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 749 in total

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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Influence of Wolbachia on host gene expression in an obligatory symbiosis.

Natacha Kremer, Delphine Charif, Hélène Henri, Frédérick F. Gavory, Patrick Wincker, Patrick Mavingui...

BMC Microbiology . 12 ( Suppl 1 ) : 1-16

DOI: 10.1186/1471-2180-12-S1-S7

Journal article

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Survey of Wolbachia and Its Phage WO in the Uzifly Exorista sorbillans (Diptera: Tachinidae)

Nm. Guruprasad, Laurence Mouton, P Sumithra, Hp. Puttaraju

Current Microbiology . 63 : 267-272

DOI: 10.1007/s00284-011-9973-6

Journal article

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Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions: Cloning reveals extreme host specificity

Pepijn Luijckx, Frida Ben-Ami, Laurence Mouton, Louis Du Pasquier, Dieter Ebert

Ecology Letters . 14 ( 2 ) : 125-131

DOI: 10.1111/j.1461-0248.2010.01561.x

Journal article

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Effect of Wolbachia infection and temperature variations on the fecundity of the Uzifly Exorista sorbillans (Diptera: Tachinidae)

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

Symbiosis . 54 : 151-158

DOI: 10.1007/s13199-011-0138-y

Journal article

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Characterisation of a large family of polymorphic collagen-like proteins in the endospore-forming bacterium Pasteuria ramosa

K. Mcelroy, Laurence Mouton, L. Du Pasquier, Q. Weihong, E. Dieter

Research in Microbiology . 162 : 701-714

DOI: 10.1016/j.resmic.2011.06.009

Journal article

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Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot...

Genome Biology and Evolution . 3 ( 3 ) : 762-781

DOI: 10.1093/gbe/evr070

Journal article

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Side effects of fungicides on the abundance and the species diversity of the natural populations of Drosophila and their hymenopterous parasitoids in orchards

J-M. Delpuech, Roland Allemand

Phytoparasitica . 39 : 429-435

DOI: 10.1007/s12600-011-0180-6

Journal article

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Does a parthenogenesis-inducing Wolbachia induce vestigial cytoplasmic incompatibility?

Ken Kraaijeveld, Barbara M Reumer, Laurence Mouton, Natacha Kremer, Fabrice Vavre, Jacques J.M. van Alphen

The Science of Nature Naturwissenschaften . 98 ( 3 ) : 175-80

DOI: 10.1007/s00114-010-0756-x

Journal article

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RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

M.-C. Carpentier, J. Charif, Vincent Lacroix, Marie-France Sagot, Fabrice Vavre

JOBIM .

Conference paper

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Rickettsia ‘In’ and ‘Out’: Two Different Localization Patterns of a Bacterial Symbiont in the Same Insect Species

Ayelet Caspi-Fluger, Moshe Inbar, Netta Mozes-Daube, Laurence Mouton, Martha Hunter, Einat Zchori-Fein

PLoS ONE . 6 ( 6 )

DOI: 10.1371/journal.pone.0021096

Journal article

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Effect of Wolbachia infection and temperature variations on the fecundity of the Uzifly Exorista sorbillans (Diptera: Tachinidae)

N.M. Guruprasad, L. Mouton, H.P. Puttaraju

Symbiosis . 54 : 151-158

Journal article

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Evolvability, epigenetics and transposable elements

Marie Fablet, C. Vieira

Biomolecular concepts . 2 : 333-341

Journal article

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Isolation and gene flow: inferring the speciation history of European house mice

Ludovic Duvaux, Khalid Belkhir, Matthieu Boulesteix, Pierre Boursot

Molecular Ecology . 20 ( 24 ) : 5248-5264

DOI: 10.1111/j.1365-294X.2011.05343.x

Journal article

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Models, algorithms, and programs for phylogeny reconciliation

Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry

Briefings in Bioinformatics . 12 ( 5 ) : 392-400

DOI: 10.1093/bib/bbr045

Journal article

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Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

Gabriel Marais, A. Forrest, E. Kamau, Jos Käfer, Vincent Daubin, D. Charlesworth

PLoS ONE . 6 : e21915

DOI: 10.1371/journal.pone.0021915

Journal article

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HDR - Evolution combinatoire Algorithmique des chromosomes

Eric Tannier

incollection . -- : 54-56

Journal article

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Euclidean nature of phylogenetic distance matrices

Damien M. de Vienne, Gabriela Aguileta, Sébastien Ollier

Systematic Biology . 60 ( 6 ) : 826--832

DOI: 10.1093/sysbio/syr066

Journal article

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