Bioinformatics, Phylogeny and Evolutionary Genomics Group

Members

Our group focuses on two main axes: phylogenomics (i.e. the inference of evolutionary history based on genomics data) and evolutionary genomics (understanding the molecular and population processes that drive genome evolution). We see genomes both as a subject of research (how do genomes evolve, why are they structured the way they are?), but also as a main source of empirical knowledge about the macroevolutionary patterns (what do they tell us about the history of life on Earth?), or about the phenotypes and life-history strategies of organisms. Our works heavily rely on methodological developments (bioinformatics, modeling and statistical inference).

Evolution of genome architecture and expression

Genomes are the result of a long-term evolutionary process, shaped by multiple evolutionary forces. Some genomic features are adaptive (i.e. are beneficial for the fitness of organisms), others result from non-adaptive processes (random drift and biased gene conversion - BGC) or are caused by conflicts between multiple levels of selection (e.g. meiotic drive or the spread of selfish genetic elements). We explore different aspects of genome architecture (base composition landscapes, genome structure and size, impact of transposable elements, …) or functioning (gene expression, lncRNAs, epigenetic landscapes, …), and try to disentangle the relative contribution of adaptive and non-adaptive processes to their evolution. For this purpose, we consider both the molecular mechanisms (mutation, repair, recombination) and the population processes (selection, drift, BGC, …) that shape genetic variation.

Phylogenomics

We are interested in reconstructing the history of life on Earth. This research unfolds along several axes. First, we develop phylogenomic databases of aligned genetic sequences (e.g. BIBI, RiboDB or HOGENOM). Second, we conduct methodological research on how to accurately reconstruct deep phylogenies, infer divergence times, reconstruct ancestral genetic sequences, gene repertoires and life-history traits. This methodological work is translated into publicly available software programs (e.g. SeaView, PhyloBayes, Coevol). Finally, we apply these approaches to several important problems, among which: reconstructing the phylogeny of animals, of archaea, or the global tree of life; using phylogenies and ancestral gene repertoires to investigate the evolution of complex systems and the emergence of molecular and cellular functions in the three domains of life; reconstructing ancestral genetic sequences, a research activity that has industrial and biotechnological applications.

Teaching and outreach

We teach at University Lyon 1 (Master Bioinfo@Lyon), INSA, ENS Lyon, we organize bioinformatics internships. We regularly give conferences on evolution (tree of life, human evolution, genetic diversity, …).
Prospective students and postdocs are invited to apply, as we often welcome visitors for internships or research projects.
 
Keywords: Molecular evolution and Population Genomics; Phylogenomics; Computational Genomics; Comparative genomics; Bioinformatics; Statistical inference.

Publications

Display of 511 to 540 publications on 1006 in total

Evolution Moléculaire

L. Duret, T. Bataillon, N. Bierne, Vincent Daubin, J. Dutheil, Christian Gautier...

Biologie évolutive . 978-2-8041-0161-9 : 114-173

Book chapter

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson, M. Bétermier, M.-H. Bré, J. Cohen, S. Duharcourt, L. Duret...

Emerging Model Organisms . 2010(1) : 1-55

Journal article

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Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, L. Duret...

BMC Genomics . 11 ( 1 ) : 547

DOI: 10.1186/1471-2164-11-547

Journal article

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Concepts et méthodes en phylogénie moléculaire

G. Perrière, Céline Brochier-Armanet

Springer . 978-2-287-99047-2

Book

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Concepts et méchodes en phylogénie moléculaire

G. Perrière, C. Brochier-Armanet

incollection . -- : 63-65

Journal article

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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

BMC Bioinformatics . 11 ( 324 ) : 13

DOI: 10.1186/1471-2105-11-324

Journal article

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Species identification of staphylococci by amplification and sequencing of the gene compared to the gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

M. Bergeron, O. Dauwalder, M. Gouy, A.-M. Freydiere, M. Bes, H. Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . : 343-354

DOI: 10.1007/s10096-010-1091-z

Journal article

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Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.

Valérie de Crécy-Lagard, Céline Brochier-Armanet, Jaunius Urbonavicius, Bernard Fernandez, Gabriela Phillips, Benjamin Lyons...

Molecular Biology and Evolution . 27 ( 9 ) : 2062-77

DOI: 10.1093/molbev/msq096

Journal article

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The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system

R. Salacha, F. Kovacic, Céline Brochier-Armanet, S. Wilhelm, J. Tommassen, A. Filloux...

Environmental Microbiology . 12 ( 6 ) : 1498-512

DOI: 10.1111/j.1462-2920.2010.02174.x

Journal article

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Statistical Potentials for Improved Structurally Constrained Evolutionary Models

Claudia L Kleinman, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe

Molecular Biology and Evolution . 27 ( 7 ) : 1546 - 1560

DOI: 10.1093/molbev/msq047

Journal article

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Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Hussein Mortada, Cristina Vieira, Emmanuelle Lerat

Journal of Molecular Evolution . 71 ( 3 ) : 180-91

DOI: 10.1007/s00239-010-9376-5

Journal article

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Detecting positive selection within genomes: the problem of biased gene conversion

A. Ratnakumar, Sylvain Mousset, S. Glémin, J. Berglund, N. Galtier, L. Duret...

Philosophical Transactions of the Royal Society B: Biological Sciences . 365 ( 1552 ) : 2571-2580

DOI: 10.1098/rstb.2010.0007

Journal article

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson, M. Bétermier, M-H. Bré, J. Cohen, S. Duharcourt, Laurent Duret...

Emerging Model Organisms . 2010 : 1-55

Journal article

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SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Manolo Gouy, Stéphane Guindon, Olivier Gascuel

Molecular Biology and Evolution . 27 : 221-224

DOI: 10.1093/molbev/msp259

Journal article

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The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre, C. Brochier-Armanet

Nature Reviews Microbiology . 8 ( 10 ) : 743-753

DOI: 10.1038/nrmicro2426

Journal article

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Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota

A. Spang, R. Hatzenpichler, Céline Brochier-Armanet, T. Rattei, P. Tischler, E. Spieck...

Trends Microbiol . 18(8) : 331-40

Journal article

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Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

C.B. Walker, J.R. La Torre, M.G. Klotz, H. Urakawa, N. Pinel, D.J. Arp...

Proceedings of the National Academy of Sciences of the United States of America . 107 ( 19 ) : 8818-23

DOI: 10.1073/pnas.0913533107

Journal article

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Structure, function, and evolution of the Thiomonas spp. genome.

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy...

PLoS Genetics . 6 ( 2 ) : e1000859

DOI: 10.1371/journal.pgen.1000859

Journal article

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A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

Nicolas Lartillot, Raphaël Poujol

Molecular Biology and Evolution . 28 ( 1 ) : 729 - 744

DOI: 10.1093/molbev/msq244

Journal article

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A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 27 ( 2 ) : 371-384

DOI: 10.1093/molbev/msp248

Journal article

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Proposals for classification methods dedicated to biological data

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy

International Journal of Biomedical Engineering and Technology (IJBET) . 3 ( 1/2 ) : 4-21

DOI: 10.1504/IJBET.2010.029649

Journal article

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The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Jean-François Gout, Daniel Kahn, Laurent Duret

PLoS Genetics . 6 ( 5 ) : e1000944

DOI: 10.1371/journal.pgen.1000944

Journal article

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Evolution of the ribosome: testing eukaryotic origins

Elie Desmond-Le Quéméner, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Archaea and the tree of life .

Conference paper

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Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis

S. Mona, K. Grunz, S. Brauer, Brigitte Pakendorf, L. Castri, H. Sudoyo...

Molecular Biology and Evolution . 26 ( 8 ) : 1865-1877

DOI: 10.1093/molbev/msp097

Journal article

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Genetic diversity and the emergence of ethnic groups in Central Asia

Evelyne Heyer, Patricia Balaresque, Mark Jobling, Lluis Quintana-Murci, Raphaelle Chaix, Laure Segurel...

BMC Genetics . 10 ( 1 ) : 49

DOI: 10.1186/1471-2156-10-49

Journal article

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Mutation Patterns in the Human Genome:More Variable Than Expected

L. Duret

PLoS Biology . 7(2) e1000028 : 803-806

Journal article

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Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea, M. Sémon, L. Duret, L.D. Hurst

Trends in Genetics . 25(12) : 519-522

Journal article

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GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier, L. Duret, S. Glémin, Vincent Ranwez

Trends in Genetics . 25(1) : 1-5

Journal article

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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

Journal article

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Phylogeny of prokaryotes: does it exist and why should we care?

Simonetta Gribaldo, Céline Brochier-Armanet

Research in Microbiology . 160 : 513-21

Journal article

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