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 91 to 120 publications on 749 in total

Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

Marie Cariou, Léa Picard, Laurent Guéguen, Stéphanie Jacquet, Andrea Cimarelli, Oliver Fregoso...

Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )

DOI: 10.1073/pnas.2206610119

Journal article

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Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet...

Current Biology - CB . 32 ( 10 ) : 2325-2333.e1-e6

DOI: 10.1016/j.cub.2022.04.014

Journal article

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From Wolbachia genomics to phenotype: molecular models of cytoplasmic incompatibility must account for the multiplicity of compatibility types

Alice Namias, Mathieu Sicard, Mylène Weill, Sylvain Charlat

Current Opinion in Insect Science . 49 : 78-84

DOI: 10.1016/j.cois.2021.12.005

Journal article

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High Stability of the Epigenome in Drosophila Interspecific Hybrids

Alejandra Bodelón, Marie Fablet, Philippe Veber, Cristina Vieira, Maria Pilar García Guerreiro

Genome Biology and Evolution . 14 ( 2 )

DOI: 10.1093/gbe/evac024

Journal article

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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

Journal article

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Sex‐related differences in aging rate are associated with sex chromosome system in amphibians

Hugo Cayuela, Jean-François Lemaître Lemaître, Jean‐paul Léna, Victor Ronget, Iñigo Martínez‐solano, Erin Muths...

Evolution - International Journal of Organic Evolution . 76 ( 2 ) : 346-356

DOI: 10.1111/evo.14410

Journal article

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Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Alexandre Laverré, Eric Tannier, Anamaria Necsulea

Genome Research . 32 ( 2 ) : 280-296

DOI: 10.1101/gr.275901.121

Journal article

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Ghost lineages highly influence the interpretation of introgression tests

Théo Tricou, Eric Tannier, Damien M. de Vienne

Systematic Biology . 71 ( 5 ) : 1147–1158

DOI: 10.1093/sysbio/syac011

Journal article

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Transposable element dynamics in the host-bacteria association of the cereal weevil Sitophilus oryzae

Mariana G. Ferrarini, Clément Goubert, Nicolas Parisot, Carlos Vargas-Chávez, Agnès Vallier, Rosario Gil...

Mobile DNA 2021 .

Poster

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Origin, evolution and global spread of SARS-CoV-2

Anna Zhukova, Luc Blassel, Frédéric Lemoine, Marie Morel, Jakub Voznica, Olivier Gascuel

Comptes Rendus Biologies . : 1-19

DOI: 10.5802/crbiol.29

Journal article

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Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Jérémy Gauthier, Hélène Boulain, Joke J F A van Vugt, Lyam Baudry, Emma Persyn, Jean-Marc Aury...

Communications Biology . 4

DOI: 10.1038/s42003-021-02480-9

Journal article

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The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Megan Wallace, Kelsey Coffman, Clément Gilbert, Sanjana Ravindran, Gregory Albery, Jessica Abbott...

Virus Evolution . 7 ( 1 ) : veab031

DOI: 10.1093/ve/veab031

Journal article

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Comparison of developmental genome expression in rodent molars reveals extensive developmental system drift

Marie Sémon, Laurent Guéguen, Coraline Petit, Carine Rey, Anne Lambert, Manon Peltier...

DOI: 10.1101/2020.04.22.043422

Preprint

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Relative time constraints improve molecular dating

Gergely J Szöllősi, Sebastian Höhna, Tom A Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

DOI: 10.1101/2020.10.17.343889

Preprint

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The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions

Vincent Mérel, Patricia Gibert, Inessa Buch, Valentina Rodriguez Rada, Arnaud Estoup, Mathieu Gautier...

Molecular Biology and Evolution . 38 ( 10 ) : 4252-4267

DOI: 10.1093/molbev/msab155

Journal article

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Infections by Transovarially Transmitted DMelSV in Drosophila Have No Impact on Ovarian Transposable Element Transcripts but Increase Their Amounts in the Soma

Marlène Roy, Barbara Viginier, Camille A Mayeux, Maxime Ratinier, Marie Fablet

Genome Biology and Evolution . 13 ( 9 )

DOI: 10.1093/gbe/evab207

Journal article

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Phenotypic and Transcriptomic Responses to Stress Differ According to Population Geography in an Invasive Species

Pierre Marin, Angelo Jaquet, Justine Picarle, Marie Fablet, Vincent Merel, Marie Laure Delignette-Muller...

Genome Biology and Evolution . 13 ( 9 ) : evab208

DOI: 10.1093/gbe/evab208

Journal article

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Natural Selection beyond Life? A Workshop Report

Sylvain Charlat, André Ariew, Pierrick Bourrat, María Ferreira Ruiz, Thomas Heams, Philippe Huneman...

Life . 11 ( 10 ) : 1051

DOI: 10.3390/life11101051

Journal article

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

Book chapter

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Transposable Element Expression and Regulation Profile in Gonads of Interspecific Hybrids of Drosophila arizonae and Drosophila mojavensis wrigleyi

Cecília Artico Banho, Daniel Siqueira Oliveira, Annabelle Haudry, Marie Fablet, Cristina Vieira, Claudia Marcia Aparecida Carareto

Cells . 10 ( 12 ) : 3574

DOI: 10.3390/cells10123574

Journal article

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DROP: Molecular voucher database for identification of Drosophila parasitoids

Chia-Hua Lue, Matthew L Buffington, Sonja Scheffer, Matthew Lewis, Tyler A Elliott, Amelia R I Lindsey...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13435

Journal article

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A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Keren Halabi, Eli Levy Karin, Laurent Guéguen, Itay Mayrose

Systematic Biology . 70 ( 3 ) : 608-622

DOI: 10.1093/sysbio/syaa087

Journal article

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Cytotype Affects the Capability of the Whitefly Bemisia tabaci MED Species To Feed and Oviposit on an Unfavorable Host Plant

Sylvain Benhamou, Isabelle Rahioui, Hélène Henri, Hubert Charles, Pedro da Silva, Abdelaziz Heddi...

mBio . 12 ( 6 ) : 1-16

DOI: 10.1128/mBio.00730-21

Journal article

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Wolbachia load variation in Drosophila is more likely caused by drift than by host genetic factors

Alexis Bénard, Hélène Henri, Camille Noûs, Fabrice Vavre, Natacha Kremer

Peer Community In Evolutionary Biology .

DOI: 10.1101/2020.11.29.402545

Journal article

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CPCN - BILAN DE MANDATURE 2016 – 2021

Olivier Coutard, Pierre-Olivier Amblard, Claude Amra, Brigitte Bacroix, Pascal Barone, Yannick Barthe...

Preprint

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