Living systems are highly integrated, with a multitude of levels of organization, from molecular and intra-cellular scales to ecosystems. Complex organisms are themselves consortia of macro- and micro-organisms, which work together with their host to build the individual. Yet, each of these organisms can function and evolve in the short term according to its own logic, possibly in conflict with other higher or lower levels, or with other time scales. The once common idea among evolutionists that natural selection results in organisms perfectly adapted to their environment is now severely undermined. Not only because, as the Red Queen explains to Alice, one has to run relentlessly to keep its place in a changing environment, or because past evolutionary history and chance constrain the possibilities of present adaptation, but also because different levels of selection have interests that are generally difficult to reconcile.
Multi-scale coevolution resets classical questions in evolutionary biology
One example, of particular interest is the question of the source of heritable variations. The phenotype of organisms in a population is influenced not only by variations in their nuclear and mitochondrial genomes, the dynamics of which is the object of population genetics, but also more and more patently by the consortium of microbes and genetic elements that constitute its microbiome and virome. The hologenome designates this complex assembly of genetic materials, which obey different rules of transmission and different evolutionary strategies. The ability of symbionts to manipulate host phenotypes or to interfere with each other influences the evolutionary dynamics of all players in ways that are yet poorly understood. In addition, new questions arise, such as the importance of co-adaptation in these systems and their consequences in maintaining cohesive biological systems.
- Symbiosis: a response to and a source of divergent selection
Using a variety of approaches combining experimental evolution, genomic, functional, phenotypic and behavioral data, we aim to test whether symbiosis facilitates diversification and to characterize the underlying microevolutionary processes.
- Ecological networks of horizontal gene transfer
We develop original methods to detect gene transfer and we investigate the factors that influence the routes of gene transfers among microbes but also among insects.
- The interplay between symbiosis, infection and immunity and its evolutionary consequences
We try to understand the intimate interaction of hosts with pathogens, symbionts and transposable elements and how it affects the extended phenotype of the host.
- Transgenerational inheritance and environment changes
We try to decipher the molecular mechanisms that underlie rapid adaptation to environment and to test for transgenerational inheritance of fitness traits.
- Intragenomic conflicts and demography
We are developing models to test whether changes in the demography of the host affect the dynamics of transposable elements.
- The determinism of phenotypic convergence
We study the genomic basis of convergent phenotypic evolution in particular in the case of animals and plants adaptation to increasing temperature and decreasing water.
- Reconciling the tree of life
We develop phylogenetic methods for “reconciling” gene/species or host/symbiont histories and use these methods to explore the bulk of extinct or undescribed species and the history of association of symbiotic microbes with their hosts.
The methods we use to tackle the questions raised by multi-scale co-evolution extend from theory, modelling and simulation to big data analysis, lab (notably on insects), and to a lesser extent, field activities.
Implication of research, responsibility of researchers and citizen sciences
From our research (some of which have immediate consequences in health, agriculture and ecology) and our concerns about the responsibility of scientists in society, we are committed to promote an “implicative” research. The implicative position means that we try to work on the link between science and society, not only through a one-way communication, applying or explaining our science, but also favoring early discussions on research projects, that may influence our research directions.
Display of 1 to 30 publications on 676 in total
An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event
Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale
Molecular Biology and Evolution . 40 ( 2 )
Approche globale des éthiques dans les relations sociétés/nature
A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius
Evolutionary Applications . 16 ( 5 ) : 1012 - 1028
Nutritional symbioses in triatomines: who is playing?
Peer Community in Evolutionary Biology . : 100629
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura
Genome Biology and Evolution . 15 ( 11 )
Sex differences in adult lifespan and aging rate across mammals: A test of the ‘Mother Curse hypothesis’
Mechanisms of Ageing and Development . 212 : 111799
Dual control of host actin polymerization by a Legionella effector pair
A quantitative, genome-wide analysis in Drosophila reveals transposable elements’ influence on gene expression is species-specific
Genome Biology and Evolution . 15 ( 9 ) : evad160
ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements
Nucleic Acids Research .
Les punaises de lit : impacts, prévention et lutte
: 257 p.
Plant choice for oviposition in the phytophagous insect Bemisia tabaci: cytotype, including symbionts, knows best!
Animal Behaviour . 200 : 147-157
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
eLife . 12 : e85993
Back to the trees: Identifying plants with Human Intelligence
LIMITS 2023 - Ninth Workshop on Computing within Limits . : 1-11
RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae)
Microbial ecology .
The for gene as one of the drivers of foraging variations in a parasitic wasp
Molecular Ecology . 32 ( 7 ) : 1760-1776
Se réapproprier la production de connaissance
AOC [Analyse Opinion Critique] . : https://aoc.media/opinion/2023/05/17/se-reapproprier-la-production-de-connaissance/
Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum
Peer Community Journal . 3 : e41
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Molecular Biology and Evolution .
Genomic characterization of viruses associated with the parasitoid Anagyrus vladimiri (Hymenoptera: Encyrtidae)
Host-symbiont-gene phylogenetic reconciliation
Peer Community Journal . : 1-22
(Epi)mutation rates and the evolution of composite trait architectures
The crisis of the scientific mind : an investigation, a tragedy and a collective redistribution of roles
Les Cahiers de Framespa : e-Storia . ( 40 )
Calculs d’inférence dans les arbres phylogénétiques
Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202
Influence of bacterial symbionts on host niche and ecological diversification: an integrative approach in a whitefly model
26.International Congress of Entomology .
Analyses of symbiotic bacterial communities in the plant pest Bemisia tabaci reveal high prevalence of Candidatus Hemipteriphilus asiaticus on the African continent
Peer Community Journal . 2
Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria
Genome Biology and Evolution . 14 ( 4 ) : evac035
Adaptation to host cell environment during experimental evolution of Zika virus
Communications Biology . 5 ( 1 ) : 1115