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 601 to 630 publications on 747 in total

Reverse Arrangement of rRNA Subunits in the Microsporidium Glugoides intestinalis

D. Refardt, L. Mouton

Journal of Eukaryotic Microbiology . 54 : 83-85

Journal article

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Insertion polymorphism of transposable elements and population structure of Anopheles gambiae M and S molecular forms in Cameroon

M. Boulesteix, F. Simard, C. Antonio-Nkondjio, P. Awono-Ambene, D. Fontenille, C. Biémont

Molecular Ecology . 16 : 441-452

Journal article

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Disrupting the timing of Wolbachia-induced male-killing

S. Charlat, N. Davies, G.K. Roderick, G.D. Hurst

Biology Letters . 3 : 154-156

Journal article

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Extraordinary flux in sex ratio

S. Charlat, E.A. Hornett, J.H. Fullard, N. Davies, G.K. Roderick, N. Wedell...

Science . 317 : 214-214

Journal article

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When can host shifts produce congruent host and parasite phylogenies? A simulation approach

Damien M de Vienne, Tatiana Giraud, J A Shykoff

Journal of Evolutionary Biology . 20 ( 4 ) : 1428--1438

Journal article

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Comparative genomics and the evolution of prokaryotes

Sophie S. Abby, Vincent Daubin

Trends in Microbiology . 15 : 135-141

Journal article

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Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Philippe Normand, Pascal Lapierre, Louis S. Tisa, Johann Peter Gogarten, Nicole Alloisio, Emilie Bagnarol...

Genome Research . 17 : 7-15

DOI: 10.1101/gr.5798407

Journal article

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Grinding up wheat: a massive loss of nucleotide diversity since domestication

A. Haudry, A. Cenci, C. Ravel, T. Bataillon, D. Brunel, C. Poncet...

Molecular Biology and Evolution . 24 : 1506-1517

Journal article

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Mitspieler der Evolution

C. Biémont, Cristina Vieira

Spektrum der Wissenschaft . S44 : 44-49

Journal article

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Effective Stochastic Local Search Algorithms for the Genomic Median Problem

Renaud Lenne, Christine Solnon, Thomas Stützle, Eric Tannier, Mauro Birattari

Doctoral Symposium on Engineering Stochastic Local Search Algorithms (SLS-DS) . : 1-5

Conference paper

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Impacts d’événements démographiques et sélectifs sur la diversité des plantes cultivées: apports de l’analyse du polymorphisme alliée à la théorie de la coalescence

Thomas Bataillon, Nathalie N. Chantret, Alberto Cenci, Marie-Françoise Gautier, Philippe Joudrier, Annabelle Haudry...

Actes du BRG . 6 : 243-257

Journal article

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A Markovian Approach for the Analysis of the Gene Structure

C. Melodelima, Laurent Guéguen, Christian Gautier, D. Piau

Prague stringology conference . 19 ( 1 ) : 19-35

Conference paper

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A computational prediction of isochores based on hidden Markov models

C. Melodelima, Laurent Guéguen, D. Piau, Christian Gautier

Gene . 385 : 41-49

Journal article

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Artifical transfer and morphological description of virus particles associated with superparasitism behaviour in a parasitoid wasp.

Julien Varaldi, M. Ravallec, C. Labrosse, M. Lopez-Ferber, M. Boulétreau, Frédéric Fleury

Journal of Insect Physiology . 52 ( 11-12 ) : 1202-1212

DOI: 10.1016/j.jinsphys.2006.09.002

Journal article

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Superparasitism evolution: adaptation or manipulation?

Sylvain Gandon, Ana R Rivero, Julien Varaldi

The American Naturalist . 167 ( 1 ) : E1-E22

DOI: 10.1086/498398

Journal article

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The virus infecting the parasitoid Leptopilina boulardi exerts a specific action on superparasitism behaviour

Julien Varaldi, S. Petit, M. Boulétreau, Frédéric Fleury

Parasitology . 132 : 747-756

Journal article

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Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans

M. Fablet, J.F. Donald, C. Biémont, Cristina Vieira

Gene . 375 : 54-62

Journal article

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Differences in genome size between closely related species: the Drosophila melanogaster species subgroup.

Matthieu Boulesteix, Michèle Weiss, Christian Biémont

Molecular Biology and Evolution . 23 ( 1 ) : 162-7

DOI: 10.1093/molbev/msj012

Journal article

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Outbreeding selects for spiteful cytoplasmic elements

J. Engelstädter, S. Charlat

Proceedings of the Royal Society B: Biological Sciences . 273 : 923-929

Journal article

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Evolution of Male Killer Suppression in a Natural Population

E.A. Hornett, S. Charlat, A.M.R. Duplouy, N. Davies, G.K. Roderick, N. Wedell...

PLoS Biology . 4 : 1643-1648

Journal article

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The evolution of cytoplasmic incompatibility types: integrating segregation inbreeding and outbreeding

J. Engelstädter, S. Charlat, A. Pomiankowski, D. Hurst G.D.

Genetics . 172 : 2601-2611

Journal article

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Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury, Olivier Jaillon, * Laurent Duret, Benjamin Noel, Claire Jubin, Betina M. Porcel...

Nature . 444 ( 7116 ) : 171-178

DOI: 10.1038/nature05230

Journal article

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Ageing and the evolution of female resistance to remating in seed beetles

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

Biology Letters . 2 : 62-64

Journal article

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Unicoloniality recognition and genetic differentiation in a native Formica ant

B. Holzer, M. Chapuisat, N. Kremer, C. Finet, L. Keller

Journal of Evolutionary Biology . 19 : 2031-2039

Journal article

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UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

L. Palmeira, Laurent Guéguen, J.R. Lobry

Molecular Biology and Evolution . 23 : 2214-2219

Journal article

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A Newly Discovered Virus Manipulates Superparasitism Behavior in a Parasitoid Wasp

Julien Varaldi, S. Gandon, A. Rivero, S. Patot, Frédéric Fleury

incollection . 2 : 119-139

Journal article

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Effect of temperature on Wolbachia density and impact on cytoplasmic incompatibility

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

Parasitology . 132 : 49-56

Journal article

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Differences in Genome Size Between Closely Related Species : The Drosophila melanogaster Species Subgroup

M. Boulesteix, M. Weiss, C. Biémont

Molecular Biology and Evolution . 23 : 162-167

Journal article

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Differences in genom size between closely related species : the drosophila melanogaster species subgroup.

M. Boulesteix, M. Weiss, C. Biemont

Molecular Biology and Evolution . ( 23 ) : 162-167

Journal article

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