COEVOL Multi-Scale Coevolution

Evolutionary Genetics of Interactions Group

The Cocoon Group

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 691 to 720 publications on 766 in total

Wolbachia infections in Drosophila melanogaster and D. simulans: polymorphism and levels of cytoplasmic incompatibility

H. Merçot, S. Charlat

Genetica . 120 : 51-59

Journal article

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Wolbachia transfer from Rhagoletis cerasi to Drosophila simulans: investigating the outcomes of host-symbiont coevolution

M. Riegler, S. Charlat, C. Stauffer, H. Merçot

Applied and Environmental Microbiology . 70 : 273-279

Journal article

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Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli

Vincent Daubin, H. Ochman

Genome Research . 14 : 1036-1042

Journal article

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Start-up entities in the origin of new genes

Vincent Daubin, H. Ochman

Current Opinion in Genetics and Development . 14 : 616-619

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Quartet mapping and the extent of lateral transfer in bacterial genomes

Vincent Daubin, H. Ochman

Molecular Biology and Evolution . 21 : 86-89

Journal article

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Sorting by reversals in subquadratic time

Eric Tannier, Marie-France Sagot

Report

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L`influence des éléments transposables sur la taille des génomes

C. Biémont, Cristina Vieira

Journal de la Société de Biologie . 198 : 413-417

Journal article

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Variation of the genome size estimate with environmental conditions in Drosophila melanogaster.

Christiane Nardon, Michèle Weiss, Cristina Vieira, Christian Biémont

Cytometry Part A . 55 ( 1 ) : 43-9

DOI: 10.1002/cyto.a.10061

Journal article

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Reduction in the sex ratio of the progeny of a parasitoid wasp (Trichogramma brassicae) surviving the insecticide chlorpyrifos

Jean-Marie Delpuech, J. Meyet

Archives of Environmental Contamination and Toxicology . 45 : 203-208

Journal article

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Divergent strategies in low temperature environment for the sibling species Drosophila melanogaster and D. simulans: Overwintering in extension border areas of France and comparison with African populations

J. Boulétreau-Merle, P. Fouillet, Julien Varaldi

Evolutionary Ecology . 17 : 523-548.

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Phenotypic plasticity of sternopleural bristle number in temperate and tropical populations of Drosophila melanogaster

B. Moreteau, Patricia Gibert, Jean-Marie Delpuech, G. Petavy, J.R. David

Genetical Research . 81 : 25-32

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Strain-specific regulation of intracellular Wolbachia density in multiply infected insects

L. Mouton, H. Henri, M. Boulétreau, F. Vavre

Molecular Ecology . 12 : 3459-3465

Journal article

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Wolbachia segregation dynamics and levels of cytoplasmic incompatibility in Drosophila sechellia

S. Charlat, P. Bonnavion, H. Mercot

Heredity . 90 : 157-161

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Characterization of non-cytoplasmic incompatibility inducing Wolbachia in two continental African populations of Drosophila simulans

S. Charlat, L. Le Chat, H. Merçot

Heredity . 90 : 49-55

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Evolutionary consequences of Wolbachia infections

S. Charlat, D. Hurst G.D., H. Mercot

Trends in Genetics . 19 : 217-223

Journal article

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G+C3 structuring along the genome: a common feature in prokaryotes

Vincent Daubin, G. Perrière

Molecular Biology and Evolution . 20 : 471-483

Journal article

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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

Emmanuelle Lerat, Vincent Daubin, Nancy Moran

PLoS Biology . 1 ( 1 ) : 101-109

DOI: 10.1371/journal.pbio.0000019

Journal article

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The source of laterally transferred genes in bacterial genomes

Vincent Daubin, E. Lerat, G. Perrière

Genome Biology . 4 : R57.1-R57.12

Journal article

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Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

C. Nardon, M. Weiss, Cristina Vieira, C. Biémont

Cytometry - Part A . 55A : 43-49

Journal article

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Infectious behavior in a parasitoid

Julien Varaldi, P. Fouillet, M. Ravallec, M. Lopez-Ferber, M. Boulétreau, Frédéric Fleury

Science . 302 ( 5652 ) : 1930

DOI: 10.1126/science.1088798

Journal article

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Between- and within-host species selection on cytoplasmic incompatibility-inducing Wolbachia in haplodiploids

F. Vavre, P. Fouillet, Frédéric Fleury

Evolution - International Journal of Organic Evolution . 57 : 421-427

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On the mechanism of Wolbachia-induced cytoplasmic incompatibility: confronting the models with the facts

D. Poinsot, S. Charlat, H. Mercot

BioEssays . 25 : 259-265

Journal article

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On a modular domination game

S. Gravier, M. Mhalla, Eric Tannier

Theoretical Computer Science . 306 : 291-303

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Worldwide distribution of transposable element copy number in natural populations of Drosophila simulans

C. Biémont, C. Nardon, G. Deceliere, D. Lepetit, C. Loevenbruck, Cristina Vieira

Evolution - International Journal of Organic Evolution . 57 : 159-167

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WORLDWIDE DISTRIBUTION OF TRANSPOSABLE ELEMENT COPY NUMBER IN NATURAL POPULATIONS OF DROSOPHILA SIMULANS

Christian Biémont, Christiane Nardon, Grégory Deceliere, David Lepetit, Catherine Lœvenbruck, Cristina Vieira

Evolution - International Journal of Organic Evolution . 57 ( 1 ) : 159-167

DOI: 10.1111/j.0014-3820.2003.tb00225.x

Journal article

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Stimulating effects of the insecticide chlorpyrifos on host searching and infestation efficacy of a parasitoid wasp.

Halitiana Rafalimanana, Laure Kaiser, Jean-Marie Delpuech

Pest Management Science . 58 ( 4 ) : 321-328

DOI: 10.1002/ps.454

Journal article

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Stimulating effects of the insecticide chlorpyrifos on host searching and infestation efficacy of a parasitoid wasp

H. Rafalimanana, L. Kaiser, Jean-Marie Delpuech

Pest Management Science . 58 : 321-328

Journal article

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Infection polymorphism and cytoplasmic incompatibility in Hymenoptera-Wolbachia associations

F. Vavre, Frédéric Fleury, Julien Varaldi, P. Fouillet, M. Boulétreau

Heredity . 88 : 361-365

Journal article

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