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 181 to 210 publications on 748 in total

The Toxin–Antidote Model of Cytoplasmic Incompatibility: Genetics and Evolutionary Implications

John Beckmann, Manon Bonneau, Hongli Chen, Mark Hochstrasser, Denis Poinsot, Mylene Weill...

Trends in Genetics . 35 ( 3 ) : 175-185

DOI: 10.1016/j.tig.2018.12.004

Journal article

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Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence

Damien M. de Vienne

Molecular Biology and Evolution . 36 ( 1 ) : 174-176

DOI: 10.1093/molbev/msy196

Journal article

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Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Damir Hasic, Eric Tannier

Journal of Combinatorial Optimization . 38 ( 2 ) : 502–544

DOI: 10.1007/s10878-019-00396-z

Journal article

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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

Journal article

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

Journal article

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Widespread Wolbachia infection in an insular radiation of damselflies (odonata, coenagrionidae)

M O Lorenzo-Carballa, Y Torres-Cambas, K Heaton, G D D Hurst, S. Charlat, H Van Gossum...

Scientific Reports .

DOI: 10.1038/s41598-019-47954-3

Journal article

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Gene transfers can date the tree of life

Adrián Davín, Eric Tannier, Tom A Williams, Bastien Boussau, Vincent Daubin, Gergely Szöllősi

Nature Ecology & Evolution . 2 ( 5 ) : 904-909

DOI: 10.1038/s41559-018-0525-3

Journal article

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Théorie des codes - 3e édition

Jean-Guillaume Dumas, Jean-Louis Roch, Eric Tannier, Sébastien Varrette

9782100781096 : 416

Book

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Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways

Olivier Duron, Olivier Morel, Valérie Noël, Marie Buysse, Florian Binetruy, Renaud Lancelot...

Current Biology - CB . 28 ( 12 ) : 1896 - 1902.e5

DOI: 10.1016/j.cub.2018.04.038

Journal article

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Cancer Is Not (Only) a Senescence Problem

Frédéric Thomas, Fabrice Vavre, Tazzio Tissot, Marion Vittecoq, Mathieu Giraudeau, Florence Bernex...

Trends in Cancer . 4 ( 3 ) : 169 - 172

DOI: 10.1016/j.trecan.2018.01.002

Journal article

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Abundance of Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) and its parasitoids on vegetables and cassava plants in Burkina Faso (West Africa)

Rahim Romba, Olivier Gnankine, Samuel Fogné Drabo, Fidèle Tiendrébéogo, Hélène Henri, Laurence Mouton...

Ecology and Evolution . 8 ( 12 ) : 6091-6103

DOI: 10.1002/ece3.4078

Journal article

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Back and forth Wolbachia transfers reveal efficient strains to control spotted wing drosophila populations

Julien Cattel, Katerina Nikolouli, Thibault Andrieux, Julien Martinez, Francis Jiggins, Sylvain Charlat...

Journal of Applied Ecology . 55 ( 5 ) : 2408-2418

DOI: 10.1111/1365-2664.13101

Journal article

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The somatic piRNA pathway controls germline transposition over generations

Bridlin Barckmann, Marianne El-Barouk, Alain Pélisson, Bruno Mugat, Blaise Maxime Li, Céline Franckhauser...

Nucleic Acids Research . 46 ( 18 ) : 9524 - 9536

DOI: 10.1093/nar/gky761

Journal article

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Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis

Marie Cariou, Céline Ribière, Stéphanie Morliere, Jean-Pierre Gauthier, Jean-Christophe Simon, Pierre Peyret...

BMC Research Notes . 11 ( 1 ) : 461

DOI: 10.1186/s13104-018-3559-3

Journal article

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Flower flies (Diptera, Syrphidae) of French Polynesia, with the description of two new species

Thibault Ramage, Sylvain Charlat, Ximo Mengual

European Journal of Taxonomy . ( 448 ) : 1-37

DOI: 10.5852/ejt.2018.448

Journal article

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Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien de Vienne, Elodie Portanier, David Fouchet, Cécile Kaerle...

BMC Evolutionary Biology . 18 ( 1 )

DOI: 10.1186/s12862-018-1289-8

Journal article

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Coexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, Cécile Kaerle...

Plume de Naturalistes . 2 : 169-190

Journal article

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Co-occurrence among three divergent plant-castrating fungi in the same Silene host species

Jessica Lee Abbate, Pierre Gladieux, Michael E Hood, Damien de Vienne, Janis Antonovics, Alodie Snirc...

Molecular Ecology . 27 ( 16 ) : 3357 - 3370

DOI: 10.1111/mec.14805

Journal article

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Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian M Altenhoff, Jaime Huerta-Cepas...

Bioinformatics . 34 ( 2 ) : 323-329

DOI: 10.1093/bioinformatics/btx542

Journal article

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

Journal article

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Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster

Lain Guio, Cristina Vieira, Josefa González

Scientific Reports . 8 ( 1 ) : 1-10

DOI: 10.1038/s41598-018-30491-w

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Involvement of a host Cathepsin L in symbiont-induced cell death

Suzanne Peyer, Natacha Kremer, Margaret Mcfall-Ngai

MicrobiologyOpen . 7 ( 5 )

DOI: 10.1002/mbo3.632

Journal article

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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

Journal article

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RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, Vincent Berry...

Bioinformatics . 34 ( 21 ) : 3646-3652

DOI: 10.1093/bioinformatics/bty389

Journal article

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Overtraining often results in topologically incorrect species trees with maximum likelihood methods

Damien M. de Vienne, Fran Supek, Toni Gabaldon

DOI: 10.1101/140780

Preprint

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A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps

Deborah Di Giovanni, D. Lepetit, Matthieu Boulesteix, Marc Ravallec, Julien Varaldi

Preprint

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Deciphering the behaviour manipulation imposed by a virus on its parasitoid host: insights from a dual transcriptomic approach

Julien Varaldi, David Lepetit

Parasitology . 145 ( 14 ) : 1979-1989

DOI: 10.1017/S0031182018000835

Journal article

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Impact of pest management practices on the frequency of insecticide resistance alleles in Bemisia tabaci (Hemiptera: Aleyrodidae) populations in three countries of West Africa

Olivier Gnankine, Omer Hema, Moussa Namountougou, Laurence Mouton, Fabrice Vavre

Crop Protection . 104 : 86 - 91

DOI: 10.1016/j.cropro.2017.10.020

Journal article

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