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.
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.
Display of 1 to 30 publications on 761 in total
A 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
Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study
Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776
Bioinformatique - 3e édition
Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
Multiple Sequence Alignment . 2231 : 241-260
Resurrection 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
A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes
Molecular Biology and Evolution . 38 ( 6 ) : 2396-2412
Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes
New Phytologist . 231 ( 4 ) : 1599-1611
Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
Scientific Reports . 11 ( 1 ) : 972
Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L
Microbiology Resource Announcements . 10 ( 8 ) : e00042-21
Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia
Microbiology Resource Announcements . 10 ( 3 ) : e01326-20
Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.
Peer Community Journal . 1 : e42
Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors
A new tool to cross and analyze TE and gene annotations
Peer Community in Genomics . : 100010
A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes
Molecular Biology and Evolution . 38 ( 3 ) : 1199-1208
Universal probabilistic programming offers a powerful approach to statistical phylogenetics
Communications Biology . 4 ( 1 )
Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution
Theoretical Population Biology . 142 : 57-66
Inferring Long-Term Effective Population Size with Mutation–Selection Models
Molecular Biology and Evolution . 38 ( 10 ) : 4573-4587
Reconstructing the History of Variation in Effective Population Size along Phylogenies
Genome Biology and Evolution . 13 ( 8 )
Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates
Frontiers in Molecular Biosciences . 8
The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
Genome Biology and Evolution . 13 ( 5 )
Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
Plos Biology . 19 ( 7 ) : e3001309
Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age
Journal of Archaeological Science . 128 : 105336
DILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Hepatitis B virus preS2Δ38–55 variants: A newly identified risk factor for hepatocellular carcinoma
JHEP Reports Innovation in Hepatology . 2 ( 5 ) : 100144
How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?
Molecular Ecology Resources . 20 ( 5 ) : 1294-1298
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria
ISME Journal .
From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria
PLoS ONE . 15 ( 4 ) : e0231839
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824