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
Stagiaire
UCBL
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
Stagiaire
UCBL
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
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 271 to 300 publications on 948 in total
Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum
BMC Genomics . 16 : 833
Journal article
see the publicationExtending the conserved phylogenetic core of \textitarchaea disentangles the evolution of the third domain of life
Molecular Biology and Evolution . 32 : 1242-54
Journal article
see the publicationConstitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11
Research in Microbiology . 166 : 205-14
Journal article
see the publicationDegeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Molecular Biology and Evolution . 32 ( 4 ) : 928-943
Journal article
see the publicationChaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae
Genetics . 200 ( 4 ) : 1275-1284
Journal article
see the publicationSex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
BMC Genomics . 16 ( 461 ) : np
Journal article
see the publicationAn evolutionary link between capsular biogenesis and surface motility in bacteria
Nature Reviews Microbiology . 13 ( 5 ) : 318--326
DOI: 10.1038/nrmicro3431
Journal article
see the publicationThe two-domain tree of life is linked to a new root for the Archaea
Proceedings of the National Academy of Sciences of the United States of America . 112 : 6670-6675
Journal article
see the publicationThe Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes
PLoS ONE . 10 ( 9 ) : 1-12
Journal article
see the publicationAssessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome
Genome Biology and Evolution . 7 : 2432-44
DOI: 10.1093/gbe/evv155
Journal article
see the publicationProbabilistic models of eukaryotic evolution: time for integration
Philosophical Transactions of the Royal Society B: Biological Sciences . 370 ( 1678 ) : 20140338
Journal article
see the publicationGenomic data do not support comb jellies as the sister group to all other animals
Proceedings of the National Academy of Sciences of the United States of America . 112 ( 50 ) : 15402-15407
Journal article
see the publicationToward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees
Molecular Biology and Evolution . 32 : 13-22
Journal article
see the publicationOccurrence of a non deleterious gene conversion event in the BRCA1 gene
Genes, Chromosomes & Cancer . 54 : 646-52
DOI: 10.1002/gcc.22278
Journal article
see the publicationEstimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing
Nucleic Acids Research . 42 ( 14 ) : 9121-30
DOI: 10.1093/nar/gku639
Journal article
see the publicationTracing Pastoralist Migrations to Southern Africa with Lactase Persistence Alleles
Current Biology - CB . 24 ( 8 ) : 875-879
Journal article
see the publicationAncient west Eurasian ancestry in southern and eastern Africa
Proceedings of the National Academy of Sciences of the United States of America . 111 ( 7 ) : 2632-2637
Journal article
see the publicationUnraveling the complex maternal history of southern African Khoisan populations
American Journal of Physical Anthropology . 153 ( 3 ) : 435-448
Journal article
see the publicationNew insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa
American Journal of Physical Anthropology . 156 ( 4 ) : 661-664
Journal article
see the publicationMigration and Interaction in a Contact Zone: mtDNA Variation among Bantu-Speakers in Southern Africa
PLoS ONE . 9 ( 6 ) : e99117
Journal article
see the publicationA high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
Molecular Ecology . 23 ( 16 ) : 4035-4058
DOI: 10.1111/mec.12810
Journal article
see the publicationWhy Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS
Molecular Biology and Evolution . 31 ( 1 ) : 212-231
Journal article
see the publicationPreserving immune diversity through ancient inheritance and admixture
Current Opinion in Immunology . 30 : 79-84
Journal article
see the publicationDeterminants of Mutation Rate Variation in the Human Germline
Annual Review of Genomics and Human Genetics . 15 ( 1 ) : 47-70
Journal article
see the publicationTroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception
Bioinformatics . 30 ( 14 ) : 2035-2042
Journal article
see the publicationMicrosatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia
European Journal of Human Genetics . 22 ( 10 ) : 1201-1207
DOI: 10.1038/ejhg.2014.2
Journal article
see the publicationA call for benchmarking transposable element annotation methods.
Mobile DNA . 6 : 13
Journal article
see the publicationSubcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells
PLoS ONE . 9 ( 3 ) : e92039
Journal article
see the publicationThe spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.
PLoS Genetics . 10 ( 5 ) : e1004282
Journal article
see the publicationThe Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes
PLoS Genetics . 10 : e1004790
Journal article
see the publication