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
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
Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Stagiaire
UCBL
Doctorante
UCBL
Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60
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 1 to 30 publications on 907 in total
The genetic legacy of the expansion of Bantu-speaking peoples in Africa
Nature . 625 : 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 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 publicationSouth Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture
PLoS ONE . 18 ( 9 ) : e0291547
Journal article
see the publicationThe genomic diversity of Taiwanese Austronesian groups: Implications for the “Into- and Out-of-Taiwan” models
PNAS Nexus . 2 ( 5 )
Journal article
see the publicationGenomic perspectives on human dispersals during the Holocene
Proceedings of the National Academy of Sciences of the United States of America . 120 ( 4 )
Journal article
see the publicationMicroAnnot: 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 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 publicationAssessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition
Molecular Biology and Evolution . 39
Journal article
see the publicationAncient genomes from the last three millennia support multiple human dispersals into Wallacea
Nature Ecology & Evolution . 6 : 1024 - 1034
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 publication