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 241 to 270 publications on 1098 in total

Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa

Sandra Oliveira, Anne-Maria Fehn, Teresa Aço, Fernanda Lages, Magdalena Gayà-Vidal, Brigitte Pakendorf...

American Journal of Physical Anthropology . 165 ( 3 ) : 518-535

DOI: 10.1002/ajpa.23378

Journal article

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High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia

Leonardo Arias, Chiara Barbieri, Guillermo Barreto, Mark Stoneking, Brigitte Pakendorf

American Journal of Physical Anthropology . 165 ( 2 ) : 238-255

DOI: 10.1002/ajpa.23345

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Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-Loth, Jazmin Sanchez, Omar Alva...

Nature Communications . 9 ( 1 ) : 932

DOI: 10.1038/s41467-018-03342-5

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The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Nicolas Brucato, Verónica Fernandes, Stéphane Mazières, Pradiptajati Kusuma, Murray Cox, Joseph Wainaina Ng'Ang'A...

American Journal of Human Genetics . 102 ( 1 ) : 58-68

DOI: 10.1016/j.ajhg.2017.11.011

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Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Leonardo Arias, Roland Schröder, Alexander Hübner, Guillermo Barreto, Mark Stoneking, Brigitte Pakendorf

Molecular Biology and Evolution . 35 ( 11 ) : 2719-2735

DOI: 10.1093/molbev/msy169

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Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Paulina Bolívar, Carina Mugal, Matteo Rossi, Alexander Nater, Mi Wang, Ludovic Dutoit...

Molecular Biology and Evolution . 35 ( 10 ) : 2475-2486

DOI: 10.1093/molbev/msy149

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Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Carina Mugal, Paulina Bolívar, Mi Wang, Krystyna Nadachowska-Brzyska, Linnéa Smeds...

Molecular Ecology . 27 ( 18 ) : 3572-3581

DOI: 10.1111/mec.14789

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Positive selection on human gamete-recognition genes

Michael Hart, Daryn Stover, Vanessa Guerra, Sahar Mozaffari, Carole Ober, Carina Mugal...

PeerJ . 6 : e4259

DOI: 10.7717/peerj.4259

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Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

Nina Marchi, Philippe Mennecier, Myriam Georges, Sophie Lafosse, Tatyana Hegay, Choduraa Dorzhu...

Scientific Reports . 8 : 9397

DOI: 10.1038/s41598-018-27047-3

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A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Diego Carriel, Pierre Simon Garcia, Florence Castelli, Patricia Lamourette, François Fenaille, Céline Brochier-Armanet...

Genome Biology and Evolution . 10 ( 11 ) : 3058-3075

DOI: 10.1093/gbe/evy228

Journal article

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Progress and Prospects in Gender Visibility at SMBE Annual Meetings

Jos Käfer, Andrea Betancourt, Avelyne S. Villain, Marie Fernandez, Clémentine Vignal, Gabriel Marais...

Genome Biology and Evolution . 10 ( 3 ) : 901-908

DOI: 10.1093/gbe/evy056

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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

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Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Clothilde Esteve, Ludmila Francescatto, Perciliz Tan, Aurélie Bourchany, Cécile de Leusse, Evelyne Marinier...

American Journal of Human Genetics . 102 ( 3 ) : 364 - 374

DOI: 10.1016/j.ajhg.2018.01.009

Journal article

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PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

L. Zucchini, C. Mercy, Ps. Garcia, C. Cluzel, V. Gueguen-Chaignon, F. Galisson...

Nature Microbiology . 3 ( 2 ) : 197-209

DOI: 10.1038/s41564-017-0069-3

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Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Khaled Fadhlaoui, Wagdi Ben Hania, Fabrice Armougom, Manon Joseph, Marie-Laure Fardeau, Gaël Erauso...

Environmental Microbiology . 20 ( 1 ) : 281-292

DOI: 10.1111/1462-2920.13995

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 35 ( 11 ) : 2819-2834

DOI: 10.1093/molbev/msy173

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

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Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

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PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Boubou Diagouraga, Julie Clément, L. Duret, Jan Kadlec, Bernard de Massy, Frédéric Baudat

Molecular Cell . 69 ( 5 ) : 853 - 865.e6

DOI: 10.1016/j.molcel.2018.01.033

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Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Nicolas Galtier, Camille Roux, Marjolaine Rousselle, Jonathan Romiguier, Emeric Figuet, Sylvain Glemin...

Molecular Biology and Evolution . 35 ( 5 ) : 1092 - 1103

DOI: 10.1093/molbev/msy015

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Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Caroline Monteil, Guy Perrière, Nicolas Menguy, Nicolas Ginet, Béatrice Alonso, Nicolas Waisbord...

Environmental Microbiology .

DOI: 10.1111/1462-2920.14364

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Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 127 : 46-54

DOI: 10.1016/j.ympev.2018.04.011

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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli...

MSphere . 3 ( 5 ) : e00405-18

DOI: 10.1128/mSphere.00405-18

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron, Ghislaine Blasquez...

Scientific Reports . 8 ( 1 ) : 5855

DOI: 10.1038/s41598-018-24034-6

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Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Christophe Lécuyer, François Atrops, Romain Amiot, Delphine Angst, Valérie Daux, Jean-Pierre Flandrois...

The Holocene .

DOI: 10.1177/0959683617752840

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Multiple convergent supergene evolution events in mating-type chromosomes

Sara E Branco, Fantin E Carpentier, Ricardo Rodriguez de La Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur...

Nature Communications . 9 ( 1 ) : 2000

DOI: 10.1038/s41467-018-04380-9

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The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

Hélène E Badouin

Second Joint Congress on Evolutionary Biology .

Conference paper

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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque...

Nature Genetics . 50 ( 6 ) : 772-777

DOI: 10.1038/s41588-018-0110-3

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Sex gap in aging and longevity: can sex chromosomes play a role?

Gabriel A.B. Marais, Jean-Michel Gaillard, Cristina Vieira, Ingrid Plotton, Damien Sanlaville, François Gueyffier...

Biology of Sex Differences . 9 ( 1 ) : 1-14

DOI: 10.1186/s13293-018-0181-y

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Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry...

Nature . 564 ( 7734 ) : 64-70

DOI: 10.1038/s41586-018-0734-6

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