GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Duret Laurent
Directeur de recherche
CNRS
Batiment Mendel 2eme étage. Bureau 12.025
Genomes are the product of various evolutionary processes: certain genomic traits that we observe today reflect functional constraints that currently operate or that have operated in the past; others result from non-adaptive processes. To identify the features of the genome that are important for its functioning, it is necessary to look for features whose mode of evolution deviates from the neutralist model: this is the basic principle of the comparative analysis of genomes, which is at the heart of all my research activity. My work follows a double logic: study the evolution of genomes to better understand how they work - and vice versa, take into account the molecular mechanisms of genome functioning in order to better interpret sequence evolution. We explore genetic diversity at different level, both across species and within species (population genomics). My work is based on bioinformatic and statistical analysis of sequences, but also relies heavily on close collaborations with ‘wet-lab' biologists.
These last years, my main focus has been on exploring the consequences of homologous recombination on genome evolution. In particular, we have discovered that in many species, recombination induces non-Mendelien inheritance, favoring the fixation of GC-alleles (gBGC – for GC-Biased Gene Conversion). This non-adaptive process has a major impact on the evolution of genomic landscapes and also on gene expression processes. We are now trying to understand how and why does gBGC evolve, and how and why do recombination rates vary in space (along chromosomes) and in time (across species).
I am also interested in understanding how the constraints imposed by the cost of gene expression shape genome evolution. We have shown that gene expression level is an important determinant of selective pressures acting on numerous features: on protein sequences, on gene dosage, on splicing accuracy, and on translation efficiency. We are now exploring how variation in the efficacy of selection contributes to the evolution of the complexity of gene expression patterns across species.
I am also working, in collaboration with researchers from Paris and Gif, on the genomics of Paramecia. This unicellular eukaryote displays many very peculiar features that make it a fantastic model to explore various topics (whole genome duplications, proliferation of selfish genetic elements, alternative splicing, transgenerational inheritance of epigenetic modifications, …).
Publications
Display of 1 to 30 publications on 174 in total
Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis.
RecomBern .
Conference paper
see the publicationHigh prevalence of Prdm9-independent recombination hotspots in placental mammals
Probabilistic Modeling in Genomics Conference : ProbGen 2024 .
Conference paper
see the publicationPrevalence of PRDM9-dependent vs PRDM9-independent recombination hotspots in animals
RecomBern .
Conference paper
see the publicationVariation in the fitness impact of translationally optimal codons among animals
Preprint
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 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 publicationPRDM9 drives the location and rapid evolution of recombination hotspots in salmonids
Preprint
see the publicationRandom genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
eLife . 13 : RP93629
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
PLoS Genetics . 20 ( 5 ) : e1011274
Journal article
see the publicationPopulation designations in biomedical research: limitations and perspectives
HLA: Immune Response Genetics . 101 ( 1 ) : 3-15
DOI: 10.1111/tan.14852
Journal article
see the publicationDILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Journal article
see the publicationMassive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
PLoS Biology . 19 ( 7 ) : e3001309
Journal article
see the publicationEvolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species
Genome Biology and Evolution . ( evaa258 )
DOI: 10.1093/gbe/evaa258
Journal article
see the publicationHow consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?
Molecular Ecology Resources . 20 ( 5 ) : 1294-1298
Journal article
see the publicationPopulation genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest
Evolutionary Applications . 13 : 442-457
DOI: 10.1111/eva.12881
Journal article
see the publicationBedrock radioactivity influences the rate and spectrum of mutation
eLife . 9 : e56830
DOI: 10.7554/eLife.56830
Journal article
see the publicationNaturally radioactive environments influence the rate and spectrum of mutation
Annual conference of the Society for Molecular Biology and Evolution .
Poster
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 publicationGC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Genome Biology . 20 ( 1 )
Journal article
see the publicationEvolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints
Nucleic Acids Research . 47 ( 10 ) : 5114-5125
DOI: 10.1093/nar/gkz182
Journal article
see the publicationUnbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
Molecular Biology and Evolution . 35 ( 3 ) : 734-742
Journal article
see the publicationLife History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods
Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912
Journal article
see the publicationPRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites
Molecular Cell . 69 ( 5 ) : 853 - 865.e6
Journal article
see the publicationCodon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion
Molecular Biology and Evolution . 35 ( 5 ) : 1092 - 1103
Journal article
see the publicationThe Red Queen model of recombination hot-spot evolution: a theoretical investigation
Philosophical Transactions of the Royal Society B: Biological Sciences .
Journal article
see the publicationThe global impact of Wolbachia on mitochondrial diversity and evolution
Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210
DOI: 10.1111/jeb.13186
Journal article
see the publicationRecombination, meiotic expression and human codon usage
eLife . 6 : e27344
Journal article
see the publicationIn vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
Genome Research . 27 ( 4 ) : 580-590
Journal article
see the publicationThe fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Genome Biology . 18 : 208
Journal article
see the publicationLess effective selection leads to larger genomes
Genome Research . 27 : 1016-1028
Journal article
see the publication