect effects may be as large as or larger than the direct effects. Including indirect effects implies that the compensation ratio (i.e., number of calves compensated per confirmed depredation) necessary to fully offset the financial impacts of wolves would need to be two to three times larger than current 7:1 compensation ratio used in Wyoming.
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Competition between organisms influences the processes governing the colonization of new habitats. As a consequence, species or populations arriving first at a suitable location may prevent secondary colonization. While adaptation to environmental variables (e.g., temperature, altitude, etc.) is essential, the presence or absence of certain species at a particular location often depends on whether or not competing species co-occur. For example, competition is thought to play an important role in structuring mammalian communities assembly. It can also explain spatial patterns of low genetic diversity following rapid colonization events or the ``progression rule'' displayed by phylogenies of species found on archipelagos. Despite the potential of competition to maintain populations in isolation, past quantitative analyses have largely ignored it because of the difficulty in designing adequate methods for assessing its impact. We present here a new model that integrates competition and dispersal into a Bayesian phylogeographic framework. Extensive simulations and analysis of real data show that our approach clearly outperforms the traditional Mantel test for detecting correlation between genetic and geographic distances. But most importantly, we demonstrate that competition can be detected with high sensitivity and specificity from the phylogenetic analysis of genetic variation in space.Joint work with L. Ranjard, D. Welch and M. Paturel.
The evolution of senescence (the physiological decline of organisms with age) poses an apparent paradox because it represents a failure of natural selection to increase the survival and reproductive performance of organisms. The paradox can be resolved if natural selection becomes less effective with age, because the death of postreproductive individuals should have diminished effects on Darwinian fitness. A substantial body of empirical work is consistent with this prediction for animals. However, such evidence is still scarce in plants. I will discuss the plausible reasons why the genetic basis of senescence in plants was not studied from an evolutionary perspective in the past. I will also present our experimental results on the quantitative genetic basis of senescence in the short-lived perennial plant Silene latifolia and their contribution to our understanding of the evolution of senescence in plants.
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Les interactions qu'elles soient sociales ou sexuelles régissent un grand nombre de comportements et stratégies développés par les animaux pour maximiser leur valeur adaptative. Qu'elles soient conflictuelles ou symbiotiques, elles sont un puissant générateur d'évolution. Je suis une biologiste évolutive intéressée par les conflits sociaux et sexuels et comment ceux-ci sont résolus. Mes travaux de thèse et de premier post-doctorat ont porté sur l'étude phénotypique, génétique et chimique de la reconnaissance de parentèle chez les insectes parasitoïdes. Lors d'un second post-doctorat, je me suis intéressée à l'évolution des systèmes de reproduction (monoandrie et polyandrie) chez les drosophiles : conflits mâles/femelles, reconnaissance du partenaire sexuel et investissement reproducteur. A l'heure actuelle, j'ai intégré un troisième niveau dans mes recherches : les microbiontes intestinaux et comment les variations des communautés de microbiontes influencent les systèmes de reconnaissance et les interactions sexuelles chez les drosophiles
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