COEVOL Multi-Scale Coevolution

Evolutionary Genetics of Interactions Group

The Cocoon Group

Functional Evolutionary Genomics 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 241 to 270 publications on 706 in total

Biodiversité, évolution et fonctionnement des écosystèmes

Isabelle Arzul, Salvador Bailon, David Bass, Pierre Boudry, Philippe Béarez, Elodie Blanchard...

Les Cahiers des prospectives . hors série : 25-33.

Book chapter

see the publication

MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Aurélie Siberchicot, Adrien Bessy, Laurent Gueguen, Gabriel A. B. Marais

Genome Biology and Evolution . 9 ( 10 ) : 2506-2509

DOI: 10.1093/gbe/evx178

Journal article

see the publication

Pitfalls in supermatrix phylogenomics

Herve Philippe, Damien M. de Vienne, Vincent Ranwez, Béatrice Roure, Denis Baurain, Frédéric Delsuc

European Journal of Taxonomy . 283 : 1-25

DOI: 10.5852/ejt.2017.283

Journal article

see the publication

Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

S. Pantalacci, Laurent Guéguen, C. Petit, A. Lambert, R. Peterkova, M. Sémon

Genome Biology . 18 : 29

DOI: 10.1186/s13059-017-1157-7

Journal article

see the publication

Genome sequencing of the behaviour manipulating virus LbFV reveals a possible new virus family

D. Lepetit, B. Gillet, S. Hughes, K. Kraaijeveld, Julien Varaldi

Genome Biology and Evolution . 8 : 3718-3738

DOI: 10.1093/gbe/evw277

Journal article

see the publication

Obligate dependence does not preclude changing partners in a Russian dolls symbiotic system

Emmanuelle Jousselin, Fabrice Vavre

Peer Community In Evolutionary Biology . : 1-2

DOI: 10.24072/pci.evolbiol.100002

Journal article

see the publication

Managing cold tolerance and quality of mass-produced Drosophila suzukii flies to facilitate the application of biocontrol through incompatible and sterile insect techniques

Katerina Nikolouli, F. Sassú, Thomas Enriquez, Patricia Gibert, Frédéric Vavre, Laurence Mouton...

Third FAO–IAEA International Conference on Area-wide Management of Insect Pests .

Poster

see the publication

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

Journal article

see the publication

High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments

Clément Goubert, Hélène Henri, Guillaume Minard, Claire Valiente Moro, Patrick Mavingui, Cristina Vieira...

Molecular Ecology . 26 ( 15 ) : 1-14

DOI: 10.1111/mec.14184

Journal article

see the publication

SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION

Henri Boutin, Damien de Vienne

Journées d'Informatique Musicale (JIM) 2017 .

Conference paper

see the publication

DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve...

Genome Biology and Evolution . 9 ( 5 ) : 1312-1319

DOI: 10.1093/gbe/evx069

Journal article

see the publication

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Guillaume Fertin, Géraldine Jean, Eric Tannier

Algorithms for Molecular Biology . 12 : 16 (11 pages)

DOI: 10.1186/s13015-017-0107-y

Journal article

see the publication

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses

Edwin Jacox, Mathias Weller, Eric Tannier, Celine Scornavacca

Bioinformatics . 33 ( 7 ) : 980-987

DOI: 10.1093/bioinformatics/btw778

Journal article

see the publication

Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

T. Boldanova, A. Suslov, M.H. Heim, A. Necsulea

EMBO Molecular Medicine . 9 : 816-834

DOI: 10.15252/emmm.201607006

Journal article

see the publication

Elicitation of superparasitization behavior from the parasitoid wasp Leptopilina boulardi by the organophosphorus insecticide chlorpyrifos

Jean-Marie Delpuech

Science of the Total Environment . 580 : 907-911

DOI: 10.1016/j.scitotenv.2016.12.037

Journal article

see the publication

Evolutionary changes in symbiont community structure in ticks

Olivier Duron, Florian Binetruy, Valérie Noël, Julie Cremaschi, Karen Mccoy, Céline Arnathau...

Molecular Ecology . 26 ( 11 ) : 2905–2921

DOI: 10.1111/mec.14094

Journal article

see the publication

Susceptibility of MED-Q1 and MED-Q3 Biotypes of Bemisia tabaci (Hemiptera: Aleyrodidae) Populations to Essential and Seed Oils

Samuel Fogné Drabo, Olivier Gnankine, Imael H N Bassolé, Roger Charles Nébié, Laurence Mouton

Journal of Economic Entomology . 110 ( 3 ) : 1031 - 1038

DOI: 10.1093/jee/tox100

Journal article

see the publication

Self and Nonself from a Genomic Perspective: Transposable Elements

Marie Fablet, Judit Salces-Ortiz, Bianca Fraga Menezes, Marlène Roy, Cristina Vieira

Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts . 2 ( 5 ) : 111-128

DOI: 10.1007/978-3-319-61569-1_6

Book chapter

see the publication

Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biemont, Vincent Daubin, Cedric Feschotte...

PLoS Biology . 15 ( 2 ) : np

DOI: 10.1371/journal.pbio.2001536

Journal article

see the publication

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost...

Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431

DOI: 10.1093/gbe/evx255

Journal article

see the publication

Comparative Methods for Reconstructing Ancient Genome Organization

Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve

Comparative Genomics: Methods and Protocols . : 343 - 362

DOI: 10.1007/978-1-4939-7463-4_13

Book chapter

see the publication

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

Valèria Romero-Soriano, Laurent Modolo, Hélène Lopez-Maestre, Bruno Mugat, Eugénie Pessia, Séverine Chambeyron...

Genome Biology and Evolution . 9 ( 6 ) : 1450 - 1470

DOI: 10.1093/gbe/evx091

Journal article

see the publication

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve, Akbar A Rafiey, Adrian A Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau...

DOI: 10.1101/127548

Other publication

see the publication

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Tom Williams, Gergely Szöllősi, Anja Spang, Peter Foster, Sarah Heaps, Bastien Boussau...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 23 ) : E4602-E4611

DOI: 10.1073/pnas.1618463114

Journal article

see the publication

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron...

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

Journal article

see the publication

Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

Journal article

see the publication

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Baptiste Saudemont, Alexandra Popa, Joanna Parmley, Vincent Rocher, Corinne Blugeon, Anamaria Necsulea...

Genome Biology . 18 : 208

DOI: 10.1186/s13059-017-1344-6

Journal article

see the publication

Impact of Wolbachia on oxidative stress sensitivity in the parasitic wasp Asobara japonica

David Monnin, Natacha Kremer, Emmanuel Desouhant, Fabrice Vavre

PLoS ONE . 5 : 10

DOI: 10.1371/journal.pone.0175974

Journal article

see the publication

Dating with transfers

Adrián Davín, Gergely J Szöllosi, Eric Tannier, Bastien Boussau, Vincent Daubin

Journées Ouvertes Biologie Informatique Mathématiques .

Conference paper

see the publication