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

Doctorante
autre
Tel: 04 72 44 81 42

Professeure des universités
UCBL
Tel: 33 04 26 23 44 76

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

Doctorant
CNRS
Tel: 04 72 44 85 60
Doctorante
UCBL

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

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
Stagiaire
UCBL

Chargée de recherche
CNRS
Tel: 04 72 43 26 28

Chercheur invité
UCBL
Technicien CDD
CNRS
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 852 in total
MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation
Preprint
see the publicationLook4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats
Preprint
see the publicationPhylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships
Systematic Entomology .
DOI: 10.1111/syen.12611
Journal article
see the publicationHow genomics can help biodiversity conservation
Trends in Genetics .
Journal article
see the publicationBridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen
Preprint
see the publicationCompositionally Constrained Sites Drive Long-Branch Attraction
Systematic Biology . 72 ( 4 ) : 767 - 780
Journal article
see the publicationIdentifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?
Systematic Biology . 72 : 616 - 638
Journal article
see the publicationGenes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale
Proceedings of the National Academy of Sciences of the United States of America . 120 ( 11 ) : e2214977120
Journal article
see the publicationRandom genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
Peer Community in Evolutionary Biology .
Journal article
see the publicationDeciphering evolutionary trajectories of lactate dehydrogenases provides new insights into allostery.
Molecular Biology and Evolution . msad223
Journal article
see the publicationThe porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations
Preprint
see the publicationProposed mechanism for the selection of lactase persistence in childhood
BioEssays . 45 ( 7 )
Journal article
see the publicationBradyrhizobium commune sp. nov., isolated from nodules of a wide range of native legumes across the Australian continent
International Journal of Systematic and Evolutionary Microbiology . 73 ( 7 ) : 005971
Journal article
see the publicationA Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size
Genome Biology and Evolution . 14 ( 5 )
DOI: 10.1093/gbe/evac058
Journal article
see the publicationHydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies
Journal of Archaeological Science . 147 : 105676
Journal article
see the publicationClimate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France
Archaeological and Anthropological Sciences . 14 ( 4 ) : 61
Journal article
see the publicationModeling the spatiotemporal spread of beneficial alleles using ancient genomes
eLife . 11
DOI: 10.7554/eLife.73767
Journal article
see the publicationGenes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale
Preprint
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 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 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 publication