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 301 to 330 publications on 749 in total

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

Wandrille Duchemin, Vincent Daubin, Eric Tannier

BMC Genomics . 16 ( Suppl 10 ) : S9

DOI: 10.1007/978-3-319-19048-8_16

Journal article

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Detection of genetically isolated entities within the Mediterranean species of Bemisia tabaci: new insights into the systematics of this worldwide pest

Laurence Mouton, Olivier Gnankiné, Hélène Henri, Gabriel Terraz, Guillaume Ketoh, Thibaud Martin...

Pest Management Science . 71 ( 3 ) : 452-458

DOI: 10.1002/ps.3834

Journal article

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Parasite-Parasite Interactions in the Wild: How To Detect Them?

Eléonore Hellard, David Fouchet, Fabrice Vavre, Dominique Pontier

Trends in Parasitology .

Journal article

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Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

Pascaline Dumas, Fabrice Legeai, Claire Lemaitre, Erwan Scaon, Marion Orsucci, Karine Labadie...

Genetica . 143 ( 3 ) : 305-316

DOI: 10.1007/s10709-015-9829-2

Journal article

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De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti).

Clément Goubert, Laurent Modolo, Cristina Vieira, Claire Valientemoro, Patrick Mavingui, Matthieu Boulesteix

Genome Biology and Evolution . 7 ( 4 ) : 1192-205

Journal article

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De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti)

Clément Goubert, Laurent Modolo, Cristina Vieira, Claire Valiente Moro, Patrick Mavingui, Matthieu Boulesteix

Genome Biology and Evolution . 7 ( 4 ) : 1192-1205

DOI: 10.1093/gbe/evv050

Journal article

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Sex and evolution

Pierre-Henri Gouyon, Damien De Vienne, Tatiana Giraud

Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507

Book chapter

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

Journal article

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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

Journal article

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Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

Florent Murat, Rongzhi R. Zhang, Sébastien Guizard, Haris Gavranovic, Raphael Flores, Delphine Steinbach...

Genome Biology and Evolution . 7 ( 3 ) : 735-749

DOI: 10.1093/gbe/evv014

Journal article

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Foundations of Coding: Compression, Encryption, Error-Correction

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

978-1-118-88144-6 : 376

Book

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The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation

Julia Schwartzman, Eric Koch, Elizabeth Heath-Heckman, Lawrence Zhou, Natacha Kremer, Margaret Mcfall-Ngai...

Proceedings of the National Academy of Sciences of the United States of America . 112 ( 2 ) : 566 - 571

DOI: 10.1073/pnas.1418580112

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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Md Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow

PLoS ONE . 10 ( 6 ) : e0129183

DOI: 10.1371/journal.pone.0129183

Journal article

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Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

Ruchi Chaudhary, Bastien Boussau, J. Gordon Burleigh, David Fernández-Baca

Systematic Biology . 64 ( 2 ) : 325-339

DOI: 10.1093/sysbio/syu128

Journal article

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Ancestral gene synteny reconstruction improves extant species scaffolding

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

BMC Genomics . 16 ( Suppl 10 ) : S11

DOI: 10.1186/1471-2164-16-S10-S11

Journal article

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Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen

BMC Bioinformatics . 16 ( Suppl 14 ) : S5

DOI: 10.1186/1471-2105-16-S14-S5

Journal article

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Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Arellano Davin, Eric Tannier, Vincent Daubin, Bastien Boussau

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)

DOI: 10.1098/rstb.2014.0335

Journal article

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Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci : testing the biological relevance of cytotypes

Gabriel Terraz, Gwenaelle Gueguen, Judit Arnó, Frédéric Fleury, Laurence Mouton

Pest Management Science . 70 ( 10 ) : 1503-1513

DOI: 10.1002/ps.3792

Journal article

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Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci : testing the biological relevance of cytotypes

Gabriel Terraz, Gwénaelle Gueguen, Frédéric Fleury, Laurence Mouton, Judit Arnó

Pest Management Science . 70 ( 10 ) : 1503-1513

DOI: 10.1002/ps.3792

Journal article

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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

DOI: 10.1093/gbe/evu077

Journal article

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Variable expression levels detected in the Drosophila effectors of piRNA biogenesis

Marie Fablet, Abdou Akkouche, Virginie Braman, Cristina Vieira

Gene . 537 ( 1 ) : 149-153

DOI: 10.1016/j.gene.2013.11.095

Journal article

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Probabilistic Graphical Model Representation in Phylogenetics

S. Höhna, Ta. Heath, Bastien Boussau

Systematic Biology . 63 ( 5 ) : 753-771

DOI: 10.1093/sysbio/syu039

Journal article

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Host Control of Insect Endogenous Retroviruses: Small RNA Silencing and Immune Response

Marie Fablet

Viruses . 6 : 4447-4464

DOI: 10.3390/v6114447

Journal article

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Wolbachia Divergence and the Evolution of Cytoplasmic Incompatibility in Culex pipiens

Célestine Atyame Nten, Pierrick Labbe, Emilie E. Dumas, Pascal Milesi, Sylvain Charlat, Philippe Fort...

PLoS ONE . 9 ( 1 ) : e87336

DOI: 10.1371/journal.pone.0087336

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Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. an

A. Sen, Vincent Daubin, D. Abrouk, I. Gifford, A. M. Berry, P. Normand

International Journal of Systematic and Evolutionary Microbiology . 64 ( Pt 11 ) : 3821-32

DOI: 10.1099/ijs.0.063966-0

Journal article

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A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids

Doris Vela, Antonio Fontdevila, Cristina Vieira, García Guerreiro María Pilar

PLoS ONE . 9 : 87 - 87

DOI: 10.1371/journal.pone.0088992.s005

Journal article

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Could interallelic interactions be a key to the epigenetic aspects of fitness-trait inbreeding depression?

C. Biemont, Cristina Vieira

Heredity . 112 : 219-20

DOI: 10.1038/hdy.2013.80

Journal article

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Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Pierre P. Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela G. Aguileta, Damien M. de Vienne...

Molecular Ecology . 23 ( 4 ) : 753-773

DOI: 10.1111/mec.12631

Journal article

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