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 747 in total

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

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L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

Journal article

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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

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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

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Lateral gene transfer, rearrangement, reconciliation

Murray Patterson, Gergely Szöllősi, Vincent Daubin, Eric Tannier

BMC Bioinformatics . 14 ( Suppl 15 ) : S4

Journal article

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

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

9782100599110 : 384

Book

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

Ashok Rajaraman, Eric Tannier, Cedric Chauve

Preprint

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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

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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

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Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization.

Natacha Kremer, Eva E R Philipp, Marie-Christine Carpentier, Caitlin A Brennan, Lars Kraemer, Melissa A Altura...

Cell Host and Microbe . 14 ( 2 ) : 183-94

DOI: 10.1016/j.chom.2013.07.006

Journal article

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Animals in a bacterial world, a new imperative for the life sciences.

Margaret Mcfall-Ngai, Michael G Hadfield, Thomas C G Bosch, Hannah V Carey, Tomislav Domazet-Lošo, Angela E Douglas...

Proceedings of the National Academy of Sciences of the United States of America . 110 ( 9 ) : 3229-36

DOI: 10.1073/pnas.1218525110

Journal article

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Efficient Exploration of the Space of Reconciled Gene Trees.

Gergely J Szöllosi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier, Vincent Daubin

Systematic Biology . 62 ( 6 ) : 901-912

DOI: 10.1093/sysbio/syt054

Journal article

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

Journal article

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Endosymbiont diversity among sibling weevil species competing for the same resource

Adrien Merville, Samuel Venner, Hélène Henri, Agnès Vallier, Frédéric Menu, Fabrice Vavre...

BMC Evolutionary Biology . 13 : 28

DOI: 10.1186/1471-2148-13-28

Journal article

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Distribution of Bemisia tabaci (Homoptera: Aleyrodidae) biotypes and their associated symbiotic bacteria on host plants in West Africa

Olivier Gnankine, Laurence Mouton, Hélène Henri, Gabriel Terraz, Thomas Houndeté, Thibaud Martin...

Insect conservation and diversity . 6 ( 3 ) : 411 - 421

DOI: 10.1111/j.1752-4598.2012.00206.x

Journal article

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Interactions et rétroactions : rôle de leur écologie et de leur évolution dans le fonctionnement des écosystèmes.

J. Roy, D. Bouchon, Dov Corenblit, Thierry Dutoit, F. Lallier, N. Niquil...

Prospectives de l’Institut Ecologie et Environnement du CNRS .

Book chapter

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Biotype status and resistance to neonicotinoids and carbosulfan in Bemisia tabaci (Hemiptera: Aleyrodidae) in Burkina Faso, West Africa

Olivier Gnankine, Laurence Mouton, Aly Savadogo, Thibaud Martin, Antoine Sanon, Roch Dabiré...

International Journal of Pest Management . 59 ( 2 ) : 95-102

DOI: 10.1080/09670874.2013.771806

Journal article

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

Journal article

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Molecular characterization of genetic diversity within the Africa/Middle East/Asia Minor and Sub-Saharan African groups of the Bemisia tabaci species complex

Hélène Henri, Gabriel Terraz, Olivier Gnankine, Frédéric Fleury, Laurence Mouton

International Journal of Pest Management . 59 ( 4 ) : 329 - 338

DOI: 10.1080/09670874.2013.869374

Journal article

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Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells

Abdou Akkouche, Thomas Grentzinger, Marie Fablet, Claudia Armenise, Nelly Burlet, Virginie Braman...

EMBO Reports . 14 ( 5 ) : 458-64

DOI: 10.1038/embor.2013.38

Journal article

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Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources

Anne Duplouy, Inaki Iturbe-Ormaetxe, Scott A Beatson, Jan M Szubert, Jeremy C Brownlie, Conor J Mcmeniman...

BMC Genomics .

Journal article

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Models and Algorithms for Genome Evolution

Cedric Chauve, Nadia El-Mabrouk, Eric Tannier

978-1-4471-5297-2 : 318

Book

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An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Annabelle A. Haudry, Adrian Platts, Emilio Vello, Douglas Hoen, Mickael Leclercq, Robert Williamson...

Nature Genetics . 45 ( 8 ) : 891 - 898

DOI: 10.1038/ng.2684

Journal article

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The first engagement of partners in the Euprymna scolopes - Vibrio fischeri symbiosis is a two-step process initiated by a few environmental symbiont cells

Melissa Altura, Elizabeth Heath-Heckman, Amani Gillette, Natacha Kremer, Anne-Marie Krachler, Caitlin Brennan...

Environmental Microbiology . : n/a - n/a

DOI: 10.1111/1462-2920.12179

Journal article

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A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

Journal article

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TPMS: a set of utilities for querying collections of gene trees.

Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière

BMC Bioinformatics . 14 : 109

DOI: 10.1186/1471-2105-14-109

Journal article

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Long PCR : A sensitive PCR protocol for amplification of Wolbachia endosymbiont in Indian honey bees

N. M. Guruprasad, M Sumithra, Laurence Mouton, H. P. Puttaraju

Journal of Entomological Research . 36 : 119--122

Journal article

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New national and regional bryophyte records, 31

L. T. Ellis, Autun L. Alegro, Halina Bednarek-Ochyra, Ryszard Ochyra, A. Bergamini, Annalena Cogoni...

Journal of Bryology . 34 ( 2 ) : 123-134

DOI: 10.1179/1743282012Y.0000000009

Journal article

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