COEVOL Multi-Scale Coevolution

The Cocoon Group

de Vienne Damien

Chargé de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 04 72 43 29 09

Email

Twitter

Research interests

I am an evolutionary biologist using and developing bioinformatics tools to explore various macro-evolutionary questions. My main projects at the moment are listed below.  

Exploring the impact of ghost lineages on evolutionary studies

To a first approximation, all species are extinct.  And most of those that are not are still unknown! When we study evolutionary processes, like introgression, horizontal gene transfer or endosymbiosis, we hope that (and do as if)  all this unknown can be neglected. We explore with simulations the effect that ghost lineages (extinct species, unknown extant species and known discarded species) can have on horizontal gene flow detection and characterization.

See these papers (from Théo Tricou's thesis) for recent publications:  
T Tricou, E Tannier and DM de Vienne. 2022. Ghost lineages highly influence the interpretation of introgression tests. Systematic Biology. In press

T Tricou, E Tannier and DM de Vienne. 2022. Ghost lineages invalidate or reverse several results on gene flow. BiorXiv.

Detecting extinct and unknown lineages thanks to horizontal gene transfers

If most species are extinct or unknown, any gene in a genome acquired through horizontal gene transfer may have originated and/or evolved for some time in species that are now extinct or still unknown. With new methods aiming at detecting horizontally acquired genes in genomes, we explore the possibility to predict where in the tree of life some species or clades are missing. This project (and the one briefly described above) has been funded by the French National Research Agency (ANR STHORIZ - 2018-2022). 

Developping tools for Phylogenomics

In the past, I developed differents tools for comparing trees (the Icong index) or for exploring forests of gene trees (Phylo-MCOA). Currently, and in collaboration with colleagues from Lyon and Montpellier, I develop Phylter, a new tool for identifying outlier sequences in phylogenomics datasets. This (still under-development) tool is available here : https://github.com/damiendevienne/phylter

Visualizing phylogenetic trees, pairs of trees, large trees and giant trees 

I am intested in new ways of visualiazing evolutionary relationships between species. My main project on this topic is Lifemap (http://lifemap.univ-lyon1.fr), a popular tool to explore in a single map the complete Tree of Life (more than 1.4 Million species).  This popular tool, also available as a mobile app for Android and Apple, has now been downloaded more than 100,000 times. It is presented in the new Science Museum in Moscow and is (or has been) presented in various exhibitions around the world. Many variations of the tool exist (R package,...) or are under construction (html widget, ...). 

 

 

Publications

Display of 1 to 30 publications on 39 in total

Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”

Théo Tricou, Eric Tannier, Damien de Vienne

PLoS Biology . 22 ( 3 ) : e3002557

DOI: 10.1371/journal.pbio.3002557

Journal article

see the publication

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

Journal article

see the publication

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

Journal article

see the publication

Vers une représentation sonore des arbres phylogénétiques

Arthur Paté, Henri Boutin, Damien de Vienne

16ème Congrès Français d'Acoustique, CFA2022 .

Conference paper

see the publication

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

see the publication

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

see the publication

L'arbre du vivant

Damien de Vienne

101 secrets de l'adn . 978-2-271-12323-7 : 358

Book chapter

see the publication

Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Adrian A Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J Szöllosi

Bioinformatics .

DOI: 10.1093/bioinformatics/btz710

Journal article

see the publication

Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence

Damien M. de Vienne

Molecular Biology and Evolution . 36 ( 1 ) : 174-176

DOI: 10.1093/molbev/msy196

Journal article

see the publication

Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien de Vienne, Elodie Portanier, David Fouchet, Cécile Kaerle...

BMC Evolutionary Biology . 18 ( 1 )

DOI: 10.1186/s12862-018-1289-8

Journal article

see the publication

Coexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, Cécile Kaerle...

Plume de Naturalistes . 2 : 169-190

Journal article

see the publication

Co-occurrence among three divergent plant-castrating fungi in the same Silene host species

Jessica Lee Abbate, Pierre Gladieux, Michael E Hood, Damien de Vienne, Janis Antonovics, Alodie Snirc...

Molecular Ecology . 27 ( 16 ) : 3357 - 3370

DOI: 10.1111/mec.14805

Journal article

see the publication

Overtraining often results in topologically incorrect species trees with maximum likelihood methods

Damien M. de Vienne, Fran Supek, Toni Gabaldon

DOI: 10.1101/140780

Preprint

see the publication

Multiple convergent supergene evolution events in mating-type chromosomes

Sara E Branco, Fantin E Carpentier, Ricardo Rodriguez de La Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur...

Nature Communications . 9 ( 1 ) : 2000

DOI: 10.1038/s41467-018-04380-9

Journal article

see the publication

Tanglegrams are misleading for visual evaluation of tree congruence

Damien M. de Vienne

Preprint

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

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SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION

Henri Boutin, Damien de Vienne

Journées d'Informatique Musicale (JIM) 2017 .

Conference paper

see the publication

RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

Journal article

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Sex and evolution

Pierre-Henri Gouyon, Damien De Vienne, Tatiana Giraud

Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507

Book chapter

see the publication

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Pierre P. Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela G. Aguileta, Damien M. de Vienne...

Molecular Ecology . 23 ( 4 ) : 753-773

DOI: 10.1111/mec.12631

Journal article

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Massive gene swamping among cheese-making Penicillium fungi

Jeanne Ropars, Gabriela Aguileta, Damien M. de Vienne, Tatiana Giraud

Microbial Cell .

DOI: 10.15698/mic2014.01.135

Journal article

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High Variability of Mitochondrial Gene Order among Fungi

Gabriela Aguileta, Damien M. de Vienne, Oliver N. Ross, Michael E Hood, Tatiana Giraud, Elsa Petit...

Genome Biology and Evolution . 6 ( 2 ) : 451-465

DOI: 10.1093/gbe/evu028

Journal article

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Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli

Thomas Bourquard, Damien Mathieu de Vienne, Jérôme Azé

EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances . E.24 : 419-430

Conference paper

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Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis

Damien M. de Vienne, Sébastien Ollier, Gabriela Aguileta

Molecular Biology and Evolution . 29 ( 6 ) : 1587--1598

DOI: 10.1093/molbev/msr317

Journal article

see the publication