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 421 to 450 publications on 1006 in total

Classification of bacterial replicons based on the Genetic Information Transmission Systems

Olivier Poirion, Bénédicte Lafay

11th RECOMB - Comparative Genomics 2013 .

Conference paper

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Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

M. Soumillon, A. Necsulea, M. Weier, D. Brawand, X. Zhang, H. Gu...

Cell Reports . 3 ( 6 ) : 2179-2190

DOI: 10.1016/j.celrep.2013.05.031

Journal article

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Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

Jérémy Andres, Florence Arsène-Ploetze, Valérie Barbe, Céline Brochier-Armanet, Jessica Cleiss-Arnold, Jean-Yves Coppée...

Genome Biology and Evolution . 5 ( 5 ) : 934-53

DOI: 10.1093/gbe/evt061

Journal article

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Phylogenetic Patterns of GC-Biased Gene Conversion in Placental Mammals and the Evolutionary Dynamics of Recombination Landscapes

Nicolas Lartillot

Molecular Biology and Evolution . 30 ( 3 ) : 489-502

DOI: 10.1093/molbev/mss239

Journal article

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An Experimentally Tested Scenario for the Structural Evolution of Eukaryotic Cys2His2 Zinc Fingers from Eubacterial Ros Homologs

Fortuna Netti, Gaetano Malgieri, Sabrina Esposito, Maddalena Palmieri, Ilaria Baglivo, Carla Isernia...

Molecular Biology and Evolution . 30 ( 7 ) : 1504 - 1513

DOI: 10.1093/molbev/mst068

Journal article

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A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

Journal article

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TPMS: a set of utilities for querying collections of gene trees.

Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière

BMC Bioinformatics . 14 : 109

DOI: 10.1186/1471-2105-14-109

Journal article

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Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

Philippe Julien, David Brawand, Magali Soumillon, Anamaria Necsulea, Angélica Liechti, Frédéric Schütz...

PLoS Biology . 10 ( 5 ) : e1001328

DOI: 10.1371/journal.pbio.1001328

Journal article

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Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

Carla Aimé, Guillaume Laval, Etienne Patin, Paul Verdu, Laure Ségurel, Raphaëlle Chaix...

Conférence Jacques Monod .

Poster

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Geographical delimitation of a partial selective sweep in African \textitDrosophila melanogaster

L. Frezal, F. Meli, Sylvain Mousset, S. Mona, M. Veuille

Molecular ecology . 21 : 5702--14

DOI: 10.1111/mec.12004

Journal article

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The genetic prehistory of southern Africa

Joseph Pickrell, Nick Patterson, Chiara Barbieri, Falko Berthold, Linda Gerlach, Tom Güldemann...

Nature Communications . 3 : 1143

DOI: 10.1038/ncomms2140

Journal article

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Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands

F. Delfin, S. Myles, Y. Choi, D. Hughes, R. Illek, M. van Oven...

Molecular Biology and Evolution . 29 ( 2 ) : 545-564

DOI: 10.1093/molbev/msr186

Journal article

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Bringing together linguistic and genetic evidence to test the Bantu expansion

C. de Filippo, K. Bostoen, M. Stoneking, Brigitte Pakendorf

Proceedings of the Royal Society B: Biological Sciences . 279 ( 1741 ) : 3256-3263

DOI: 10.1098/rspb.2012.0318

Journal article

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The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

A. Mey, Hervé Acloque, Emmanuelle Lerat, S. Gounel, V. Tribollet, S. Blanc...

Retrovirology . 9 ( 1 ) : 21

DOI: 10.1186/1742-4690-9-21

Journal article

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Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Ellen Miranda Leffler, Kevin Bullaughey, Daniel R Matute, Wynn Meyer, Laure Ségurel, Aarti A. Venkat...

PLoS Biology . 10 ( 9 ) : e1001388

DOI: 10.1371/journal.pbio.1001388

Journal article

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A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

A. Auton, A. Fledel-Alon, S. Pfeifer, O. Venn, L. Segurel, T. Street...

Science . 336 ( 6078 ) : 193-198

DOI: 10.1126/science.1216872

Journal article

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The ABO blood group is a trans-species polymorphism in primates

Laure L. Segurel, Emma E. E. E. Thompson, Timothée T. Flutre, Jessica J. Lovstad, Aarti A. Venkat, Susan W. S. W. Margulis...

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 45 ) : 18493 - 18498

DOI: 10.1073/pnas.1210603109

Journal article

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Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

Eugénie Pessia, Alexandra Popa, Sylvain Mousset, Clément Rezvoy, Laurent Duret, G. Marais

Genome Biology and Evolution . 4 : 787-794

DOI: 10.1093/gbe/evs052

Journal article

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Toward community standards in the quest for orthologs

Christophe Dessimoz, Toni Gabaldon, David Roos, Erik L L Sonnhammer, Javier Herrero, Alfonso Valencia...

Bioinformatics . 28 ( 6 ) : 900-904

DOI: 10.1093/bioinformatics/bts050

Journal article

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Simplified detection of food-borne pathogens: An in situ high affinity capture and staining concept

T. Junillon, A. Vimont, D. Mosticone, B. Mallen, F. Baril, C. Rozand...

Journal of Microbiological Methods . 91 : 501--505

DOI: 10.1016/j.mimet.2012.09.015

Journal article

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Les défis de la systématique face au monde microbien

Céline Brochier-Armanet, Simonetta Gribaldo

incollection . 328 : 49-52

Journal article

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Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

V. de Crécy-Lagard, F. Forouhar, Céline Brochier-Armanet, L. Tong, Jf. Hunt

Biology Direct . 7 : 1--13

DOI: 10.1186/1745-6150-7-32

Journal article

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A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, Nelly Burlet...

Journal of Environmental Radioactivity . 113 : 83-86

DOI: 10.1016/j.jenvrad.2012.04.001

Journal article

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Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.

Béatrice Py, Catherine Gerez, Sandra Angelini, Rémy Planel, Daniel Vinella, Laurent Loiseau...

Molecular Microbiology . 86 ( 1 ) : 155-71

DOI: 10.1111/j.1365-2958.2012.08181.x

Journal article

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Spotlight on the Thaumarchaeota

C. Brochier-Armanet, Simonetta Gribaldo, Patrick Forterre

The International Society of Microbiologial Ecology Journal . 6 : 227-230

DOI: 10.1038/ismej.2011.145

Journal article

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The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean-Marc Aury, Cyril Denby Wilkes...

PLoS Genetics . 8 ( 10 ) : e1002984

DOI: 10.1371/journal.pgen.1002984

Journal article

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Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archea

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

BMC Evolutionary Biology . 12 : 226

DOI: 10.1186/1471-2148-12-226

Journal article

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