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 211 to 240 publications on 1098 in total

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Sandra Oliveira, Alexander Hübner, Anne-Maria Fehn, Teresa Aço, Fernanda Lages, Brigitte Pakendorf...

European Journal of Human Genetics . 27 ( 3 ) : 475-483

DOI: 10.1038/s41431-018-0304-2

Journal article

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Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels

Ana Lokmer, Amandine Cian, Alain Froment, Nausicaa Gantois, Eric Viscogliosi, Magali Chabé...

PLoS ONE . 14 ( 2 ) : e0211139

DOI: 10.1371/journal.pone.0211139

Journal article

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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

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Article 22. Crise du stockage: conserver les molécules d'ADN ou les données informatiques de l'ADN ?

Dominique D. Joly, Guy Perriere

101 Secrets de l'ADN. CNRS Editions, Paris, pp 90-91 . : 90-91

Book chapter

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Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Jean-Pierre Flandrois, Céline Brochier-Armanet, Jérôme Briolay, Danis Abrouk, Guillaume P Schwob, Philippe Normand...

Research in Microbiology . 170 ( 6-7 ) : 280-287

DOI: 10.1016/j.resmic.2019.06.005

Journal article

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Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA

Eaazhisai Kandiah, Diego Carriel, Pierre Simon Garcia, Jan Felix, Manuel Banzhaf, George Kritikos...

Structure .

DOI: 10.1016/j.str.2019.10.003

Journal article

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The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis

Romain Pardoux, Anouchka Fiévet, Cíntia Carreira, Céline Brochier-Armanet, Odile Valette, Zorah Dermoun...

Scientific Reports . 9 ( 1 ) : 360-373

DOI: 10.1038/s41598-018-37021-8

Journal article

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Description Osteo-Oto-Hepato-Enteric (O2HE) syndrome, a new recessive autosomal syndrome secondary to loss of function mutations in the UNC45A gene

L. Faivre, Clothilde Esteve, L. Francescatto, P. L. Tan, A. Bourchany, C. Delafoulhouze...

European Journal of Human Genetics . 27 ( 1 ) : 795-796

Journal article

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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira

Genes . 10 ( 4 ) : 258

DOI: 10.3390/genes10040258

Journal article

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Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Romain Lannes, Carène Rizzon, Emmanuelle Lerat

Genes . 10 ( 3 ) : 249

DOI: 10.3390/genes10030249

Journal article

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Homme/femme, mâle/femelle : la détermination du sexe dans l’espèce humaine et le reste du vivant

Gabriel Marais, Jos Käfer

Sexe & genre: De la biologie à la sociologie .

Book chapter

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Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards.

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzatti, Mélissa Mary...

DOI: 10.1101/771790

Preprint

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P2857 Quantifying drivers of antimicrobial resistance in a large network of hospital wards: a meta-population approach.

Julie Teresa Shapiro, Leboucher Gilles, Anatole Luzzati, Jean Francois Sauzon, Olivier Dauwalder, Pascale Girardo...

29TH ECCMID .

Conference paper

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Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Darbellay, Anamaria Necsulea

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msz212

Journal article

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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

Journal article

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Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints

Florian Massip, Marc Laurent, Caroline Brossas, José miguel Fernández-Justel, Maria Gomez, Marie-Noëlle Prioleau...

Nucleic Acids Research . 47 ( 10 ) : 5114-5125

DOI: 10.1093/nar/gkz182

Journal article

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Alexandre Duprey, Najwa Taïb, Simon Leonard, Tiffany Garin, Jean-Pierre Flandrois, William Nasser...

Environmental Microbiology . 21 ( 8 ) : 2809-2835

DOI: 10.1111/1462-2920.14627

Journal article

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Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Claire Siebert, Helena Lindgren, Sabrina Ferré, Corinne Villers, Sandrine Boisset, Julien Pérard...

Emerging microbes & infections . 8 ( 1 ) : 808-822

DOI: 10.1080/22221751.2019.1615848

Journal article

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Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Lorine Bethencourt, Hasna Boubakri, Najwa Taïb, Philippe Normand, J. Armengaud, Pascale P Fournier...

Research in Microbiology . 170 ( 4-5 ) : 202-213

DOI: 10.1016/j.resmic.2019.04.002

Journal article

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Evolutionary placement of Methanonatronarchaeia

Monique Aouad, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

Nature Microbiology .

DOI: 10.1038/s41564-019-0359-z

Journal article

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GeneSpy, a user-friendly and flexible genomic context visualizer

Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet

Bioinformatics . 35 ( 2 ) : 329-331

DOI: 10.1093/bioinformatics/bty459

Journal article

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Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Dominique D. Joly, Celine Brochier-Armanet

101 secrets de l’ADN. CNRS Éditions, Paris, pp 39-41 . : 39-41

Book chapter

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Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

Paris Veltsos, Kate Ridout, Melissa Toups, Santiago González-Martínez, Aline Muyle, Olivier Emery...

Genetics . 212 ( 3 ) : 815-835

DOI: 10.1534/genetics.119.302045

Journal article

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

Journal article

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Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems

Hélène Martin, Fantin E Carpentier, Sophie Gallina, Cécile Godé, Eric Schmitt, Aline Muyle...

Genome Biology and Evolution . 11 ( 2 ) : 350-361

DOI: 10.1093/gbe/evz001

Journal article

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Genomic imprinting mediates dosage compensation in a young plant XY system.

Aline Muyle, Niklaus Zemp, Cécile Fruchard, Radim Cegan, Jan Vrána, Clothilde Deschamps...

DOI: 10.1101/179044

Preprint

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Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia

Nguyen Thuy Duong, Enrico Macholdt, Nguyen Dang Ton, Leonardo Arias, Roland Schröder, Nguyen van Phong...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-29989-0

Journal article

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Genetic structure and sex-biased gene flow in the history of southern African populations

Vladimir Bajić, Chiara Barbieri, Alexander Hübner, Tom Tom Güldemann, Christfried Naumann, Linda Gerlach...

American Journal of Physical Anthropology . 167 ( 3 ) : 656-671

DOI: 10.1002/ajpa.23694

Journal article

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