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 271 to 300 publications on 766 in total

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve, Akbar A Rafiey, Adrian A Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau...

DOI: 10.1101/127548

Other publication

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Adaptation-adaptabilité : comprendre la réponse adaptative avec pour objectif de la prédire

Nicolas Bierne, Malika Ainouche, M. Gouy, Pierre-Alexandre Gagnaire, Guillaume Mitta, Y. Lemaho...

Prospectives de l’Institut Ecologie et environnement du CNRS : compte-rendu des journées des 22, 23 et 24 février 2017, CNRS, Bordeaux, CNRS . : 127-141

Book chapter

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Integrative modeling of gene and genome evolution roots the archaeal tree of life

Tom Williams, Gergely Szöllősi, Anja Spang, Peter Foster, Sarah Heaps, Bastien Boussau...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 23 ) : E4602-E4611

DOI: 10.1073/pnas.1618463114

Journal article

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Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron...

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

Journal article

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Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

Journal article

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How Long Does Wolbachia Remain on Board?

Marc Bailly-Bechet, Patricia Martins-Simões, Gergely Szöllősi, Gladys Mialdea, Marie-France Sagot, Sylvain Charlat

Molecular Biology and Evolution . 34 ( 5 ) : 1183 - 1193

DOI: 10.1093/molbev/msx073

Journal article

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Impact of Wolbachia on oxidative stress sensitivity in the parasitic wasp Asobara japonica

David Monnin, Natacha Kremer, Emmanuel Desouhant, Fabrice Vavre

PLoS ONE . 5 : 10

DOI: 10.1371/journal.pone.0175974

Journal article

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Dating with transfers

Adrián Davín, Gergely J Szöllosi, Eric Tannier, Bastien Boussau, Vincent Daubin

Journées Ouvertes Biologie Informatique Mathématiques .

Conference paper

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Diploid male production correlates with genetic diversity in the parasitoid wasp Venturia canescens : a genetic approach with new microsatellite markers

Marie Collet, Chloé Vayssade, Alexandra Auguste, Laurence Mouton, Emmanuel Desouhant, Thibaut Malausa...

Ecology and Evolution . 6 ( 18 ) : 6721 - 6734

DOI: 10.1002/ece3.2370

Journal article

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Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases

C. Goubert, G. Minard, Cristina Vieira, Matthieu Boulesteix

Heredity . 117 ( 3 ) : 125-34

DOI: 10.1038/hdy.2016.35

Journal article

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Nucleotide, gene and genome evolution : a score to bind them all

Wandrille Duchemin, Vincent Daubin, Eric Tannier

Journées Ouvertes Biologie Informatique Mathématiques .

Conference paper

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Genome Rearrangements on both Gene Order and Intergenic Regions

Guillaume Fertin, Géraldine Jean, Eric Tannier

WABI 2016 . 9838 : 162-173

Conference paper

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Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?

Claire Lays, Eric Tannier, Thomas Henry

Microbial Cell . 3 ( 11 ) : 576-578

DOI: 10.15698/mic2016.11.543

Journal article

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Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels

Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine Bérard

Journées Ouvertes Biologie Informatique Mathématiques .

Conference paper

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SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

F. Pouyet, M. Bailly-Bechet, Dominique Mouchiroud, Laurent Guéguen

Genome Biology and Evolution . 8 : 2427-41

DOI: 10.1093/gbe/evw165

Journal article

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Additional heritable virus in the parasitic wasp Leptopilina boulardi: prevalence, transmission and phenotypic effects

Julien Martinez, David Lepetit, Marc Ravallec, Frédéric Fleury, Julien Varaldi

Journal of General Virology . 97 : 523-535

DOI: 10.1099/jgv.0.000360

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

Journal article

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Influence of oxidative homeostasis on bacterial density and cost of infection in Drosophila–Wolbachia symbioses

David Monnin, Natacha Kremer, C. Berny, Hélène Henri, Adeline Dumet, Yann Voituron...

Journal of Evolutionary Biology . 29 : 1211-1222

DOI: 10.1111/jeb.12863

Journal article

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Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

Journal article

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Efficient gene tree correction guided by genome evolution

Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen...

PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)

DOI: 10.1371/journal.pone.0159559

Journal article

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Wolbachia -mediated protection against viruses in the invasive pest Drosophila suzukii

Julien Cattel, Julien Martinez, F. Jiggins, L. Mouton, P. Gibert

Insect Molecular Biology . 25 ( 5 ) : 595-603

DOI: 10.1111/imb.12245

Journal article

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Wolbachia in European Populations of the Invasive Pest Drosophila suzukii: Regional Variation in Infection Frequencies

Julien Cattel, Rupinder Kaur, Patricia Gibert, Julien Martinez, Antoine Fraimout, Francis Jiggins...

PLoS ONE . 11 ( 1 ) : e0147766

DOI: 10.1371/journal.pone.0147766

Journal article

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The draft genome sequence of the rice weevil Sitophilus oryzae as a model to explore the host-symbiont interactions in a nascent stage of endosymbiosis

Carlos Vargas-Chavez, Nicolas Parisot, Clément Goubert, Patrice Baa-Puyoulet, Severine Balmand, M. Boulesteix...

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) .

Poster

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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In silico experimental evolution provides independent and challenging benchmarks for comparative genomics

Priscila Biller, Eric Tannier, Guillaume Beslon, Carole Knibbe

Journées ouvertes Biologie Informatique Mathématiques . : 79-82

Conference paper

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