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
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”
PLoS Biology . 22 ( 3 ) : e3002557
Journal article
see the publicationEndoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
eLife . 12 : e85993
DOI: 10.7554/eLife.85993
Journal article
see the publicationPhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets
Molecular Biology and Evolution . 40 ( 11 ) : msad234
Journal article
see the publicationVers une représentation sonore des arbres phylogénétiques
16ème Congrès Français d'Acoustique, CFA2022 .
Conference paper
see the publicationtidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
Journal article
see the publicationGhost lineages can invalidate or even reverse findings regarding gene flow
PLoS Biology . 20 ( 9 ) : e3001776
Journal article
see the publicationGhost lineages highly influence the interpretation of introgression tests
Systematic Biology . 71 ( 5 ) : 1147–1158
Journal article
see the publicationGlobal survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Journal article
see the publicationZombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages
Bioinformatics .
Journal article
see the publicationTanglegrams Are Misleading for Visual Evaluation of Tree Congruence
Molecular Biology and Evolution . 36 ( 1 ) : 174-176
Journal article
see the publicationCoexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
BMC Evolutionary Biology . 18 ( 1 )
Journal article
see the 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
Journal article
see the 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
Journal article
see the publicationOvertraining often results in topologically incorrect species trees with maximum likelihood methods
DOI: 10.1101/140780
Preprint
see the publicationMultiple convergent supergene evolution events in mating-type chromosomes
Nature Communications . 9 ( 1 ) : 2000
Journal article
see the publicationPitfalls in supermatrix phylogenomics
European Journal of Taxonomy . 283 : 1-25
DOI: 10.5852/ejt.2017.283
Journal article
see the publicationSONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION
Journées d'Informatique Musicale (JIM) 2017 .
Conference paper
see the publicationLifemap: Exploring the Entire Tree of Life
PLoS Biology . 14 ( 12 )
Journal article
see the publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Journal article
see the publicationSex and evolution
Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507
Book chapter
see the publicationDegeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Molecular Biology and Evolution . 32 ( 4 ) : 928-943
Journal article
see the publicationFungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes
Molecular Ecology . 23 ( 4 ) : 753-773
DOI: 10.1111/mec.12631
Journal article
see the publicationMassive gene swamping among cheese-making Penicillium fungi
Microbial Cell .
Journal article
see the publicationHigh Variability of Mitochondrial Gene Order among Fungi
Genome Biology and Evolution . 6 ( 2 ) : 451-465
DOI: 10.1093/gbe/evu028
Journal article
see the 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
Conference paper
see the publicationLineage selection and the maintenance of sex
PLoS ONE . 8 ( 6 ) : e66906
Journal article
see the publicationPhylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis
Molecular Biology and Evolution . 29 ( 6 ) : 1587--1598
Journal article
see the publicationEfficient Prediction of Co-Complexed Proteins Based on Coevolution
PLoS ONE . 7 ( 11 ) : 1-13
Journal article
see the publication