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, …).
Display of 1 to 30 publications on 160 in total
Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
Plos Biology . 19 ( 7 ) : e3001309
DILS: Demographic inferences with linked selection by using ABC
Molecular Ecology Resources .
Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species
Genome Biology and Evolution . ( evaa258 )
Bedrock radioactivity influences the rate and spectrum of mutation
eLife . 9 : e56830
How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?
Molecular Ecology Resources . 20 ( 5 ) : 1294-1298
Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest
Evolutionary Applications . 13 : 1-16
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Genome Biology . 20 ( 1 )
Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints
Nucleic Acids Research . 47 ( 10 ) : 5114-5125
Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites
Molecular Cell . 69 ( 5 ) : 853 - 865.e6
Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
Molecular Biology and Evolution . 35 ( 3 ) : 734-742
Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods
Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912
Codon 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
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Genome Biology . 18 ( 1 )
The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Philosophical Transactions of the Royal Society B: Biological Sciences .
In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
Genome Research . 27 ( 4 ) : 580-590
Less effective selection leads to larger genomes
Genome Research . 27 : 1016-1028
Recombination, meiotic expression and human codon usage
eLife . 6 : e27344
The global impact of Wolbachia on mitochondrial diversity and evolution
Journal of Evolutionary Biology .
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes
Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620
How and how much does RAD-seq bias genetic diversity estimates?
BMC Evolutionary Biology . 16 : 240
Optimization of multiplexed RADseq libraries using low-cost adaptors
Genetica . 143 ( 2 ) : 139-143
Occurrence of a non deleterious gene conversion event in the BRCA1 gene
Genes, Chromosomes and Cancer . 54 : 646-52
Quantification of GC-biased gene conversion in the human genome
Genome Research . 25 ( 8 ) : 1215 - 1228
GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands
PLoS Genetics . 11 ( 2 ) : 1-20
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.
PLoS Genetics . 10 ( 5 ) : e1004282
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome
Molecular Biology and Evolution . 31 : 23-36
The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes
PLoS Genetics . 10 : e1004790
Comparative population genomics in animals uncovers the determinants of genetic diversity
Nature . 515 ( 7526 ) : 261-263
XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells
Epigenetics and Chromatin: Interactions and processes . 6 ( Suppl 1 ) : O33