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 511 to 540 publications on 766 in total

Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

Journal article

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RECOMB Satellite Workshop on Comparative Genomics

Eric Tannier

8. Annual RECOMB Satellite Workshop on Comparative Genomics . 978-3-642-16181-0 : 303

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Comparative Genomics

Eric Tannier

incollection . 6938 : 1-12

Journal article

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RECONSTRUCTING ORIGINS OF LOSS OF SELF-INCOMPATIBILITY AND SELFING IN NORTH AMERICAN ARABIDOPSIS LYRATA: A POPULATION GENETIC CONTEXT

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 ( 12 ) : 3495 - 3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 : 3495-3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae.

Haris Gavranović, Eric Tannier

Pacific Symposium on Biocomputing . 15 : 21-30

DOI: 10.1142/9789814295291_0004

Conference paper

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Theory and examples of reciprocal influence between hosts and pathogens, from short-term to long term interactions: coevolution, cospeciation and pathogen speciation following host shifts

Aurélien Tellier, Damien M. de Vienne, Tatiana Giraud, Michael Hood, Guislaine Refrégier

Host-Pathogen Interactions: Genetics, Immunology, and Physiology . 978-1608762866

Book chapter

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Computing the likelihood of sequence segmentation under Markov modelling

Laurent Guéguen

Preprint

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Evolution and manipulation of parasitoid eggload

Sylvain Gandon, Julien Varaldi, Frédéric Fleury, Ana R Rivero

Evolution - International Journal of Organic Evolution . 63 ( 11 ) : 2974-2984

DOI: 10.1111/j.1558-5646.2009.00776.x

Journal article

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A new case of Wolbachia dependence in the genus Asobara: evidence for parthenogenesis induction in Asobara japonica

N. Kremer, D. Charif, H. Henri, M. Bataille, G. Prévost, K. Kraaijeveld...

Heredity . 103 ( 3 ) : 248-256

DOI: 10.1038/hdy.2009.63

Journal article

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Molecular detection and identification of Rickettsia endosymbiont in different biotypes of Bemisia tabaci

G. Gueguen, Jean-Marc Rolain, E. Zchori-Fein, F. Vavre, Frédéric Fleury, Didier Raoult

Clinical Microbiology and Infection . -- : 1-2

Journal article

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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

Journal article

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Genomes as documents of evolutionary history

Bastien Boussau, Vincent Daubin

Trends in Ecology & Evolution . 1192 : 1-9

Journal article

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Identification of a polymorphic collagen-like protein in the crustacean bacteria Pasteuria ramosa

L. Mouton, E. Traunecker, K. Mcelroy, L. Du Pasquier, D. Ebert

Research in Microbiology . 160 : 792-799

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, S. Martinez...

FASEB Journal . 23 : 54-62

Journal article

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Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira, M. Fablet, E. Lerat

genome dyn stab . -- : 115-123

Journal article

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Rapidly Shifting Sex Ratio across a Species Range

E.A. Hornett, S. Charlat, N. Wedell, C.D. Jiggins, G.D.D. Hurst

Current Biology . 19 : 1628-1631

Journal article

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Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Ravi D. Barabote, Gary Xie, David H. Leu, Philippe Normand, Anamaria Necsulea, Vincent Daubin...

Genome Research . ( 19 ) : 1033-1043

DOI: 10.1101/gr.084848.108

Journal article

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Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

Journal article

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Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

Journal article

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Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

Eric Tannier

RECOMB International Workshop on Comparative Genomics . 5817 : 1-12

DOI: 10.1007/978-3-642-04744-2_1

Conference paper

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Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes

Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul, Eric Tannier

Journal of Computational Biology . 16 ( 10 ) : 1287-1309

DOI: 10.1089/cmb.2009.0088

Journal article

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Combinatorics of Genome Rearrangements

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, Stéphane Vialette

978-0-262-06282-4 : 312

Book

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Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

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Maintenance of adaptive differentiation by Wolbachia induced bidirectional cytoplasmic incompatibility: the importance of sib-mating and genetic systems.

Antoine Branca, Fabrice Vavre, Jean-François Silvain, Stéphane Dupas

BMC Evolutionary Biology . 9 : 185

DOI: 10.1186/1471-2148-9-185

Journal article

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Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum

Damien de Vienne, G Refrégier, Me Hood, A Guigue, B Devier, E Vercken...

Journal of Evolutionary Biology . 22 ( 4 ) : 683--698

Journal article

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A Virus-Shaping Reproductive Strategy in a Drosophila Parasitoid

Julien Varaldi, Sabine Patot, Maxime Nardin, Sylvain Gandon

Advances in Parasitology . 70 : 334-359

DOI: 10.1016/S0065-308X(09)70013-2

Journal article

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Molecular Detection Penetrance and Transmission of an Inherited Virus Responsible for Behavioral Manipulation of an Insect Parasitoid

S. Patot, D. Lepetit, D. Charif, Julien Varaldi, Frédéric Fleury

Applied and Environmental Microbiology . 75 ( 3 ) : 703-710

DOI: 10.1128/AEM.01778-08

Journal article

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Wolbachia interferes with ferritin expression and iron metabolism in insects.

Natacha Kremer, Denis Voronin, Delphine Charif, Patrick Mavingui, Bertrand Mollereau, Fabrice Vavre

PLoS Pathogens . 5 ( 10 ) : e1000630

DOI: 10.1371/journal.ppat.1000630

Journal article

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