Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87

Doctorante
UCBL
Tel: 04 72 44 81 42

Doctorant
CNRS

Stagiaire
UCBL
Tel: 04 72 44 81 42

Doctorante
autre
Tel: 04 72 44 81 42

Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
Contrat à durée déterminée
UCBL
Tel: 04 72 44 81 42
Doctorant
autre
Tel: 04 72 44 81 42

Directeur de recherche
CNRS
Tel: 33 04 72 44 62 97

Professeur d'université émérite
UCBL
Tel: 04 72 44 85 60

Doctorante
UCBL
Tel: 04 72 44 81 42

Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Stagiaire
UCBL
Tel: 04 72 44 81 42

Doctorant
CNRS
Tel: 04 72 44 85 60

Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60

Stagiaire
UCBL
Tel: 04 72 44 81 42

Directeur de recherche
CNRS
Tel: 04 72 44 84 87

Chargée de recherche
CNRS
Tel: 04 72 43 13 44

Professeure des universités émérite
UCBL
Tel: 04 72 44 81 42

Maître de conférences
UCBL
Tel: 04 72 43 35 83
Chargée de recherche
CNRS
Tel: 04 72 44 81 42

Chargée de recherche
CNRS
Tel: 04 72 43 35 82

Directeur de recherche
CNRS
Tel: 33 04 72 44 62 96

Chargée de recherche
CNRS
Tel: 04 72 43 26 28
Stagiaire
UCBL
Tel: 04 72 44 81 42

Chercheur invité
UCBL
Stagiaire
UCBL
Tel: 04 72 44 81 42

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 1 to 30 publications on 813 in total
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale
Preprint
see the publicationRecent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements
Frontiers in Genetics . 13
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology and Evolution . 37 ( 3 ) : 197-202
Journal article
see the publicationPopulation designations in biomedical research: limitations and perspectives
HLA: Immune Response Genetics .
DOI: 10.1111/tan.14852
Journal article
see the publicationModelling the spatiotemporal spread of beneficial alleles using ancient genomes
Preprint
see the publicationCodiversification of gut microbiota with humans
Science . 377 ( 6612 ) : 1328-1332
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology & Evolution . 37 ( 3 ) : 197-202
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology & Evolution .
Journal article
see the publicationProtein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual mutations
Molecular Biology and Evolution . 39 ( 9 ) : msac186
Journal article
see the publicationGOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements
Preprint
see the publicationAn Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias
Molecular Biology and Evolution . 39
Journal article
see the publicationIdentifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?
Preprint
see the publicationRecent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements
Frontiers in Genetics . 13
Journal article
see the publicationA divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
BMC Ecology and Evolution . 22 ( 1 ) : 1-12
Journal article
see the publicationLong-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
Journal article
see the publicationThe human gut microbiome and health inequities
Proceedings of the National Academy of Sciences of the United States of America . 118 ( 25 ) : e2017947118
Journal article
see the publicationNo evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas
Ecology and Evolution . 11 ( 12 ) : 7634-7646
DOI: 10.1002/ece3.7596
Journal article
see the publicationElevated rates of horizontal gene transfer in the industrialized human microbiome
Cell . 184 ( 8 ) : 2053-2067.e18
Journal article
see the publicationChanges in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations
Frontiers in Cellular and Infection Microbiology . 11 : 533528
Journal article
see the publicationThe Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study
Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776
Journal article
see the publicationDILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Journal article
see the publicationMassive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
Plos Biology . 19 ( 7 ) : e3001309
Journal article
see the publicationSeaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
Multiple Sequence Alignment . 2231 : 241-260
Book chapter
see the publicationResurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties
Molecular Biology and Evolution . : 1-44
Journal article
see the publicationStructural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
Scientific Reports . 11 ( 1 ) : 972
Journal article
see the publicationNatural Selection beyond Life? A Workshop Report
Life . 11 ( 10 ) : 1051
DOI: 10.3390/life11101051
Journal article
see the publicationQuantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution
Theoretical Population Biology . 142 : 57-66
Journal article
see the publicationInferring Long-Term Effective Population Size with Mutation–Selection Models
Molecular Biology and Evolution . 38 ( 10 ) : 4573-4587
Journal article
see the publication