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 661 to 690 publications on 768 in total

Prevalence and penetrance variation of male-killing Wolbachia across Indo-Pacific populations of the butterfly Hypolimnas bolina

S. Charlat, E.A. Hornett, E.A. Dyson, P.P. Ho, N.T. Loc, M. Schilthuizen...

Molecular Ecology . 14 : 3525-3530

Journal article

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Evolutionary origins of genomic repertoires in bacteria

E. Lerat, Vincent Daubin, H. Ochman, N.A. Moran

PLoS Biology . 3 : 0807-0814

Journal article

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Perfect Sorting by Reversals

Marie-France Sagot, Eric Tannier

: 13

Report

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Is genome size influenced by colonization of new environments in dipteran species ?

C. Nardon, G. Deceliere, C. Loevenbruck, M. Weiss, Cristina Vieira, C. Biémont

Molecular Ecology . 14 : 869-878

Journal article

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New regulatory regions of Drosophila 412 retrotransposable element generated by recombination

N. Mugnier, C. Biémont, Cristina Vieira

Molecular Biology and Evolution . 22 : 747-757

Journal article

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Adaptive male effects on female ageing in seed beetles

A.A. Maklakov, N. Kremer, G. Arnqvist

Proceedings of the Royal Society B: Biological Sciences . 272 : 2485-2489

Journal article

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Wolbachia requierement for oogenesis : occurence within the genus Asobara (Hynoptera, Braconidae) and evidence for intraspecific variation in A. tabida.

F. Dedeine, F. Vavre, M. Bouletreau

Heredity . 95 : 394-400

Journal article

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Superparasitism acceptance and patch-leaving mechanisms in parasitoids: A comparison between two sympatric wasps

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

Animal Behaviour . 69 : 1227-1234

Journal article

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Cost induced by viral particles manipulating superparasitism behaviour in the parasitoid Leptopilina boulardi

Julien Varaldi, M. Boulétreau, Frédéric Fleury

Parasitology . 131 : 161-168

Journal article

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Évaluation des effets sublétaux d'insecticides sur des insectes auxiliaires entomophages

Laure Kaiser, Jean-Marie Delpuech, Jean-Noël Reboulet, Nicolas Desneux, Halitiana Rafalimanana, Marcel Thaon...

incollection . -- : 85-96

Journal article

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Efficient procedure for purification of obligate intracellular Wolbachia pipientis and representative amplification of its génome by multiple-pisplacement amplification

Patrick Mavingui, Van Tran Van, Estelle Labeyrie, Edwige Rancès, Fabrice Vavre, Pascal Simonet

Applied and Environmental Microbiology . 71 ( 11 ) : 6910-6917

DOI: 10.1128/AEM.71.11.6910-6917.2005

Journal article

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Wolbachia requirement for oogenesis: occurrence within the genus Asobara (Hymenoptera Braconidae) and evidence for intraspecific variation in A. tabida

F. Dedeine, M. Boulétreau, F. Vavre

Heredity . -- : 267-282

Journal article

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Exploring the evolution of Wolbachia compatibility types: a simulation approach

S. Charlat, C. Calmet, Olivier Andrieu, H. Mercot

Genetics . 170 : 495-507

DOI: 10.1534/genetics.103.015198

Journal article

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Interactions between inherited bacteria and their hosts: The Wolbachia paradigm

Z. Veneti, M. Reuter, H. Montenegro, E.A. Hornett, S. Charlat, D. Hurst G.D.

incollection . -- : 119-141

Journal article

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A bunch of fun-guys: the whole-genome view of yeast evolution

H. Ochman, Vincent Daubin, E. Lerat

Trends in Genetics . 21 : 1-3

Journal article

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Examining bacterial species under the specter of gene transfer and exchange

H. Ochman, E. Lerat, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 102 : 6595-6599

Journal article

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Perfect sorting by reversals

M.-F. Sagot, Eric Tannier

International Computing and Combinatorics Conference . 3595 : 42-51

DOI: 10.1007/11533719_7

Conference paper

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What transposable elements tell us about genome organization and evolution: the case of Drosophila

C. Biémont, Cristina Vieira

Cytogenetics and Genome Researchearch . 110 : 25-34

Journal article

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Cytogenetic mechanism and genetic consequences of thelytoky in the wasp Trichogramma cacoeciae

F. Vavre, J.H. de Jong, R. Stouthamer

Heredity . 93 : 592-596

Journal article

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Virulence multiple infections and regulation of symbiotic population in the Wolbachia-Asobara tabida symbiosis

L. Mouton, F. Dedeine, H. Henri, M. Boulétreau, N. Profizi, F. Vavre

Genetics . 168 : 181-189

Journal article

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, Bastien Boussau, V. Laudet

Molecular Biology and Evolution . 21 : 580-586

Journal article

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, B. Boussau, V. Laudet

Molecular Biology and Evolution . 21 ( 3 ) : 580-586

Journal article

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Incipient evolution of Wolbachia compatibility types

S. Charlat, M. Riegler, I. Baures, D. Poinsot, C. Stauffer, H. Mercot

Evolution - International Journal of Organic Evolution . 58 : 1901-1908

Journal article

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Natural Wolbachia infections in the Drosophila yakuba species complex do not induce cytoplasmic incompatibility but fully rescue the wRi modification

S. Zabalou, S. Charlat, A. Nirgianaki, D. Lachaise, H. Mercot, K. Bourtzis

Genetics . 167 : 827-34

Journal article

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What maintains noncytoplasmic incompatibility inducing Wolbachia in their hosts: a case study from a natural Drosophila yakuba population

S. Charlat, J.W. Ballard, H. Mercot

Journal of Evolutionary Biology . 17 : 322-330

Journal article

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Comment on "The origins of genome complexity

Vincent Daubin, N.A. Moran

Science . 306 : 978a-978a

Journal article

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Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test

M. Zelwer, Vincent Daubin

Molecular Phylogenetics and Evolution . 33 : 687-693

Journal article

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On Metric Generators of Graphs

András Sebő, Eric Tannier

Mathematics of Operations Research . 29 : 383-393

Journal article

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Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans

Cristina Vieira, C. Biémont

Genetica . 120 : 115-123

Journal article

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Diversity distribution and specificity of WO phage infection in Wolbachia of four insect species

L. Gavotte, F. Vavre, H. Henri, M. Ravallec, R. Stouthamer, M. Boulétreau

Insect Molecular Biology . 13 : 147-153

Journal article

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