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 301 to 330 publications on 1006 in total

GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Carina Mugal, Claudia Weber, Hans Ellegren

BioEssays . 37 ( 12 ) : 1317-1326

DOI: 10.1002/bies.201500058

Journal article

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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

Reto Burri, Alexander Nater, Takeshi Kawakami, Carina Mugal, Pall Olason, Linnea Smeds...

Genome Research . 25 ( 11 ) : 1656-1665

DOI: 10.1101/gr.196485.115

Journal article

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Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

Carina Mugal, Peter Arndt, Lena Holm, Hans Ellegren

G3 . 5 ( 3 ) : 441-447

DOI: 10.1534/g3.114.015545

Journal article

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Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

Elise R Morton, Joshua Lynch, Alain Froment, Sophie Lafosse, Evelyne Heyer, Molly M. Przeworski...

PLoS Genetics . 11 ( 11 ) : e1005658

DOI: 10.1371/journal.pgen.1005658

Journal article

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Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

Anne-Laure Bechy-Loizeau, Jean-Pierre Flandrois, Hafid Abaibou

Life Sciences in Space Research . 6 : 29-35

DOI: 10.1016/j.lssr.2015.06.002

Journal article

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Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

C. Bouchiat, J. Saison, S. Boisset, Jean-Pierre Flandrois, B. Issartel, O. Dauwalder...

Open Forum Infectious Diseases . 2 ( 2 )

DOI: 10.1093/ofid/ofv047

Journal article

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Adaptation in toxic environments: arsenic Genomic Islands in the bacterial genus $Thiomonas$

Kelle Freel, Martin Krueger, Julien Farasin, Céline Brochier-Armanet, Valérie Barbe, Jérémy Andres...

PLoS ONE . 10 ( 9 ) : 0139011

DOI: 10.1371/journal.pone.0139011

Journal article

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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

Journal article

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Quantification of GC-biased gene conversion in the human genome

Sylvain Glemin, Peter F. Arndt, Messer W. Philip, Petrov M. Dmitri, Nicolas Galtier, L. Duret

Genome Research . 25 ( 8 ) : 1215 - 1228

DOI: 10.1101/gr.185488.114

Journal article

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Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri, Marie Cariou, Gabriel Terraz, Sonia Martinez, Adil El Filali, Marine Veyssière...

Genetica . 143 ( 2 ) : 139-143

DOI: 10.1007/s10709-015-9828-3

Journal article

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Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d'identifier les déterminants de la pathogénicité

Amandine Campan-Fournier, Christine Oger, Christophe Ginevra, Vincent Navratil, Anne-Gaëlle Ranc, G. Perrière...

JOBIM 2015 - 16èmes Journées Ouvertes en BIologie, Informatique et Mathématiques .

Poster

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Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns

H. Philippon, Céline Brochier-Armanet, G. Perriere

BMC Evolutionary Biology . 15 : 226

DOI: 10.1186/s12862-015-0498-7

Journal article

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Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer, Camille Rustenhloz, Véronique Leh-Louis, Guy Perrière

BMC Microbiology . 15 ( 1 ) : 221

DOI: 10.1186/s12866-015-0564-8

Journal article

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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy

BMC Bioinformatics . 16 ( 1 ) : 251

DOI: 10.1186/s12859-015-0692-z

Journal article

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A Toolbox for Nonlinear Regression in R: The Package nistools

F. Baty, C. Ritz, Sandrine Charles, M. Brutsche, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Journal of Statistical Software . 66 : 1-21

Journal article

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Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization

Daniel Vinella, Frédéric Fischer, Egor Vorontsov, Julien Gallaud, Christian Malosse, Valérie Michel...

PLoS Pathogens . 11 ( 12 ) : e1005312

DOI: 10.1371/journal.ppat.1005312

Journal article

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Exploration of Frankia genomes to identify genetic determinants involved in sporogenesis: Towards promising tracks to understand in plant sporuration

Lorine Bethencourt, N. Taib, J. Briolay, P. Fournier, M.P. Fernandez, Céline Brochier-Armanet...

18th International Meeting on Frankia and Actinorhizal plants .

Poster

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Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, Emilia M. F. Mauriello...

PLoS Genetics . 11 ( 8 ) : e1005460

DOI: 10.1371/journal.pgen.1005460

Journal article

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Taxonomy and Phylogeny of Prokaryotes

Pierre Caumette, Céline Brochier-Armanet, Philippe Normand

Environmental Microbiology: Fundamentals and Applications . 978-94-017-9118-2 : 145-190

DOI: 10.1007/978-94-017-9118-2_6

Book chapter

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Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia

Wajdi Ben Hania, Khaled Fadhlaoui, Céline Brochier-Armanet, Cecile Persillon, Anne Postec, Moktar Hamdi...

Standards in Genomic Sciences . 10

DOI: 10.1186/1944-3277-10-12

Journal article

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Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

Stéphanie Borland, Anne Oudart, Claire Prigent-Combaret, Céline Brochier-Armanet, Florence Wisniewski-Dyé

BMC Genomics . 16 : 833

DOI: 10.1186/s12864-015-1962-x

Journal article

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Extending the conserved phylogenetic core of \textitarchaea disentangles the evolution of the third domain of life

C. Petitjean, P. Deschamps, P. Lopez-Garcia, D. Moreira, Céline Brochier-Armanet

Molecular Biology and Evolution . 32 : 1242-54

Journal article

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Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

S. Koechler, F. Arsene-Ploetze, Céline Brochier-Armanet, F. Goulhen-Chollet, A. Heinrich-Salmeron, B. Jost...

Research in Microbiology . 166 : 205-14

Journal article

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

Journal article

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Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

Hélène Badouin, Michael E Hood, Jerome Gouzy, Gabriela Aguileta, Sophie Siguenza, Michael H Perlin...

Genetics . 200 ( 4 ) : 1275-1284

DOI: 10.1534/genetics.115.177709

Journal article

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Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Michael H Perlin, Joelle J. Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan Goldberg...

BMC Genomics . 16 ( 461 ) : np

DOI: 10.1186/s12864-015-1660-8

Journal article

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An evolutionary link between capsular biogenesis and surface motility in bacteria

Rym Agrebi, Morgane Wartel, Céline Brochier-Armanet, Tam Mignot

Nature Reviews Microbiology . 13 ( 5 ) : 318--326

DOI: 10.1038/nrmicro3431

Journal article

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The two-domain tree of life is linked to a new root for the Archaea

Kasie Raymann, Céline Brochier-Armanet, Simonetta Gribaldo

Proceedings of the National Academy of Sciences of the United States of America . 112 : 6670-6675

DOI: 10.1073/pnas.1420858112

Journal article

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The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

Abdel Belkorchia, Cyrielle Gasc, Valérie Polonais, Nicolas Parisot, Nicolas Gallois, Céline Ribière...

PLoS ONE . 10 ( 9 ) : 1-12

DOI: 10.1371/journal.pone.0139075

Journal article

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Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

R. A. Wiberg, D. L. Halligan, R. W. Ness, A. Necsulea, H. Kaessmann, P. D. Keightley

Genome Biology and Evolution . 7 : 2432-44

DOI: 10.1093/gbe/evv155

Journal article

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