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 481 to 510 publications on 1006 in total

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

C. Chureau, S. Chantalat, A. Romito, A. Galvani, Laurent Duret, P. Avner...

Human Molecular Genetics . 20 : 705-718

DOI: 10.1093/hmg/ddq516

Journal article

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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

T. Rouxel, J. Grandaubert, Jk. Hane, Claire Hoede, Angela P. van de Wouw, A. Couloux...

Nature Communications . 2 : 202

DOI: 10.1038/ncomms1189

Journal article

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Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections

Thomas Bigot, Vincent Daubin, G. Perrière

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) . : 111-112

Conference paper

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Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Sébastien Terrat, Richard Christen, Samuel S. Dequiedt, Pierre-Alain Maron, Christophe Mougel, Guy Perriere...

1ères Rencontres bioinformaticiens et statisticiens de l’INRA . : 1 p.

Conference paper

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Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

M. Groussin, Manolo Gouy

Molecular Biology and Evolution . 28 : 2661-2674

DOI: 10.1093/molbev/msr098

Journal article

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Pendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre

J.C. Bertrand, Céline Brochier-Armanet, Manolo Gouy, F. Westall

incollection . 2-35311-022-3 9782353110223 : 94-U259

Book chapter

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Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.

Céline Brochier-Armanet, Philippe Deschamps, Purificación López-García, Yvan Zivanovic, Francisco Rodríguez-Valera, David Moreira

The International Society of Microbiologial Ecology Journal . 5 ( 8 ) : 1291-302

DOI: 10.1038/ismej.2011.16

Journal article

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A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System

S. Coumes-Florens, Céline Brochier-Armanet, A. Guiseppi, F. Denizot, M. Foglino

PLoS ONE . 6 : e15951

DOI: 10.1371/journal.pone.0015951

Journal article

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Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

J. Luciano, R. Agrebi, A.V. Le Gall, M. Wartel, F. Fiegna, A. Ducret...

PLoS Genetics . 7 ( 9 ) : 1409-1418

DOI: 10.1371/journal.pgen.1002268

Journal article

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Characterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia

H. Trigui, Salma Masmoudi, Céline Brochier-Armanet, S. Maalej, S. Dukan

Int J Microbiol . -- : 347-58

Journal article

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Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes

A. Heinrich-Salmeron, A. Cordi, Céline Brochier-Armanet, D. Halter, C. Pagnout, E. Abbaszadeh-Fard...

Applied and Environmental Microbiology . 77 : 4685-92

DOI: 10.1128/AEM.02884-10

Journal article

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On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.

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

Research in Microbiology . 162 ( 1 ) : 53-70

DOI: 10.1016/j.resmic.2010.10.004

Journal article

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A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120

C. Boileau, L. Eme, Céline Brochier-Armanet, A. Janicki, C-C. Zhang, A. Latifi

New Phytologist . 191 : 1108-1118

DOI: 10.1111/j.1469-8137.2011.03774.x

Journal article

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Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Sylvie Auxilien, Anette Rasmussen, Simon Rose, Céline Brochier-Armanet, Clotilde Husson, Dominique Fourmy...

RNA . 17 ( 1 ) : 45-53

DOI: 10.1261/rna.2323411

Journal article

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Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3As(T) sp. nov.

D. Slyemi, D. Moinier, Céline Brochier-Armanet, V. Bonnefoy, D. B. Johnson

Archives of Microbiology . 193 : 439-449

DOI: 10.1007/s00203-011-0684-y

Journal article

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Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

A. Amouric, Céline Brochier-Armanet, D. B. Johnson, V. Bonnefoy, K. B. Hallberg

Microbiology . 155 : 111-122

DOI: 10.1099/mic.0.044537-0

Journal article

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An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales

C. Le Fourn, G. Brasseur, Céline Brochier-Armanet, L. Pieulle, A. Brioukhanov, B. Ollivier...

Environmental Microbiology . 13 : 2132-45

DOI: 10.1111/j.1462-2920.2011.02439.x

Journal article

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Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.

Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina Vieira

Gene . 473 ( 2 ) : 100-9

DOI: 10.1016/j.gene.2010.11.009

Journal article

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Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis

Hana Trigui, Salma Masmoudi, Céline Brochier-Armanet, Aude Barani, Gérald Grégori, Michel Denis...

Extremophiles . 15 : 347-358

DOI: 10.1007/s00792-011-0364-5

Journal article

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Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Sylvie Auxilien, Anette Rasmussen, Simon Rose, Céline Brochier-Armanet, Clotilde Husson, Dominique Fourmy...

RNA . 17 ( 1 ) : 45-53

DOI: 10.1261/rna.2323411

Journal article

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An efficient method to find potentially universal population genetic markers applied to metazoans

A. Chenuil, Thierry B. Hoareau, E. Egea, G. Penant, C. Rocher, D. Aurelle...

BMC Evolutionary Biology . 10 ( 276 ) : 1-17

DOI: 10.1186/1471-2148-10-276

Journal article

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Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia

Cesare de Filippo, Patricia Heyn, Lawrence Barham, Mark Stoneking, Brigitte Pakendorf

American Journal of Physical Anthropology . 141 ( 3 ) : 382-394

DOI: 10.1002/ajpa.21155

Journal article

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Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Carina Mugal, J. Wolf, H. von Grünberg, H. Ellegren

Genome Biology and Evolution . 2 : 19-28

DOI: 10.1093/gbe/evp056

Journal article

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Molecular evolution of genes in avian genomes

Ki Woong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen B W Wolf, Niclas Backström...

Genome Biology . 11 ( 6 ) : 17 p.

DOI: 10.1186/gb-2010-11-6-r68

Journal article

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Phylogénie moléculaire

Samuel Blanquart, Alexis Criscuolo, Christophe J Douady, Emmanuel Douzery, Nicolas Lartillot, Herve Philippe...

Biologie évolutive . 9782804101619

Book chapter

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In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

Evelyne Heyer, Begoña Martínez-Cruz, Renaud Vitalis, Laure Ségurel, Frédéric Austerlitz, Myriam Georges...

European Journal of Human Genetics .

DOI: 10.1038/ejhg.2010.153

Journal article

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Mode de vie et diversité génétique dans les populations humaines d'Asie Centrale

Laure Ségurel

Thesis

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Frequency of the AGT Pro11Leu polymorphism in humans: Does diet matter?

Laure Ségurel, Sophie Lafosse, Evelyne Heyer, Renaud Vitalis

Annals of Human Genetics . 74 ( 1 ) : 57-64

DOI: 10.1111/j.1469-1809.2009.00549.x

Journal article

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Looking for signatures of sex-specific demography and local adaptation on the X chromosome.

Evelyne Heyer, Laure Segurel

Genome Biology . 11 ( 1 ) : 203

DOI: 10.1186/gb-2010-11-1-203

Journal article

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