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 421 to 450 publications on 768 in total

Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

G.J. Szollosi, Vincent Daubin

Methods in Molecular Biology . 856 : 29-51

Journal article

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Preserving Inversion Phylogeny Reconstruction

Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier

WABI 2012 - 12th International Workshop on Algorithms in Bioinformatics . : 1-13

DOI: 10.1007/978-3-642-33122-0_1

Conference paper

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Modulation of Symbiont Lipid A Signaling by Host Alkaline Phosphatases in the Squid-Vibrio Symbiosis

B. Rader, Natacha Kremer, M. Apicella, W. Goldman, M. Mcfall-Ngai

mBio . 3 ( 3 )

DOI: 10.1128/mBio.00093-12

Journal article

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Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis

Damien M. de Vienne, Sébastien Ollier, Gabriela Aguileta

Molecular Biology and Evolution . 29 ( 6 ) : 1587--1598

DOI: 10.1093/molbev/msr317

Journal article

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Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

Jean Bérard, Laurent Guéguen

Systematic Biology . 61 ( 3 ) : 510-521

DOI: 10.1093/sysbio/sys024

Journal article

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Effects of deltamethrin on the specific discrimination of sex pheromones in two sympatric Trichogramma species

Jean-Marie Delpuech, C. Dupont, R. Allemand

Ecotoxicology and Environmental Safety . 84 : 32--38

DOI: 10.1016/j.ecoenv.2012.06.007

Journal article

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Complete Genome Sequence of "Candidatus Portiera aleyrodidarum" BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci.

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

Journal of Bacteriology . 194 ( 23 ) : 6654-6655

DOI: 10.1128/JB.01793-12

Journal article

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Evolution and control of host-microbe symbiosis in arthropods: an RNAseq-based transcriptomic analysis

Yves Moné, F. Chevalier, M.C. Carpentier, N. Kremer, Patrick Mavingui, V. Raquin...

7. International Wolbachia conference . 978-2-911320-44-6

Conference paper

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Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Jonathan Romiguier, Emeric Figuet, Nicolas Galtier, Emmanuel J.P. Douzery, Bastien Boussau, Julien y Dutheil...

PLoS ONE . 7 ( 3 ) : e33852

DOI: 10.1371/journal.pone.0033852

Journal article

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Efficient selection of branch-specific models of sequence evolution.

Julien y Dutheil, Nicolas Galtier, Jonathan Romiguier, Emmanuel J.P. Douzery, Vincent Ranwez, Bastien Boussau

Molecular Biology and Evolution . 29 ( 7 ) : 1861-1874

DOI: 10.1093/molbev/mss059

Journal article

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A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

Jj. Fong, Jm. Brown, Mk. Fujita, Bastien Boussau

PLoS ONE . 7 : e48990

DOI: 10.1371/journal.pone.0048990

Journal article

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Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex

L. Mouton, M. Thierry, H. Henri, R. Baudin, O. Gnankine, Bernard Reynaud...

BMC Microbiology . 12(Suppl 1) : 1-15

DOI: 10.1186/1471-2180-12-S1-S10

Journal article

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tirant, a newly discovered active endogenous retrovirus in Drosophila simulans.

Abdou Akkouche, Rita Rebollo, Nelly Burlet, Caroline Esnault, Sonia Martinez, Barbara Viginier...

Journal of Virology . 86 ( 7 ) : 3675-3681

DOI: 10.1128/JVI.07146-11

Journal article

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Mod/Resc Parsimony Inference: Theory and application

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Information and Computation . 213 : 23-32

DOI: 10.1016/j.ic.2011.03.008

Journal article

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Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes

Elsa Petit, Tatiana Giraud, Damien M. de Vienne, Marco A Coelho, Gabriela Aguileta, Joelle J. Amselem...

Evolution - International Journal of Organic Evolution . 66 ( 11 ) : 3519-3533

DOI: 10.1111/j.1558-5646.2012.01703.x

Journal article

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Evolution of Prokaryotic Pangenomes

Florent Lassalle, Vincent Daubin

Horizontal Gene Transfer in Microorganisms . 978-1-908230-10-2 : 23-32

Book chapter

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Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North-American Arabidopsis lyrata

A. Haudry, H.G. Zha, M. Stift, B.K. Mable

Molecular Ecology . 21 : 1130-1142

DOI: 10.1111/j.1365-294X.2011.05435.x

Journal article

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International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.

Abdelkader Aïnouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Gaël Cristofari, Jean-Marc Deragon...

Mobile DNA . 3 ( 1 ) : 17

DOI: 10.1186/1759-8753-3-17

Journal article

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Transposon proliferation in an asexual parasitoid.

Ken Kraaijeveld, Brechtje Zwanenburg, Benjamin Hubert, Cristina Vieira, Sylvia de Pater, Jacques J.M. van Alphen...

Molecular Ecology . 21 ( 16 ) : 3898-3906

DOI: 10.1111/j.1365-294X.2012.5582.x

Journal article

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Linearization of ancestral multichromosomal genomes

Ján Maňuch, Murray Patterson, Roland Wittler, Cedric Chauve, Eric Tannier

BMC Bioinformatics . 13 ( Suppl 19 ) : S11

DOI: 10.1186/1471-2105-13-S19-S11

Journal article

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Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, Eric Tannier

Bioinformatics . 28 ( 18 ) : i382-i388

DOI: 10.1093/bioinformatics/bts374

Journal article

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

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High-resolution melting technology: a new tool for studying the Wolbachia endosymbiont diversity in the field.

H. Henri, Laurence Mouton

Molecular Ecology Resources . 12 ( 1 ) : 75-81

DOI: 10.1111/j.1755-0998.2011.03064.x

Journal article

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