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Le séquençage et l'assemblage de génomes de référence à partir de données PacBio et Oxford Nanopore
Depuis 2015, les avancées des technologies de séquençage PacBio et Oxford Nanopore ont bouleversé les projets de séquençages génomiques. Les chromosomes bactériens et les bras chromosomiques des génomes eucaryotes peuvent être assemblés en une seule séquence. La qualité des assemblages atteint si ce n'est dépasse les assemblages de références Sanger des années 2000, les centromères et télomères alors souvent non résolus deviennent désormais analysables. Les résultats sur plusieurs espèces de bactéries, champignons et plantes seront présentés afin d'illustrer les réussites de cette rupture technologique mais aussi les cas qui restent encore non parfaitement résolus.
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Evolution des ornements colorés chez les oiseaux dans le temps et l'espace
Le séminaire présentera les trois axes de recherche en écologie évolutive et comportementale développés par Claire Doutrelant (CEFE, Montpellier). Le premier axe de recherche porte sur la variation spatio-temporelle et l'évolution des ornements colorés chez les oiseaux (en particulier chez les femelles). Le deuxième axe de recherche porte sur la coopération et la dynamique de populations d'une espèce d'oiseau à reproduction coopérative, le républicain social. Le 3ème axe porte sur l'évolution en milieu insulaire par des comparaisons de plusieurs espèces vivant en milieu insulaire et continental.
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Allocation au sexe chez les mammifères
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La Formule de Bayes : Exemples d'application au-delà de la démarche Diagnostiquen nL'inscription est gratuite mais obligatoire au plus tard le mardi 31 octobre 2017 par courriel à paola.damaso@chu-lyon.frn
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Immune function and the island syndrome
Life on isolated oceanic islands often means life in the absence of (or at least with fewer) top predators and large herbivores. Such a change in prey-predator and plant-herbivore interactions likely translates into slackened natural selection on the animals and plants that are normally being eaten. One consequence is high population densities on islands. Another is that over evolutionary time island organisms lose their defenses against predation and herbivory. The extent to which similar dynamics underlie changes in host defenses against parasites (i.e., immune function) is less clear. The host-parasite interaction can be seen as ecologically analogous to prey-predator and plant-herbivore interactions, and some instances of island animals being hard hit by infectious diseases have been described. If the selective pressures imposed by parasites are reduced on islands compared to on continents and if immune defenses incur costs, then the immune system architecture is expected to differ between animal hosts on living on islands and continents. In my presentation, I will explore this hypothesis by reviewing current literature and examining the breadth and consistency of results. If the hypothesis is well supported, then changes in the immune system might be appropriately recognized as a physiological aspect of the island syndrome. I will end by introducing plans for a new direction in this line of research: an examination of immunological and physiological changes associated with the reverse island syndrome. Under this scenario, low or fluctuating population densities on islands, for example due to severe environmental variation, appears to lead to a reverse set of life history changes in island animals. To date, however, little is known about the interaction between parasites and hosts defenses in this system.
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Fidelity of parent-offspring transmission and the evolution of social behaviour in structured populations
The theoretical investigation of how spatial structure affects the evolution of social behavior has mostly been done under the assumption that parent-offspring strategy transmission is perfect, i.e., for genetically transmitted traits, that mutation is very weak or absent. In this talk, we investigate the evolution of social behavior in structured populations under arbitrary mutation probabilities. We consider spatially structured populations of fixed size N, in which two types of individuals,A and B, corresponding to two types of social behavior, are competing. Under the assumption of small phenotypic differences (weak selection), we provide a formula for the expected frequency of type A individuals in the population, and deduce conditions for the long-term success of one strategy against another. We then illustrate this result with three common life-cycles (Wright-Fisher,Moran Birth-Death and Moran Death-Birth),and specific population structures. Qualitatively, we find that some life-cycles (Moran Birth-Death,Wright-Fisher, when social interactions affect fecundities) prevent the evolution of altruistic behavior, confirming previous results obtained with perfect strategy transmission. Imperfect strategy transmission also alters the balance between the benefits and costs of staying next to one's kin, leading to surprising results in subdivided populations, in that higher emigration probabilities can be favourable to the evolution of altruistic strategies.
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Genomic evidence for ameiotic evolution and genetic exchanges in the bdelloid rotifer Adineta vaga.
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Magnetic biomineralization: multi-faceted evolutionary history of a complex prokaryotic function
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Pathology 2.0 : how omics technologies and bioinformatics are changing the rules
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Effective normalization for copy number variation in Hi-C data
Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data. Chromosome conformation data, such as Hi-C, is not different. The most widely used type of normalization of Hi-C data casts estimations of unwanted effects as a matrix balancing problem, relying on the assumption that all genomic regions interact as much as any other. Here, we show that these approaches, while very effective on fully haploid or diploid genome, fail to correct for unwanted effects in the presence of copy number variations. We propose a simple extension to matrix balancing methods that properly models the copy-number variation effects. Our approach can either retain the copy-number variation effects or remove it. We show that this leads to better downstream analysis of the three-dimensional organization of rearranged genome.
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Mechanisms of lineage-specific genome evolution in Mammals
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ECOLOGICAL-GENETIC FACTORS DETERMINING THE STRUCTURE AND FUNCTIONS OF THE MARMOT ALARM CALL
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Adult sex ratios and primate sex roles
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The rise of phenomics: photogrammetry technique applied to a study of allometry in deer antler size
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Le projet AURAGEN : présentation du projet et retombées attendues
Dans le cadre du projet France Médecine Génomique annoncé par le Premier ministre en juin 2016, deux projets pilotes de plateformes de séquençage très haut débit ont été retenues : les projets SeqOIA (Paris-Île-de-France) et AURAGEN (région Auvergne Rhône Alpes). Après quelques rappels sur le contexte du plan France Médecine génomique, le projet AURAGEN sera détaillé avec ses 5 axes : pré analytique, analytique, post analytique, médico-économique et formation. Il s'agit d'un projet de génomique qui sera inclus dans le parcours de soins des patients présentant une maladie rare ou un cancer. Nous présenterons également les projets pilotes en lien avec le plan France médecine génomique et les retombées attendues tant au niveau diagnostique que de la recherche.
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Alternative splicing in human parasites
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Male violence and sexual intimidation in wild chacma baboons
Sexual intimidation is frequent in humans, but its evolutionary origin remain speculative because few animal studies have investigated comparable, long-term forms of sexual violence. In our study, we focused on a population of wild chacma baboons and showed that males intimidate females to mate with them, and that sexual violence is the main source of injuries for females. Aggression and matings were found to be decoupled temporally, which may explain why some forms of sexual violence have been largely overlooked in well-studied animal populations. This study suggests that long-term sexual coercion may be widespread across mammalian societies, with important implications for understanding the evolution of mate choice and sexual conflict in mammals, as well as the origins of human sexual violence.
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Costs of compensatory and accelerated growth in a hibernating mammal
Yellow-bellied marmots (Marmota flaviventer) live in highly seasonal environments and have limited time for development and fat accumulation. An increase in body mass is a strong determinant of overwinter survival, thus immature marmots (juveniles and yearlings) starting the active season with low body mass may exhibit compensatory growth. Additionally, adults may exhibit accelerated fat accumulation to compensate for mass loss during hibernation. We investigated the potential costs of accelerated growth in a wild population of yellow-bellied marmots, using individual survival and longevity as proxies for fitness. Mass measurements from 2002-2015 were used to calculate individual seasonal growth rates. We estimated annual survival from 130 adults, 239 yearlings and 643 juveniles and longevity from 76 females. Individuals were distributed in two areas that differ in elevation, down- and up-valley, where the latter is an overall harsher environment. As results, juvenile survival increased with growth rate, with location and initial body mass changing the shape of this association. For yearlings, both location and initial body mass influenced the relationship between growth rate and survival. Yearlings exhibiting compensatory growth had had lower survival up-valley, and higher survival down-valley. No significant effect was found for longevity or adult annual survival. Thus, yearlings appear to represent the development stage in which the costs of rapid growth are the highest, and compensatory growth may be beneficial depending on the environmental conditions. Juveniles benefit from accelerated growth, which suggests that the conflicting demands of structural growth and fat accumulation vs. body maintenance may be less drastic at this developmental stage. Overall, the benefits and costs of rapid growth are age- and site- dependent and the costs of compensatory growth be seen in the short-term in this species, instead of paid later in life.
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Penser les origines de la vie et sa définition : deux objectifs distincts, mais indissociables. Aspects épistémologiques et historiques.
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The nature of individual and collective reactions to danger in humans: evidence from interviews with survivors of the Bataclan attacks
Individual and collective reactions to threat are largely conceived as individualistic and anti-social: when exposed to threat, humans would revert to self-preservative motives, trying to flee as fast as possible, sometimes at the expense of others. This conception, which can be traced back to the non-empirical conclusions of sociologist and social psychologist Gustave Le Bon, has met immediate intellectual success and is widespread both in academic and lay audiences. However, more recent work based on interviews with survivors from a diversity of disasters has consistently shown a very different pattern: humans do not display self-preservative behaviour when exposed to threat. In fact, they show a high degree of pro-sociality in such contexts, even when their life is directly at risk. Those results remain questionable. In particular, it is not clear how the type of danger people are exposed to can modulate their individual and collective responses to it. Another important issue is the methodology being used in those studies, which does not allow comparing between different moments of the event. Indeed, it is possible that immediate reactions to threat are self-preservative, with prosocial responses overcoming individualistic ones later on. Finally, previous work does not distinguish between genuine altruistic acts (where the action is immediately costly to the agent - eg exposing oneself to danger to help another person) and apparent altruistic behaviour (clearing an access, which directly benefits the agent). We have conducted interviews with survivors from the attacks at the Bataclan (13-11-2015 in Paris) asking them to describe with precision their own actions and others' at different moments of the attacks. In this talk, I will try to clarify the interplay between individualistic and prosocial motives and their temporality during collective exposure to deadly threat, drawing from our work with survivors from the Bataclan attacks. I will also suggest future directions to better understand the evolution of prosocial traits in such circumstances, in humans and other social species.