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 361 to 390 publications on 768 in total

Reductive genome evolution at both ends of bacterial population size spectrum

Bérénice Batut, Carole Knibbe, Gabriel Marais, Vincent Daubin

Nature Reviews Microbiology . 12 ( 12 ) : 841-850

DOI: 10.1038/nrmicro3331

Journal article

see the publication

Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Hemalatha Golaconda Ramulu, Mathieu Groussin, Emmanuel Talla, Rémi Planel, Vincent Daubin, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 75 : 103 - 117

DOI: 10.1016/j.ympev.2014.02.013

Journal article

see the publication

Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid

Martha H. Ramírez-Bahena, Ludovic Vial, Florent Lassalle, Benjamin Diel, David Chapulliot, Vincent Daubin...

Molecular Phylogenetics and Evolution . 73 : 202-207

DOI: 10.1016/j.ympev.2014.01.005

Journal article

see the publication

A Bayesian Method for Analyzing Lateral Gene Transfer

Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad, Jens Lagergren

Systematic Biology . 63 ( 3 ) : 409 - 420

DOI: 10.1093/sysbio/syu007

Journal article

see the publication

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Robert Williamson, Emily Josephs, Adrian Platts, Khaled Hazzouri, Annabelle A. Haudry, Mathieu Blanchette...

PLoS Genetics . 10 ( 9 )

DOI: 10.1371/journal.pgen.1004622

Journal article

see the publication

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Marc Bailly-Bechet, Annabelle Haudry, Emmanuelle Lerat

Mobile DNA . 5 : 13

DOI: 10.1186/1759-8753-5-13

Journal article

see the publication

The Drosophila Su(var)3–7 Gene Is Required for Oogenesis and Female Fertility, Genetically Interacts with piwi and aubergine, but Impacts Only Weakly Transposon Silencing

Denis Basquin, Anne Spierer, Flora Begeot, Dmitry E Koryakov, Anne-Laure Todeschini, Stéphane Ronsseray...

PLoS ONE . 9 ( 5 ) : e96802

DOI: 10.1371/journal.pone.0096802

Journal article

see the publication

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Claudia M A Carareto, Eric H Hernandez, Cristina Vieira

Gene . 537 ( 1 ) : 93-99

DOI: 10.1016/j.gene.2013.11.080

Journal article

see the publication

The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution

Y. Moné, David Monnin, Natacha Kremer

Proceedings of the Royal Society B: Biological Sciences . 281 ( 1785 ) : 20133112 - 20133112

DOI: 10.1098/rspb.2013.3112

Journal article

see the publication

A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide

Caitlin Brennan, Jason Hunt, Natacha Kremer, Benjamin Krasity, Michael Apicella, Margaret Mcfall-Ngai...

eLife . 3

DOI: 10.7554/eLife.01579

Journal article

see the publication

The dual nature of haemocyanin in the establishment and persistence of the squid - vibrio symbiosis

Natacha Kremer, Julia Schwartzman, Rene Augustin, Lawrence Zhou, Edward G. Ruby, Stéphane Hourdez...

Proceedings of the Royal Society B: Biological Sciences . 281 ( 1785 ) : 20140504

DOI: 10.1098/rspb.2014.0504

Journal article

see the publication

Exposure to hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni.

David Roquis, Julie M. J. Lepesant, Emanuel Villafan, Jérôme Boissier, Cristina Vieira, Celine Cosseau...

Frontiers in Genetics . 5 : 207

DOI: 10.3389/fgene.2014.00207

Journal article

see the publication

Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

Elias a G Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia M A Carareto, Cristina Vieira

Genome Biology and Evolution . 6 : 1806 - 1817

DOI: 10.1093/gbe/evu141

Journal article

see the publication

The Genome of Cardinium cBtQ1 Provides Insights into Genome Reduction, Symbiont Motility, and Its Settlement in Bemisia tabaci

Diego Santos-Garcia, Pierre-Antoine Rollat-Farnier, Francisco Beitia, Einat Zchori-Fein, Fabrice Vavre, Laurence Mouton...

Genome Biology and Evolution . 6 ( 4 ) : 1013-1030

Journal article

see the publication

The sublethal effects of deltamethrin on Trichogramma behaviors during the exploitation of host patches

Jean-Marie Delpuech, Maxime Delahaye

Science of the Total Environment . 447 : 274-279

DOI: 10.1016/j.scitotenv.2012.12.096

Journal article

see the publication

The influence of male wing shape on mating success in Drosophila melanogaster

Bf. Menezes, Fm. Vigoder, Aa. Peixoto, J. Varaldi, Bc. Bitner-Mathé

Animal Behaviour . 85 : 1217--1223

DOI: 10.1016/j.anbehav.2013.03.008

Journal article

see the publication

Distribution of endosymbiotic reproductive manipulators reflects invasion process and not reproductive system polymorphism in the little fire ant Wasmannia auropunctata

Olivier REY, Arnaud Estoup, Benoit Facon, Anne Loiseau, Alexandre Aebi, Olivier Duron...

PLoS ONE . 8 ( 3 ) : e58467

DOI: 10.1371/journal.pone.0058467

Journal article

see the publication

The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy

Biology Letters . 9 ( 5 ) : 20130608

DOI: 10.1098/rsbl.2013.0608

Journal article

see the publication

On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data

Igor Nor, Jan Engelstädter, Olivier Duron, Max Reuter, Marie-France Sagot, Sylvain Charlat

The American Naturalist . 182 ( 1 ) : 15-24

DOI: 10.1086/670612

Journal article

see the publication

Eloge de l'ADN poubelle

Laurent Duret, Sylvain Charlat

Pour la science . 81 : 10--17

Journal article

see the publication

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Marie Cariou, Laurent Duret, Sylvain Charlat

Ecology and Evolution . 3 ( 4 ) : 846-852

DOI: 10.1002/ece3.512

Journal article

see the publication

Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli

Thomas Bourquard, Damien Mathieu de Vienne, Jérôme Azé

EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances . E.24 : 419-430

Conference paper

see the publication

L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

Journal article

see the publication

Lateral Gene Transfer from the Dead.

Gergely J Szöllosi, Eric Tannier, Nicolas Lartillot, Vincent Daubin

Systematic Biology . 62 ( 3 ) : 386-397

DOI: 10.1093/sysbio/syt003

Journal article

see the publication

Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

Subarna Thakur, Philippe Normand, Vincent Daubin, Louis S. Tisa, Arnab Sen

BMC Genomics . 14 ( 1 )

DOI: 10.1186/1471-2164-14-474

Journal article

see the publication

Lateral gene transfer, rearrangement, reconciliation

Murray Patterson, Gergely Szöllősi, Vincent Daubin, Eric Tannier

BMC Bioinformatics . 14 ( Suppl 15 ) : S4

Journal article

see the publication

Théorie des Codes : compression, cryptage, correction, 2e edition

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

9782100599110 : 384

Book

see the publication

The genome of the medieval Black Death agent (extended abstract)

Ashok Rajaraman, Eric Tannier, Cedric Chauve

Preprint

see the publication

Gene tree correction guided by orthology

Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk

BMC Bioinformatics . 14 ( Suppl 15 ) : S5

Journal article

see the publication

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Cedric Chauve, Nadia El-Mabrouk, Laurent Gueguen, Magali Semeria, Eric Tannier

Models and Algorithms for Genome Evolution . 19 : 47-62

Book chapter

see the publication