COEVOL Multi-Scale Coevolution
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.
Integrating methods
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.
Publications
Display of 1 to 30 publications on 595 in total
A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
Systematic Biology . 70 ( 3 ) : 608-622
Articles
see the publicationDROP: Molecular voucher database for identification of Drosophila parasitoids
Molecular Ecology Resources .
Articles
see the publicationThe worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions
Molecular Biology and Evolution .
Articles
see the publicationWolbachia load variation in Drosophila is more likely caused by drift than by host genetic factors
Peer Community in Evolutionary Biology .
Articles
see the publicationChromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
Communications Biology . 4 ( 1 )
Articles
see the publicationSeaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
Multiple Sequence Alignment . 2231 : 241-260
Book chapters
see the publicationReconciling Gene trees with Species Trees
Phylogenetics in the Genomic Era . : 3.2:1--3.2:23
Book chapters
see the publicationDGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes
Nucleic Acids Research . 48 ( 18 ) : e103-e103
DOI: 10.1093/nar/gkaa680
Articles
see the publicationL’épistémologie des sciences biologiques et géologiques : une occasion d’enseigner l’incertitude ?
Raisons éducatives . N°24
Articles
see the publicationWolbachia host shifts: routes, mechanisms, constraints and evolutionary consequences
Biological Reviews .
DOI: 10.1111/brv.12663
Articles
see the publicationGenome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes
Current Biology - CB . 30 ( 19 ) : R1083-R1085
Articles
see the publicationSuperparasitism by a parasitoid wasp: The absence of sublethal effects from the neonicotinoid insecticide imidacloprid enlightens the specificity of the cholinergic pathway involved
Ecotoxicology and Environmental Safety . 201
Articles
see the publicationHow consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?
Molecular Ecology Resources . 20 ( 5 ) : 1294-1298
Articles
see the publicationGenomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
Molecular Biology and Evolution .
Articles
see the publicationExperimental evolution of virulence and associated traits in a Drosophila melanogaster - Wolbachia symbiosis
Peer Community in Evolutionary Biology .
Articles
see the publicationSuperparasitism by a parasitoid wasp: The absence of sublethal effects from the neonicotinoid insecticide imidacloprid enlightens the specificity of the cholinergic pathway involved
Ecotoxicology and Environmental Safety . 201 : 110809
Articles
see the publicationEndosymbiont diversity in natural populations of Tetranychus mites is rapidly lost under laboratory conditions
Heredity . 124 ( 4 ) : 603-617
Articles
see the publicationGenomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses
Molecular Biology and Evolution . 37 ( 9 ) : 2661-2678
Articles
see the publicationHomology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
Genes . 11 ( 2 ) : 170
Articles
see the publicationEvolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
BMC Biology . 18 ( 1 ) : 1-20
Articles
see the publicationAncestral Genome Organization as a Diagnosis Tool for Phylogenomics
Phylogenetics in the Genomic Era . : 2.5:1--2.5:19
Book chapters
see the publicationTreerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Articles
see the publicationA transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore
Cells .
DOI: 10.3390/cells9081776
Articles
see the publicationCombining sterile and incompatible insect techniques for the population suppression of Drosophila suzukii
Journal of Pest Science . 93 ( 2 ) : 647 - 661
Articles
see the publicationStress & Symbiosis: Heads or Tails?
Frontiers in Ecology and Evolution . : 1-9
Articles
see the publicationA behavior-manipulating virus relative as a source of adaptive genes for Drosophila parasitoids
Molecular Biology and Evolution . 37 ( 10 ) : 2791-2807
Articles
see the publicationCAARS: comparative assembly and annotation of RNA-Seq data
Bioinformatics . 35 ( 13 ) : 2199-2207
Articles
see the publicationL'enseignement de l'évolution : redonner une place à l'épistémologie des sciences historiques
RDST - Recherches en didactique des sciences et des technologies .
Articles
see the publicationTracing Human Ancestral Migrations Using Symbiotic Bacteria
Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .
Congress proceedings
see the publication