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 541 to 570 publications on 747 in total

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.

Adriana Granzotto, Fabrício R Lopes, Emmanuelle Lerat, Cristina Vieira, Claudia M A Carareto

BMC Evolutionary Biology . 9 : 174

DOI: 10.1186/1471-2148-9-174

Journal article

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High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.)

Aurélie A. Berard, Marie-Christine Le Paslier, Mireille M. Dardevet, Florence F. Exbrayat-Vinson, Isabelle I. Bonnin, Alberto A. Cenci...

Plant Biotechnology Journal . 7 ( 4 ) : 364-374

DOI: 10.1111/j.1467-7652.2009.00404.x

Journal article

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Databases of Homologous Gene Families for Comparative Genomics

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, L. Duret...

BMC Bioinformatics . 10 (Suppl.6) :S3 : 13

DOI: 10.1186/1471-2105-10-S6-S3

Journal article

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[Prophylaxis of thromboembolic disease in obstetrics after the French guidelines publication]

C. Chauleur, Cristina Vieira, P. Seffert

Gynécologie Obstétrique & Fertilité . 36 ( 1 ) : 23-34

DOI: 10.1016/j.gyobfe.2007.07.043

Journal article

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Do vertically transmitted symbionts co-existing in a single host compete or cooperate? A modelling approach

E. Vautrin, S. Genieys, Sandrine Charles, F. Vavre

Journal of Evolutionary Biology . 21 : 145-161

Journal article

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Inherited intracellular ecosystem: symbiotic bacteria share bacteriocytes in whiteflies

Y. Gottlieb, M. Ghanim, G. Gueguen, S. Kontsedalov, F. Vavre, Frédéric Fleury...

FASEB Journal . 22 : 1-9

Journal article

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The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event ?

Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler...

BMC Evolutionary Biology . 8:336 : 1-19

DOI: 10.1186/1471-2148-8-336

Journal article

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Genetic and Immunological Comparison of the Cladoceran Parasite Pasteuria ramosa with the Nematode Parasite Pasteuria penetrans

L.M. Schmidt, L. Mouton, G. Nong, D. Ebert, J.F. Preston

Applied and Environmental Microbiology . 74 : 259-264

Journal article

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Variable-Number-of-Tandem-Repeats Analysis of Genetic Diversity in Pasteuria ramosa

L. Mouton, D. Ebert

Current Microbiology . 56 : 447-452

Journal article

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High Genetic Differentiation between the M and S Molecular Forms of Anopheles gambiae in Africa

C. Esnault, M. Boulesteix, J.B. Duchemin, A.A. Koffi, F. Chandre, R. Dabiré...

PLoS ONE . 3 : 1-7

Journal article

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You can`t keep a good parasite down: evolution of a male-killer suppressor uncovers cytoplasmic incompatibility

E.A. Hornett, A.M. Duplouy, N. Davies, G.K. Roderick, N. Wedell, G.D. Hurst...

Evolution international journal of organic evolution . 62 : 1258-1263

Journal article

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Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution

Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 3 ) : 348-356

DOI: 10.1109/TCBB.2008.16

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

: 26

Report

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Prédiction de synténies dans le génome ancestral des amniotes

F. Boyer, C. Chauve, Eric Tannier

Journées Ouvertes de Biologie, Informatique et Mathématiques, JOBIM 2008 . : 141-148

Conference paper

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Perfect DCJ rearrangement

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

RECOMB-CG: Comparative Genomics . LNCS ( 5267 ) : 158-169

DOI: 10.1007/978-3-540-87989-3_12

Conference paper

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Advances on Stochastic Local Search Algorithms for the Genomic Median Problem

Renaud Lenne, Christine Solnon, Thomas Stützle, Eric Tannier

International Conference on Metaheuristics and Nature Inspired Computing (META) . 4872 : 266-276

Conference paper

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Multichromosomal Genome Median and Halving Problems

Eric Tannier, C. Zheng, D. Sankoff

International Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 1-13

DOI: 10.1007/978-3-540-87361-7_1

Conference paper

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A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

C. Chauve, Eric Tannier

PLoS Computational Biology . 4 : 391-410

Journal article

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Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot

Eric Tannier

incollection . -- : 860-863

Journal article

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The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome

N. Mugnier, Laurent Guéguen, Cristina Vieira, C. Biémont

Gene . 411 : 87-93

Journal article

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Losing helena: The extinction of a drosophila line-like element

Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont, Cristina Vieira

BMC Genomics . 9 : 1-11

DOI: 10.1186/1471-2164-9-149

Journal article

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In response to comment on ‘A congruence index for testing topological similarity between trees’

Damien de Vienne, Tatiana Giraud, Olivier C Martin

Bioinformatics . 25 ( 1 ) : 150--151

DOI: 10.1093/bioinformatics/btn535

Journal article

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Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont

R. Cordaux, S. Pichon, A. Ling, P. Perez, C. Delaunay, F. Vavre...

Molecular Biology and Evolution . 25 ( 9 ) : 1889-1896

DOI: 10.1093/molbev/msn134

Journal article

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Is symbiosis evolution influenced by the pleiotropic role of programmed cell death in immunity an development ?

F. Vavre, N. Kremer, B.A. Pannebakker, B. Loppin, Patrick Mavingui

Insect Symbiosis . 3 : 57-76

Book chapter

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Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

Journal article

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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

Journal article

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Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

J. Dutheil, Bastien Boussau

BMC Evolutionary Biology . 8:255 : 31-42

Journal article

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Phylogenetic Characterization and Prevalence of “Spirobacillus cienkowskii ” a Red-Pigmented Spiral-Shaped Bacterial Pathogen of Freshwater Daphnia Species

J.L.M. Rodrigues, M.A. Duffy, A.J. Tessier, D. Ebert, L. Mouton, T.M. Schmidt

Applied and Environmental Microbiology . 74 : 1575-1582

Journal article

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The effects of multiple infections on the expression and evolution of virulence in a daphnia-endoparasite system

F. Ben-Ami, L. Mouton, D. Ebert

Evolution - International Journal of Organic Evolution . 62-7 : 1700-1711

Journal article

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