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Simultaneous Bayesian gene tree construction and reconciliation.
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Host specialization in South American brood parasitic cowbirds
Juan Carlos Reboreda est professeur à la faculté de Sciences de l'Université de Buenos Aires. Il travaille en écologie évolutive et écologie du comportement des oiseaux, en particulier des parasites de nichée. Juan Carlos est Secrétaire de Recherche (équivalent de "Vice-president pour la Recherche" en termes français) de sa fac et il vient dans le cadre de cette fonction. Avec lui, des collègues chiliens (et avec la participation de Fred Menu, Dominique Allainée, Manu, etc) on est en train de mettre en place l'internalisation de notre master (master 1: échange d'étudiants, master 2: implantation en Amérique du Sud d'un mastère "écologie quantitative" dans un sens large.
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Population genomics of Group B Streptococcus - evolution of human versus animal isolates.
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The evolutionary rate of a sexually selected trait: the case of sperm design
Postcopulatory sexual selection is thought to be an important force driving the evolution of sperm design. Yet, despite numerous theoretical and empirical studies of the relationship between sperm design and sperm competition (as one postcopulatory sexual selection mechanism) is still poorly understood. A series of comparative studies in several taxonomic groups have found inconclusive and sometimes even contradictory results suggesting that in different taxonomic groups the evolution of sperm design in the context of sperm competition show markedly different patterns. We conducted the largest to date comparative study including over 250 species of passerine birds to investigate the relationship between sperm design and sperm competition and to determine the evolutionary rate of sperm design as a sexually selected trait. We did so in three ways: (I) we investigated the relationship between sperm design and sperm competition at different phylogenetic levels its association with the underlying phylogeny; (II) we tested the interspecific, the intraspecific and the intra-male variation of sperm design in the context of sperm competition; (III) we performed experiments to improve our understanding of the behavioural mechanisms influencing sperm design and function. Our results provide new insights into the evolution of sperm design as a sexually selected trait.
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Paléogénomique des plantes.
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Distorsion de ségrégation des chromosome sexuels et conflit génétique: bases génétiques et évolution chez Drosophila simulans.
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Le séquençage de transcriptomes: limitations méthodologiques et applications à la régulation de l'épissage.
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Titre à venir
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Usage du code: des phages au HIV.
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Congruent evolution of genetic and environmental robustness in microRNA.
Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic robustness, whether it evolves directly by natural selection or it is a correlated byproduct of other phenotypic traits, is, however, unresolved. Examining micro-RNA (miRNA) genes of several eukaryotic species, Borenstein and Ruppin (Borenstein E, Ruppin E. 2006. Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci USA. 103: 6593) showed that the structure of miRNA precursor stem loops exhibits significantly increased mutational robustness in comparison with a sample of random RNA sequences with the same stem-loop structure. The observed robustness was found to be uncorrelated with traditional measures of environmental robustness--implying that miRNA sequences show evidence of the direct evolution of genetic robustness. These findings are surprising as theoretical results indicate that the direct evolution of robustness requires high mutation rates and/or large effective population sizes only found among RNA viruses, not multicellular eukaryotes. We demonstrate that the sampling method used by Borenstein and Ruppin introduced significant bias that lead to an overestimation of robustness. Introducing a novel measure of environmental robustness based on the equilibrium thermodynamic ensemble of secondary structures of the miRNA precursor sequences, we demonstrate that the biophysics of RNA folding induces a high level of correlation between genetic (mutational) and environmental (thermodynamic) robustness, as expected from the theory of plastogenetic congruence introduced by Ancel and Fontana (Ancel LW, Fontana W. 2000. Plasticity, evolvability, and modularity in RNA. J Exp Zool. 288: 242-283). In light of theoretical considerations, we believe that this correlation strongly suggests that genetic robustness observed in miRNA sequences is the byproduct of selection for environmental robustness.
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Titre à venir
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Inheritance patterns of DNA methylation in Arabidopsis: molecular mechanisms and phenotypic consequences.
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The Dynamics of Phenotypic Change and thenShrinking Sheep of St. Kilda.
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Facteurs impliques dans la variabilite de methylation des elements transposables.
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Evolutionary genetics of a mimicry supergene in Heliconius butterflies.
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Species Influence: assessing species-induced incongruities innphylogenetic inference.
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Titre à venir
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Creating dynamic maps of biodiversity: examples in R + Google Earth
The seminar will focus on application of open source tools for analysis of biodiversity data. The focus is put on R statistical computing environment and its various Environometrics and Spatial packages. There are three main opportunities for using R: (1) vitality and high speed of development of R, (2) academic openness of developers and their willingness to collaborate, and (3) increasing sympathy for spatial data analysis and visualization. Spatial statisticians generally believe that geostatistical techniques are suited only for modeling of features that are inherently continuous (spatial fields); discrete objects (points, lines, polygons) should be analyzed using point pattern analysis and similar methods. A method is suggested that tries to bridge this gap by combining the strong points of various packages in R with the geographical analysis capabilities of the open source GIS. The presenter will demonstrates how to combine geostatistical techniques with conceptually different techniques --- point pattern analysis and Niche analysis --- to allow prediction of species' distributions using regression-kriging.References: 1. Hengl, T., Sierdsema, H., Radovic, A., Dilo, A., 2009. Spatial prediction of species' distributions from occurrence-only records: combining point pattern analysis, ENFA and regression-kriging. Ecological Modelling, in press. 2. Hengl, T., 2007. A Practical Guide to Geostatistical Mapping of Environmental Variables. EUR 22904 EN Scientific and Technical Research series, Office for Official Publications of the European Communities, Luxemburg, 143 pp. ISBN: 978-92-79-06904-8 3. Hengl T., Heuvelink G.B.M., Rossiter D.G., 2007. About regression-kriging: from equations to case studies. Computers and Geosciences, 33(10): 1301-1315