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Vibrio diversity and oyster mortality: the hypothesis of a new polymicrobial disease
Vibrios have been associated with successive mortality outbreaks ofCrassostrea gigas) in France that have resulted in losses up to 100% of production. Given the near monoculture of C. gigas in Europe, there is an urgent need to understand the epidemiology of these outbreaks, particularly the role of Vibrio in the diseases.The study of the Vibrios distribution on fine phylogenetic and spatial scales has demonstrated that vibrios coexisting in the water column can be divided into closely related populations, which pursue different lifestyles i.e. ecological population (Hunt et al., 2008). However, a link between ecological populations and pathogenicity has not been demonstrated, and it is unclear whether pathogenicity is a trait primarily linked to clones or to populations comprising a large number of distinct genotypes.In the presentVibrio populations in an intensive oyster cultivation area. We demonstrate that Vibrio populations do not assemble neutrally in oysters from water column populations i.e. specific genotypes colonize the oysters. Combining experimental ecology, high throughput infection assay and genome sequencing, we showed that the onset of disease in oysters is associated with progressive replacement of diverse, benign colonizers by members of a phylogenetically coherent virulent population together with quorum sensing pheromone producers. Analyses of oyster mortality following experimental infection suggest that disease onset can be facilitated by the presence of non-virulent strains. Oyster disease may thus represent a new form of polymicrobial disease, in which non-pathogenic strains contribute to increased mortality.Hunt DE, et al. (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320(5879):1081-1085.Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. (2014) Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. Dec 9. doi: 10.1038/ismej.2014.233
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Lessons from 30 years of natural disturbances in the Bavarian Forest National Park
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Transposable element evolution in Drosophila
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Similarities and differences between evolutionary processes in linguistics and biology
Among biologist as well as linguists, it is now widely accepted that there are many striking parallels between the evolution of life forms and the history of languages. Starting from the rise of language studies as a scientific discipline in the early 19th century, up to today's recent "quantitative turn" in historical linguistics, scholars from both disciplines have repeatedly pointed to similarities between the respective research objects in biology and linguistics. During the last two decades, this has lead to a new school of ''quantitative historical linguistics''. Based on the key assumption that the characteristic processes of language change and biological evolution are so similar that the methods designed for one discipline may also be used in the other one, methods which were originally designed to study biological evolution (methods for phylogenetic reconstruction, sequence alignment, or biological network analysis) have now repeatedly been applied to linguistic data.Unfortunately, not all analogies which have been made between evolutionary processes in linguistics and biology reflect true similarities in the processes. Striking differences between the research objects of both disciplines are often ignored. In the talk, I will review proposed similarities between evolutionary processes in the two disciplines and discuss their methodological implications.
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Bad luck of cancer - or misinterpreted statistics?
A recent paper in Science (January 2015) claimed that the majority, 64% to be precise, of cancers is due to bad luck, so non-preventable. The message was spread quickly through media, including serious ones like BBC (and also radio Slovenia, if I may add). And while the paper has been criticized by many, the authors seem to stick to the original message.In this talk I'll give my view of the paper and try to defend a counter message that their analysis gives them absolutely no grounds to make such a claim. The arguments that I'll present have, to my knowledge, not appeared in published reactions to the paper. Obviously, if I am right, they are wrong, and vice versa. If I was Bayesian, I would, at present, give a 0.99 prior probability to the first option. Either way, it should be fun.
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Human sex differences in height : A costly evolution due to gender hierarchy.
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Titre à venir
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Understanding molecular evolution: insights from animals and plants
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Dispersion des vers de terre en Agroécosytèmes : résultats du projet Edisp
La dispersion est un processus central pour le maintien de la biodiversité dans les paysages. Cependant les patterns de dispersion et leurs déterminants sont encore mal documentés, en particulier chez les organismes du sol. En conséquence, une grande partie des déterminants de la biodiversité des sols n'est toujours pas comprise.Nous exposons les résultats d'un projet ANR de quatre ans sur la dispersion des vers de terre, un organisme clé dans le maintien de nombreux services écosystémiques. Avec une combinaison d'approches (1) de terrain multi-échelle, (2) de (méta) communauté, (3) de génétique du paysage, et (4) d'expérience en laboratoire, nous avons identifié des mécanismes centraux qui permettent aux vers de terre de disperser dans un agro-écosystème de manière adaptée, et nous montrons l'importance de la dispersion pour le maintien de la diversité spécifique et génétique.Nos résultats suggèrent également que la dispersion passive joue un rôle sous estimé dans la dynamique spatiale de ces organismes.
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Baiting for phylogenetic fishing
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Phylogenetic Fate Mapping
We are exploring techniques using single cell genomic sequencing in human beings for the purpose of defining phylogenetic trees to explain the relationship of cells within defined human tissues. I will discuss how we used single cell exome and whole genome sequencing to identify patient and donor adipocytes in human white adipose tissue biopsies taken from bone marrow recipients and discuss future projects using similar methods to explore cellular identities in human tissue samples.
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Beyond Jarman-Bell: how principles of digestive physiology can and cannot inform on ecological diversification.
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Evaluation quantitative et qualitative d'un dispositif de surveillance basé sur le principe de la déclaration obligatoire : l'exemple de la surveillance de la brucellose chez les bovins en France
La surveillance de la brucellose chez les bovins, maladie pour laquelle la France est indemne depuis 2005, a pour objectif principal d'assurer la détection de tout nouveau foyer qui surviendrait sur le territoire. Cette surveillance repose principalement sur la surveillance évènementielle (clinique) : celle-ci impose aux éleveurs et aux vétérinaires la déclaration de tout avortement chez les bovins, suivi du dépistage de la femelle ayant avorté vis- à-vis de la brucellose. Toutefois, en amont de ce travail, il était admis par l'ensemble des acteurs, sans que cela ait été rigoureusement évalué, que cette surveillance souffrait d'une forte sous-déclaration et nécessitait d'être améliorée.Les objectifs de l'évaluation de ce dispositif étaient : 1) de quantifier le niveau de sous-déclaration et estimer l'effet de différents facteurs sur le processus de déclaration ; 2) d'analyser le processus de décision conduisant les éleveurs et les vétérinaires à participer ou non au dispositif.Afin de répondre au premier objectif, le principe des méthodes de capture-recapture unilistes a été retenu. L'ensemble des observations a pu être modélisé à l'aide des méthodes MCMC et de deux modèles multi-réponses, le modèle de Poisson enflé en zéro (ZIP) et le modèle hurdle. La deuxième étude a consisté à mener des entretiens semi-directifs auprès de 12 éleveurs et de leurs 8 vétérinaires.
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Soutenance de thèse de Lisa Nicvert
Méthodes statistiques et outils logiciels pour l'analyse et l'inférence de réseaux écologiques et le traitement de données multi-espèces
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Séminaire département Ecologie Evolutive
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Soutenance de thèse de Luca Nesterenko
Apprentissage automatique pour l’evolution moléculaire
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Seminar: Rebekka Müller-Widmann
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Séminaire interne LBBE
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Séminaire interne LBBE