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 766 in total

Influence of secondary symbionts on host plant utilization and selection in the whitefly Bemisia tabaci.

Sylvain Benhamou, Isabelle Rahioui, Hélène Henri, Zainab Belgaidi, Hubert Charles, Pedro da Silva...

10th congress of the International Symbiosis Society (ISS) - 3rd International Conference on Holobionts (joint meeting) .

Poster

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Role of symbionts in insects' ecological diversification: cytotype influences exploitation of an unfavorable host plant in the sap-feeder Bemisia tabaci (Hemiptera: Aleyrodidae).

Sylvain Benhamou, Isabelle Rahioui, Zainab Belgaidi, Hélène Henri, Hubert Charles, Pedro da Silva...

Rencontres du Groupe Régional de Recherche en Microbiologie des Interactions (G-RREMI) 2022 .

Poster

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Analyses of symbiotic bacterial communities in the plant pest Bemisia tabaci reveal high prevalence of Candidatus Hemipteriphilus asiaticus on the African continent

Laurence Mouton, Hélène Henri, Rahim Romba, Zainab Belgaidi, Olivier Gnankiné, Fabrice Vavre

Peer Community Journal . 2 ( e20 )

DOI: 10.24072/pcjournal.103

Journal article

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Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria

Théophile Grébert, Laurence Garczarek, Vincent Daubin, Florian Humily, Dominique Marie, Morgane Ratin...

Genome Biology and Evolution . 14 ( 4 ) : evac035

DOI: 10.1093/gbe/evac035

Journal article

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Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

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Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Rui Borges, Bastien Boussau, Sebastian Höhna, Ricardo Pereira, Carolin Kosiol

Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346

DOI: 10.1111/2041-210X.13980

Journal article

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Relative Time Constraints Improve Molecular Dating

Gergely Szöllõsi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

Systematic Biology . 71 ( 4 ) : 797-809

DOI: 10.1093/sysbio/syab084

Journal article

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Vers une représentation sonore des arbres phylogénétiques

Arthur Paté, Henri Boutin, Damien de Vienne

16ème Congrès Français d'Acoustique, CFA2022 .

Conference paper

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Larval density in the invasive Drosophila suzukii : immediate and delayed effects on life-history traits

Alicia Reyes-Ramírez, Zaïnab Belgaidi, Patricia Gibert, Thomas Pommier, Aurélie Siberchicot, Laurence Mouton...

DOI: 10.1101/2022.10.06.511120

Preprint

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High-throughput genomics and transcriptomics to decipher host-symbiont molecular dialogue in the cereal weevil Sitophilus oryzae and Sodalis pierantonius endosymbiotic association

Nicolas Parisot, Mariana Galvão Ferrarini, Clément Goubert, Carlos Vargas-Chávez, Agnès Vallier, Benjamin Gillet...

10th congress of the International Symbiosis Society (ISS) - 3rd International Conference on Holobionts (joint meeting) .

Poster

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

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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 . 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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Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes

Cecilia Banho, Vincent Mérel, Thiago Oliveira, Claudia Carareto, Cristina Vieira

Scientific Reports . 11 ( 1 ) : 9844

DOI: 10.1038/s41598-021-89366-2

Journal article

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Oxidative and radiation stress induces transposable element transcription in Drosophila melanogaster

Daniel Siqueira de Oliveira, Marcos Trindade Rosa, Cristina Vieira, Elgion Loreto

Journal of Evolutionary Biology . 34 ( 4 ) : 628-638

DOI: 10.1111/jeb.13762

Journal article

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