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 271 to 300 publications on 1098 in total

A Survey and a Positive Psychology Intervention on French PhD Student Well-being

Gabriel Marais, Rebecca Shankland, Pascale Haag, Robin Fiault, Briget Juniper

International Journal of Doctoral Studies . 13 : 109-138

DOI: 10.28945/3948

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...

Nature Plants . 4 ( 9 ) : 677-680

DOI: 10.1038/s41477-018-0221-y

Journal article

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Integrative Mobilizable Element (IMEs): a reservoir of antibiotic resistance genes in the zoonotic pathogen Streptococcus suis

Virginie Libante, Nombre Yves, Charles Coluzzi, Gérard Guédon, Marcelo Gottschalk, Nahuel Fittipaldi...

GDR 3546 - Les elements mobiles du mécanisme aux populations, une approche intégrative .

Conference paper

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L'exploration des génomes par l'outil ICEFinder révèle la forte prévalence et l'extrême diversité des ICE et des IME de streptocoques

Charles Coluzzi

Thesis

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A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Chloé C. Ambroset, Valentin Loux, Thomas Lacroix...

Frontiers in Microbiology . 8 : 16

DOI: 10.3389/fmicb.2017.00443

Journal article

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The obscure world of integrative and mobilizable elements

Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot, Nathalie N. Leblond-Bourget

Genes . 8 ( 11 ) : 337

DOI: 10.3390/genes8110337

Journal article

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The palaeolatitudinal distribution of fossil wood genera as a proxy for European Jurassic terrestrial climate

Marc Philippe, Sara Puijalon, Guillaume C Suan, Sylvain Mousset, Frédéric Thévenard, Emanuela Mattioli

Palaeogeography, Palaeoclimatology, Palaeoecology . 466 ( 373–381 )

DOI: 10.1016/j.palaeo.2016.11.029

Journal article

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Genomic landscape of human diversity across Madagascar

Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Ignace Rakoto, Nelly Rabetokotany, Bodo Ravololomanga...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 32 ) : E6498-E6506

DOI: 10.1073/pnas.1704906114

Journal article

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Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Takeshi Kawakami, Carina Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds...

Molecular Ecology . 26 ( 16 ) : 4158-4172

DOI: 10.1111/mec.14197

Journal article

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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Ludovic Dutoit, Nagarjun Vijay, Carina Mugal, Christen Bossu, Reto Burri, Jochen Wolf...

Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756

DOI: 10.1098/rspb.2016.2756

Journal article

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Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Reto Burri, Alexander Nater, Carina Mugal, Hans Ellegren

Molecular Ecology Resources . 17 ( 4 ) : 586-597

DOI: 10.1111/1755-0998.12602

Journal article

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

Journal article

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Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Magali Chabé, Ana Lokmer, Laure Ségurel

Trends in Parasitology . 33 ( 12 ) : 925-934

DOI: 10.1016/j.pt.2017.08.005

Journal article

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Microbiome intestinal ancien et problématiques médicales contemporaines

Philippe Charlier, Anaïs Augias, Philippe Sansonetti, Céline Bon, Sean Kennedy, Laure Ségurel

Médecine/Sciences . 33 : 984-990

DOI: 10.1051/medsci/20173311016

Other publication

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Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Nina Marchi, Tatyana Hegay, Philippe Mennecier, Myriam Georges, Romain Laurent, Mark Whitten...

American Journal of Physical Anthropology . 162 ( 4 ) : 627-640

DOI: 10.1002/ajpa.23151

Journal article

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MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Aurélie Siberchicot, Adrien Bessy, Laurent Gueguen, Gabriel A. B. Marais

Genome Biology and Evolution . 9 ( 10 ) : 2506-2509

DOI: 10.1093/gbe/evx178

Journal article

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The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou, Laurent Duret, Sylvain Charlat

Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210

DOI: 10.1111/jeb.13186

Journal article

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The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille, L. Duret, Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences .

DOI: 10.1098/rstb.2016.0463

Journal article

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d18O-Derived incubation temperatures of oviraptorosaur eggs.

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . : 1-15

DOI: 10.1111/pala.12311

Journal article

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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

The International Society of Microbiologial Ecology Journal . 11 ( 11 ) : 2407-2425

DOI: 10.1038/ismej.2017.122

Journal article

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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda, Martin Dohrmann, Walker Pett, Herve Philippe, Omar Rota-Stabelli, Nicolas Lartillot...

Current Biology . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

Journal article

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Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Sara E Branco, Hélène E Badouin, Ricardo E Rodríguez de La Vega, Jerome Gouzy, Fantin E Carpentier, Gabriela E Aguileta...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 27 ) : 7067-7072

DOI: 10.1073/pnas.1701658114

Journal article

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Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Helene Badouin, Pierre Gladieux, Jerome Gouzy, Sophie Siguenza, Gabriela Aguileta, Alodie Snirc...

Molecular Ecology . 26 ( 7 )

DOI: 10.1111/mec.13976

Journal article

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Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

T. Boldanova, A. Suslov, M.H. Heim, A. Necsulea

EMBO Molecular Medicine . 9 : 816-834

DOI: 10.15252/emmm.201607006

Journal article

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

Journal article

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On the rarity of dioecy in flowering plants

Jos Käfer, Gabriel Marais, Jr. Pannell

Molecular Ecology . 26 : 1225-1241

DOI: 10.1111/mec.14020

Journal article

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In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey, Julie a J Clément, J Buard, B Leblanc, I Gut, M Gut...

Genome Research . 27 ( 4 ) : 580-590

DOI: 10.1101/gr.217240.116

Journal article

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