Damien M. de Vienne

Damien M. de Vienne

@damdevienne.bsky.social

Research director @CNRS (LBBE, Lyon, FR). Phylogenetics/phylogenomics, Ghost lineages, Tree of Life, Horizontal Gene Transferts. Creator of Lifemap (https://lifemap.cnrs.fr). Currently visitor at FORTH (Crete, Greece) in Stamatakis' lab (2025-2027).

110 followers119 following38 posts

Damien M. de Vienne reposted

Nicolas Bierne
@couplingdmi.bsky.social

📢 Save the date, submit your abstract, spread the word! ERA 2027 - Evolutionary Responses to Anthropogenic Drivers 📅 20–21 April 2027 📍Nantes, France 🇫🇷 With a fantastic lineup of keynote speakers: @tatianagiraud.bsky.social, Daniel Streicker, Ophélie Ronce & Bruno Ernande! 🔗 era2027.sciencesconf.org

era2027.sciencesconf.orgERA 2027 - Evolutionary Responses to Anthropogenic drivers - Sciencesconf.orgSciencesconf.org

Damien M. de Vienne reposted

CNRS Biologie
@cnrsbiologie.bsky.social

#ResultatScientifique🔎| Dans PLOS Genetics, des scientifiques proposent une méthode pour mieux estimer le risque de porter un variant génétique associé à la maladie de Charcot et à la démence fronto-temporale. ✍️ Dominique de Vienne et Damien de Vienne buff.ly/Corh0aA

buff.lyMaladie de Charcot et démence fronto-temporale : réévaluer les risques en tenant compte de l'âgeDans un article publié dans PLOS Genetics, des scientifiques proposent une méthode pour mieux estimer la probabilité de porter un variant génétique associé à la maladie de Charcot et à la démence…
Damien M. de Vienne
@damdevienne.bsky.social

...all this under idealized condition 😉. On the way, we illustrate (Fig1 ) how HGTs can reveal ghost nodes in gene trees. Not only nodes of type 1 that lie along the branches of the Sampled Species Tree (SST) but also ghost nodes of type 2 having no descendant at all in the SST!

Damien M. de Vienne
@damdevienne.bsky.social

🌍🎉 New languages in Lifemap! In addition to French 🇫🇷 and English 🇬🇧, Lifemap is now available in: 🇬🇷 Ελληνικά 🇪🇸 Español 🇩🇪 Deutsch A big thank you to Lucía Martín Fernández 🇪🇸, Noah Wahl 🇩🇪 and Georgios Koutsovoulos 🇬🇷 for translation review and corrections! 🙏 🔗 lifemap.cnrs.fr

Damien M. de Vienne
@damdevienne.bsky.social

🌳 Lifemap update!! - Lifemap now includes synonyms for taxa that have them. - 🔎 Searching with a synonym retrieves the correct taxon. Synonyms (if any) are also displayed in the taxon box! Well, this seems like an obvious feature, but it was missing!! 😅 see you there! lifemap.cnrs.fr

Damien M. de Vienne
@damdevienne.bsky.social

New paper out in PLOS Genetics! doi.org/10.1371/jour... Written with my dad (Prof. emeritus D de Vienne), we revisit genetic risk estimation for relatives of C9orf72 repeat expansion carriers. This variant is the most common genetic cause of ALS and FTD, two major neurodegenerative disorders. 1/3

doi.orgAge-based risk estimates for C9orf72RE-related diseases: Theoretical developments and added value for genetic counselingAuthor summary Amyotrophic lateral sclerosis and frontotemporal dementia are often linked to a mutation called C9orf72 repeat expansion. Relatives of mutation carriers are usually informed of a 50% (c...
Damien M. de Vienne
@damdevienne.bsky.social

In genetic counselling, a child of a carrier is usually told to have a 50% risk of carrying the variant (Mendelian proportion) This estimate ignores the age-dependent penetrance of ALS/FTD. When this information is integrated using a Bayesian framework, the probabilities become very different: 2/3

Damien M. de Vienne
@damdevienne.bsky.social

First slide ready for my talk tomorrow (fr) in a "Large Scales" webinar series #FRBioEEnVIS. Tree of Life is a large-scale object: biodiversity × deep time. Visualizing it ( #Lifemap) helps us grasp its scale and identify biases in its analysis (ghosts). Let's see if I can make that case tomorrow. 🙂

Damien M. de Vienne
@damdevienne.bsky.social

Well... An interesting and somewhat disturbing first experience as a speaker at a virtual conference. Alone in my office, in front of my computer, with no sound and no view of the audience... At least the experience matched my topic: ghosts. 👻

Damien M. de Vienne
@damdevienne.bsky.social

📣 The article presenting pylifemap is now published in Methods Ecol Evol @methodsinecoevol.bsky.social! Read it here: besjournals.onlinelibrary.wiley.com/doi/10.1111/... ...If you want to map your data onto the NCBI taxonomy as visualized in Lifemap, give it a try! lifemap-tol.github.io/pylifemap/

besjournals.onlinelibrary.wiley.compylifemap: Mapping data onto the tree of lifeThe need to visualize data associated with NCBI Taxonomy Identifiers is growing in various biological fields ranging from comparative genomics to metagenomics and metabarcoding, and even for outre...

Damien M. de Vienne reposted

Pint of Science FR
@pintofscience.fr

🎉ÇA Y EST !! Le programme #pint26 est en ligne dans (presque) toutes les villes. 👉 pintofscience.fr 🎫 Ouverture de la billetterie lundi 13 avril à 8h, vous avez deux semaines pour repérer vos soirées préférées ! 📅 Festival du 18 au 20 mai 2026. 👓🧠 Alors, quelle soirée vous tente le plus?

Damien M. de Vienne reposted

Marie Fablet
@mariefablet.bsky.social

We are recruting an assistant engineer for 18 months at LBBE (Lyon, France) in molecular biology of Drosophila. The project is to study the interactions between response to viral infections and control of transposable elements. emploi.cnrs.fr/Offres/CDD/U...

emploi.cnrs.frPortail Emploi CNRS - Offre d'emploi - Assistant Ingénieur / Assistante ingénieure (H/F) en biologie moléculaire et zootechnie des drosophilesAssurez-vous que votre profil candidat soit correctement renseigné avant de postuler
Damien M. de Vienne
@damdevienne.bsky.social

Finally! Thrilled to share our new work on ghosts and horizontal gene flow! After showing that ghost lineages (extinct, unknown, unsampled) can distort gene flow detection, we now show that gene flow signals can be used to detect, quantify, and place ghost species in the Tree of Life!(1/2)

Evolutionary Journal of the Linnean Society@evojlinnsoc.bsky.social

Who you gonna call? EVOLUTIONARY SCIENTISTS! Ghost species (no, not species of ghost) are extinct, unknown & unsampled taxa...and they vastly outnumber those included in phylogenetics. This hidden diversity can complicate phylogenetic signals of horizontal gene flow, impacting their study...(1/2)🧪

Damien M. de Vienne
@damdevienne.bsky.social

There’s still work ahead to turn this proof of concept into a method usable on real data. This is one of the focus of Enzo Marsot’s PhD, co-first author on this article, where he develops deep learning models for this goal. Stay tuned! (2/2)

Damien M. de Vienne
@damdevienne.bsky.social

Our new work on the overlooked impact of ghosts for HGT detection and simulation has just been published in MBE @molbioevol.bsky.social !

Molecular Biology and Evolution@molbioevol.bsky.social

Tannier, @damdevienne.bsky.social et al. simulated horizontal gene transfer (HGT) with ghost lineages, finding that, when only 1% of potential donors are sampled, ca. 50% of SPR-inferred HGTs misidentify donors. 🔗 doi.org/10.1093/molbev/msaf128 #evobio #HGT

doi.orgHGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and RegraftingAbstract. When a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient gen
Damien M. de Vienne
@damdevienne.bsky.social

Hi, tonight I will give my conference on "Exploring the tree of Life", a special type of immersive experience with animations projected under the dome of the planetarium!!

CNRS Rhône Auvergne@cnrs-rhoneauvergne.bsky.social

#Évènement🎟️| Ce soir on se pose au ciné ou on se pose des questions❓ En compagnie de @damdevienne.bsky.social du #LBBE visionner les 5️⃣ grandes crises biologiques : le tout assis confortablement sous la voute du planétarium😎 #ÉchappéesInattendues ➕d'info 👇 echappeesinattendues.cnrs.fr/event/voyage...

Damien M. de Vienne
@damdevienne.bsky.social

New preprint to (finaly) present the proof of concept that detection of HGTs can help reveal invisible (ghost) lineages along the branches of a species tree. More work on that coming soon! www.biorxiv.org/content/10.1...

biorxiv.orgGene flow can reveal ghost lineagesGhost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of hor...
Damien M. de Vienne
@damdevienne.bsky.social

New preprint on a funny obvservation: treating horizontal gene transfers (HGTs) as Subtree Pruning and Regrafting (SPRs) operations (as is commonly done) assumes that no ghost lineages are around... which is unlikely! www.biorxiv.org/content/10.1...

biorxiv.orgHGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and RegraftingWhen a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the ...

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