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 and Enzo Marsot theses) for recent publications and preprints: 

Tannier E., Tricou T., Benali S., de Vienne D.M. HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting. BiorXiv.
Tricou T., Tannier E., de Vienne D.M. 2024. Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”. Plos Biology. 22:e3002557.

Tricou T., Tannier E., de Vienne D.M. 2022a. Ghost lineages highly influence the interpretation of introgression tests. Systematic Biology. 71:1147–1158.

Tricou T., Tannier E., de Vienne D.M. 2022b. Ghost lineages can invalidate or even reverse findings regarding gene flow. Plos Biology. 20:e3001776.

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. Multiple approaches for this purpose are explored. This project (and the one briefly described above) has been funded by the French National Research Agency (ANR STHORIZ - 2018-2022). A recent preprint explains the rationale behind this idea: 

Tricou T.,Marsot M., Boussau B., Tannier T., de Vienne DM. 2025. Gene flow can reveal ghost lineages. BiorXiv.

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). Recently, in collaboration with colleagues from Lyon and Montpellier, I developed Phylter, a new tool for identifying outlier sequences in phylogenomics datasets, and Zombi, a tool for simulating the evolution of genomes along the branches of a species tree, that accounts for ghost lineages. 

Comte A., Tricou T., Tannier E., Joseph J., Siberchicot A., Penel S., Allio R., Delsuc F., Dray S., de Vienne D.M. 2023. PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets. Molecular Biology and Evolution. 40:msad234.

Davín A.A., Tricou T., Tannier E., de Vienne D.M.*, Szöllhosi G.J.* 2019. Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages. Bioinformatics. 36(4): 1286–1288.

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

I am interested in new ways of visualiazing evolutionary relationships between species. My main project on this topic is Lifemap (https://lifemap.cnrs.fr), a popular tool to explore in a single map the complete Tree of Life (more than 2.1 Million species from the NCBI taxonomy).  This popular, used by ~20,000 users every month is present in some exhibitions, and used for teaching at all levels. Other visualization-related publications are given below. 

de Vienne D.M. 2019b. Tanglegrams are misleading for visual evaluation of tree congruence. Molecular Biology and Evolution. 36:174–176.

Penel S., de Vienne D.M. 2022. tidy tree: a new layout for phylogenetic trees. Molecular Biology and Evolution. 39:msac204.

de Vienne D.M. 2016. Lifemap: exploring the entire tree of life. PLoS biology. 14:e2001624.
 

 

Publications

Display of 31 to 43 publications on 43 in total

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

see the publication

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

Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes

Elsa Petit, Tatiana Giraud, Damien M. de Vienne, Marco A Coelho, Gabriela Aguileta, Joelle J. Amselem...

Evolution - International Journal of Organic Evolution . 66 ( 11 ) : 3519-3533

DOI: 10.1111/j.1558-5646.2012.01703.x

Journal article

see the publication

Euclidean nature of phylogenetic distance matrices

Damien M. de Vienne, Gabriela Aguileta, Sébastien Ollier

Systematic Biology . 60 ( 6 ) : 826--832

DOI: 10.1093/sysbio/syr066

Journal article

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Theory and examples of reciprocal influence between hosts and pathogens, from short-term to long term interactions: coevolution, cospeciation and pathogen speciation following host shifts

Aurélien Tellier, Damien M. de Vienne, Tatiana Giraud, Michael Hood, Guislaine Refrégier

Host-Pathogen Interactions: Genetics, Immunology, and Physiology . 978-1608762866

Book chapter

see the publication

Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum

Damien de Vienne, G Refrégier, Me Hood, A Guigue, B Devier, E Vercken...

Journal of Evolutionary Biology . 22 ( 4 ) : 683--698

Journal article

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Phylogenetic determinants of potential host shifts in fungal pathogens

Damien de Vienne, Me Hood, T Giraud

Journal of Evolutionary Biology . 22 ( 12 ) : 2532--2541

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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Speciation in fungi

Tatiana Giraud, Guislaine Refrégier, Mickaël Le Gac, Damien M. de Vienne, Michael E Hood

Fungal Genetics and Biology . 45 ( 6 ) : 791--802

DOI: 10.1016/j.fgb.2008.02.001

Journal article

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When can host shifts produce congruent host and parasite phylogenies? A simulation approach

Damien M de Vienne, Tatiana Giraud, J A Shykoff

Journal of Evolutionary Biology . 20 ( 4 ) : 1428--1438

Journal article

see the publication