Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Stagiaire
CNRS
Stagiaire
UCBL
Doctorante
UCBL
Tel: 04 72 44 81 42
Doctorant
CNRS
Doctorante
autre
Tel: 04 72 44 81 42
Stagiaire
UCBL
Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
Stagiaire
UCBL
Directeur de recherche
CNRS
Tel: 33 04 72 44 62 97
Professeur d'université émérite
UCBL
Tel: 04 72 44 85 60
Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Doctorante
UCBL
Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60
Stagiaire
UCBL
Directeur de recherche
CNRS
Tel: 04 72 44 84 87
Stagiaire
UCBL
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
Doctorant
CNRS
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
Chercheur invité
UCBL
Stagiaire
UCBL
Ingénieur de recherche 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 91 to 120 publications on 907 in total
Evolutionary relationships between Archaea and eukaryotes
Nature Ecology & Evolution . 4 : 20-21
Journal article
see the publicationDetecting sex-linked genes using genotyped individuals sampled in natural populations
Preprint
see the publicationThe Bayesian Approach to Molecular Phylogeny
Phylogenetics in the Genomic Era . : 1.4:1--1.4:17
Book chapter
see the publicationPhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models
Phylogenetics in the Genomic Era . : 1.5:1--1.5:16
Book chapter
see the publicationAn efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
Genome Research . 30 ( 2 ) : 164-172
Journal article
see the publicationThe wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication
Genome Biology . 21 ( 1 ) : 223
Journal article
see the publicationAn Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice
Genes . 11 ( 9 ) : 1046
Journal article
see the publicationA Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
Journal of Clinical Microbiology . 58 ( 6 )
DOI: 10.1128/JCM.00060-20
Journal article
see the publicationEvidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Genes . 11 ( 7 ) : 787
Journal article
see the publicationFrom conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria
PLoS ONE . 15 ( 4 ) : e0231839
Journal article
see the publicationIsotopic systematics point to wild origin of mummified birds in Ancient Egypt
Scientific Reports . 10 ( 1 )
Journal article
see the publicationThe Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France
Journal of Archaeological Science: Reports . 34 : 102595
Journal article
see the publicationMetapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards
eLife . 9
DOI: 10.7554/eLife.54795
Journal article
see the publicationDickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)
International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514
Journal article
see the publicationδ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?
Journal of African Earth Sciences . 162 : 103702
Journal article
see the publicationProbabilistic programming: a powerful new approach to statistical phylogenetics
Preprint
see the publicationFitting diversification models on undated or partially dated trees
Peer Community In Evolutionary Biology . : 100088
Other publication
see the publicationPhylogenomics and Genome Annotation
Phylogenetics in the Genomic Era . : 4.1:1--4.1:26
Book chapter
see the publicationBedrock radioactivity influences the rate and spectrum of mutation
eLife . 9 : e56830
DOI: 10.7554/eLife.56830
Journal article
see the publicationMultiple Deeply Divergent Denisovan Ancestries in Papuans
Cell .
Journal article
see the publicationEvidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia
Genome Biology and Evolution . 11 ( 3 ) : 748-758
DOI: 10.1093/gbe/evz028
Journal article
see the publicationThe role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola
European Journal of Human Genetics . 27 ( 3 ) : 475-483
Journal article
see the publicationUse of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels
PLoS ONE . 14 ( 2 ) : e0211139
Journal article
see the publicationGlobal survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Journal article
see the publicationArticle 22. Crise du stockage: conserver les molécules d'ADN ou les données informatiques de l'ADN ?
101 Secrets de l'ADN. CNRS Editions, Paris, pp 90-91 . : 90-91
Book chapter
see the publicationTaxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon
Research in Microbiology . 170 ( 6-7 ) : 280-287
Journal article
see the publicationStructure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA
Structure .
Journal article
see the publicationThe bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis
Scientific Reports . 9 ( 1 ) : 360-373
Journal article
see the publicationDescription Osteo-Oto-Hepato-Enteric (O2HE) syndrome, a new recessive autosomal syndrome secondary to loss of function mutations in the UNC45A gene
European Journal of Human Genetics . 27 ( 1 ) : 795-796
Journal article
see the publicationOn the Importance to Acknowledge Transposable Elements in Epigenomic Analyses
Genes . 10 ( 4 ) : 258
Journal article
see the publication