Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
Enseignant-chercheur CPJ
UCBL
Directeur de recherche
CNRS
Tel: 33 04 72 44 62 97
Professeur d'université émérite
UCBL
Tel: 04 72 44 85 60
Ingénieur d'études CDD
CNRS
Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Doctorante
UCBL
Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60
Directeur de recherche
CNRS
Tel: 04 72 44 84 87
Doctorant
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
Doctorant
UCBL
Chercheur invité
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 1 to 30 publications on 975 in total
Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions
Preprint
see the publicationSMALL RUMINANTS VERSUS ENDOGENOUS RETROVIRUSES: AN EVOLUTIVE SHOWDOWN STILL IN PROGRESS IN THE DOMESTIC GOAT GENOME
International congress on transposable elements .
Poster
see the publicationA genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats
Preprint
see the publicationSMBE Secretary’s Report
Molecular Biology and Evolution . 41 ( 6 )
Journal article
see the publicationLook4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats
Mobile DNA . 15 ( 1 ) : 8
Journal article
see the publicationDiversité et diversification des Pectobacteriaceae, une famille de bactéries phytopathogènes d’importance mondiale
Cahiers Scientifiques de la Fondation Pierre Vérots . ( 10 ) : 19-29
Journal article
see the publicationISMB/ECCB 2023 organization benefited from the strengths of the French bioinformatics community
Bioinformatics Advances . 4 ( 1 ) : vbae040
Journal article
see the publicationBradyrhizobium hardenbergiae sp. nov., isolated from Hardenbergia violacea in Australia, represents a novel basal lineage of the B. elkanii supergroup
Preprint
see the publicationA Wright–Fisher graph model and the impact of directional selection on genetic variation
Theoretical Population Biology . 159 : 13-24
Journal article
see the publicationInvestigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam
PLoS ONE . 19 ( 6 ) : e0304964
Journal article
see the publicationComplete mitochondrial genomes of patients from Thailand with cardiovascular diseases
PLoS ONE . 19 ( 7 ) : e0307036
Journal article
see the publicationGTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes
NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064
Journal article
see the publicationRegulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids
BMC Biology . 22 ( 1 ) : 124
Journal article
see the publicationHigh prevalence of PRDM9-independent recombination hotspots in placental mammals
Proceedings of the National Academy of Sciences of the United States of America . 121 ( 23 ) : e2401973121
Journal article
see the publicationLncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma
Preprint
see the publicationPersistent homology reveals strong phylogenetic signal in 3D protein structures
PNAS Nexus . 3 ( 4 ) : 158
Journal article
see the publicationThe genetic legacy of the expansion of Bantu-speaking peoples in Africa
Nature . 625 ( 7995 ) : 540–547
Journal article
see the publicationPRDM9 drives the location and rapid evolution of recombination hotspots in salmonids
Preprint
see the publicationThe role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome †
Proceedings of the Royal Society B: Biological Sciences . 291 ( 2015 )
Journal article
see the publicationEvidence that genetic drift not adaptation drives fast‐Z and large‐Z effects in Ficedula flycatchers
Molecular Ecology .
DOI: 10.1111/mec.17262
Journal article
see the publicationDescription of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov
Systematic and Applied Microbiology . 47 ( 2-3 ) : 126497
Journal article
see the publicationMicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation
International Journal of Molecular Sciences . 25 ( 2 ) : 880
DOI: 10.3390/ijms25020880
Journal article
see the publicationRandom genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
eLife . 13 : RP93629
Journal article
see the publicationA first step towards the characterization of endogenous retroviruses’ evolutionary history and impact on small ruminant genomes
CNET 2023 : 24th National Congress on Transposable Elements 2023 .
Conference paper
see the publicationOVINE β-ENDOGENOUS RETROVIRUSES : FROM INTEGRATION TO COPY-SPECIFIC TRANSCRIPTION
XXVèmes Journées Francophones de Virologie .
Poster
see the publicationMitigation of the diagenesis risk in biological apatite δ18O interpretation
Palaeogeography, Palaeoclimatology, Palaeoecology . 630 : 111812
Journal article
see the publicationδ2H and δ18O of river water from a high-altitude humid plain of the southern Alps: Implications for the interpretation of the isotopic compositions of bioapatite from humans living close to mountain areas
Journal of Archaeological Science: Reports . 49 : 104020
Journal article
see the publicationGenomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand
Nature Communications . 14 ( 1 ) : 8527
Journal article
see the publicationGenome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry
Science Advances . 9 ( 38 )
Journal article
see the publication