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:
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).
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 develop Phylter, a new tool for identifying outlier sequences in phylogenomics datasets, or Zombi, a tool for simulating the evolution of genomes along the branches of a species tree, that accounts for ghost lineages.
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, 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, Etc). Other visualization-related publications are given below.
de Vienne D.M. 2016. Lifemap: exploring the entire tree of life. PLoS biology. 14:e2001624.
Publications
Affichage des publications 1 à 30 sur 41 au total
Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”
PLoS Biology . 22 ( 3 ) : e3002557
Article dans une revue
voir la publicationEndoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
eLife . 12 : e85993
DOI: 10.7554/eLife.85993
Article dans une revue
voir la publicationPhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets
Molecular Biology and Evolution . 40 ( 11 ) : msad234
Article dans une revue
voir la publicationVers une représentation sonore des arbres phylogénétiques
16ème Congrès Français d'Acoustique, CFA2022 .
Acte de congrès
voir la publicationtidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
Article dans une revue
voir la publicationGhost lineages can invalidate or even reverse findings regarding gene flow
PLoS Biology . 20 ( 9 ) : e3001776
Article dans une revue
voir la publicationGhost lineages highly influence the interpretation of introgression tests
Systematic Biology . 71 ( 5 ) : 1147–1158
Article dans une revue
voir la publicationL'arbre du vivant
101 secrets de l'adn . 978-2-271-12323-7 : 358
Chapitre d'ouvrage
voir la publicationZombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages
Bioinformatics .
Article dans une revue
voir la publicationGlobal survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Article dans une revue
voir la publicationTanglegrams Are Misleading for Visual Evaluation of Tree Congruence
Molecular Biology and Evolution . 36 ( 1 ) : 174-176
Article dans une revue
voir la publicationCo-occurrence among three divergent plant-castrating fungi in the same Silene host species
Molecular Ecology . 27 ( 16 ) : 3357 - 3370
DOI: 10.1111/mec.14805
Article dans une revue
voir la publicationCoexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
BMC Evolutionary Biology . 18 ( 1 )
Article dans une revue
voir la publicationCoexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie
Plume de Naturalistes . 2 : 169-190
Article dans une revue
voir la publicationOvertraining often results in topologically incorrect species trees with maximum likelihood methods
DOI: 10.1101/140780
Pré-publication
voir la publicationMultiple convergent supergene evolution events in mating-type chromosomes
Nature Communications . 9 ( 1 ) : 2000
Article dans une revue
voir la publicationTanglegrams are misleading for visual evaluation of tree congruence
Pré-publication
voir la publicationPitfalls in supermatrix phylogenomics
European Journal of Taxonomy . 283 : 1-25
DOI: 10.5852/ejt.2017.283
Article dans une revue
voir la publicationSONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION
Journées d'Informatique Musicale (JIM) 2017 .
Acte de congrès
voir la publicationLifemap: Exploring the Entire Tree of Life
PLoS Biology . 14 ( 12 )
Article dans une revue
voir la publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Article dans une revue
voir la publicationSex and evolution
Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507
Chapitre d'ouvrage
voir la publicationDegeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Molecular Biology and Evolution . 32 ( 4 ) : 928-943
Article dans une revue
voir la publicationFungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes
Molecular Ecology . 23 ( 4 ) : 753-773
DOI: 10.1111/mec.12631
Article dans une revue
voir la publicationMassive gene swamping among cheese-making Penicillium fungi
Microbial Cell .
Article dans une revue
voir la publicationHigh Variability of Mitochondrial Gene Order among Fungi
Genome Biology and Evolution . 6 ( 2 ) : 451-465
DOI: 10.1093/gbe/evu028
Article dans une revue
voir la publicationIdentification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli
EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances . E.24 : 419-430
Acte de congrès
voir la publicationLineage selection and the maintenance of sex
PLoS ONE . 8 ( 6 ) : e66906
Article dans une revue
voir la publication