Pierre de Villemereuil

Object: Postdoc Position Building a phylogenetic model for horizontal transfers of transposable elements A postdoctoral position (24 months) is available to work at EGCE (Gif-sur-Yvette, France, CNRS / Université Paris-Saclay) from January 2026. Transposable elements (TEs) are repetitive DNA sequences capable of promoting their own mobility. They are widespread across the tree of life and often represent a substantial fraction of eukaryotic genomes. Beyond their ability to invade genomes, TEs are frequently reported to undergo horizontal transfer, enabling their colonization of new hosts. However, understanding and predicting how horizontal transfers shape the distribution of TEs among species is far from straightforward. In particular, estimates of transfer rates based on documented cases are both biased and approximate, since transfers occurring close to speciation events are virtually undetectable. This project aims to develop explicit phylogenetic models of TE evolution that incorporate horizontal transfers, and to use these models to obtain statistical estimates of key evolutionary dynamics of TE families across species (e.g., horizontal transfer and extinction rates). The postdoctoral project will focus on exploring the impact of horizontal transfers on the distribution of TE presence/absence among related species, using statistical and/or computational approaches.

Context The position will be part of a 4-year collaborative project funded by the French National Agency (ANR). The research consortium gathers two departments (from Paris-Saclay university and from Université Lyon 1), and involves 7 Pls and 5 postdocs and PhD students devoted to distinct workpackages of the project. The postdoc will be based at EGCE, which is part of the Institute for Ecology and Evolution (IDEEV). The institute offers an exciting and active scientific life, it is located on the new research campus of Paris-Saclay, 35 km south of Paris. Relevant references Gilbert C et al. 2018. Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Cur. Opin. Genet. Dev. 49:15-24. Le Rouzic A et al. 2013. Reconstructing the Evolutionary History of Transposable Elements. Genome Biol. Evol. 5:77-86. Wallau GL et al. 2016. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila. Mol Biol Evol 33:1094-1109. Profile We are looking for a motivated early career theoretical biologist, with a PhD in theoretical evolutionary biology. Skills in statistics, programming, bio-informatics, and phylogenetic models will be appreciated. Application Formal applications (CV and cover letter) have to be deposited on the CNRS job portal https://emploi.cnrs.fr/Offres/CDD/UMR9191-ARNLER-006/Default.aspx?lang=EN.

Come and join our team! A 2-year postdoc position is available in our "Genome Evolution" department at Univ Paris Saclay. We want to play with phylogenetic models accounting for horizontal transfers of transposable elements. Application& details on the official portal: emploi.cnrs.fr/Offres/CDD/U...

A New Method to Uncover Signatures of Divergent and Stabilizing Selection in Quantitative Traits Abstract. While it is well understood that the pace of evolution depends on the interplay between natural selection, random genetic drift, mutation, and ge

This method is strongly inspired by previous by O Ovaskainen and J Merila :
academic.oup.com/genetics/art...

The key differences are that we use a different test statistics and a quite generally applicable estimator of co-ancestry developed by J Goudet and B Weir:
journals.plos.org/plosgenetics...

We show in the paper that doing so results in calibrated tests of neutrality, even in the face of highly structured scenario, contrary to classical Qst-Fst comparison. 🎉

The clever trick is since both estimates (using between- or within-population co-ancestry) refer to the same ancestral VA, they should be equal under neutrality.

LogAV thus compare these estimates as the Log-ratio of Ancestral Variances (hence the name) to 0 (the expectation under neutrality).

Instead of summarising co-ancestry with a global Qst, or Fst, index, LogAV uses the full, carefully designed, matrices of between- and within-population co-ancestry to refer to the same ancestral additive genetic variance.

As such, it fully accounts for the actual population structure.

A method for identifying local adaptation in structured populations Species occupy diverse, heterogeneous environments, which expose populations to spatially varied selective pressures. Populations in different environments can diverge due to local adaptation. However...

In 2020, O Gaggiotti, J Goudet and I showed that Qst-Fst comparison was uncalibrated with high population structure.

During her PhD with us, Isa do O developed LogAV: a method that accounts for any population structure while testing for local adaptation :
journals.plos.org/plosgenetics...

Apprentissage du logiciel R | École Pratique des Hautes Études L’EPHE − PSL propose une formation pratique à l’utilisation du logiciel libre R pour la gestion et la manipulation des données avant l’analyse statistique (non traitée dans cette formation).Le contenu...

Marre de passer vos journées à Ctrl+C/Ctrl+V vos données dans un tableur et devoir tout refaire à cause d'un soucis de formatage imprévu ? 😡

Suivez la formation @ephe-psl.bsky.social (27 janvier au 5 février) pour apprendre à utiliser R pour traiter vos données :👇
www.ephe.psl.eu/formations-q...

Sujet de stage M2 sur la "dock mussel", cet écotype de moules hybrides qui habite dans les ports. L'objectif est de tester si la dock mussel s’est adaptée grâce à sa variance génétique d’admixture ou si l’admixture n’est que le corolaire du contact secondaire entre les deux espèces parentales.

📢 Postdoc Opportunity – Université Paris-Saclay
🌾🧬💻 Reproductive isolation between crops and their wild relatives
Candidates with PhD in evolutionary genomics & programming skills.
👉 Full description & how to apply: [https://moulon.inrae.fr/en/]
#Postdoc #EvolutionaryGenomics #Speciation

I guess it also depends on the type of article. You can have an LLM write up a literature review for you somewhat easily (this says nothing about the quality of the output...) for example.

Le fiston d'un copain, atteint d'une myopathie, aimerait suivre une L1 de physique/maths. Mais #Grenoble ayant été particulièrement "rétive" 😖 il s'est inscrit au #Bourget et cherche à salarier un.e accompagnant.e. Auriez-vous la gentillesse de faire tourner cette annonce d'emploi ?
👇

The software logo, text that reads "Harpy" and a badge beside the text that indicates it's version 3.0

My lil' baby turns 3.0 today! Most notable features:
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options

#bioinformatics #genomics #linkedreads

GAUTIER Mathieu / baypass public · GitLab GitLab Community Edition

For those interested: 🚀 BayPass v3.1 released!
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits

📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...

With #eseb2025 coming to a close, it is time to start making plans for 2026. Interested in the interface of evolution 🧬 and ecology 🌳? Come to our #ExE conference hosted by @uniexecec.bsky.social in beautiful #Cornwall. Leave your email address at tinyurl.com/EvolxEcol to join our mailing list!

I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species
yeamanlab.weebly.com/uploads/5/7/...

I'm trying to revive an abandoned #bioinformatics software written Go. I have no experience with Go (or similar langs), but doing my best. Does anyone here have even middling experience with Go that can lend some wisdom or time towards this effort?

Figure showing cognitive task administered to wild great tits in the field.

We have a new paper out on the genetic vs. environmental drivers of cognition along an urban gradient: doi.org/10.1007/s100...

@lauragervais.bsky.social @dhanyabharath.bsky.social @annecharmantier.bsky.social @denisreale.bsky.social

#inhibitorycontrol #greattits #animalcognition

Théo Bodineau: The impact of nocturnal warming and prey availability during reproduction in a viviparous lizard In this week’s blog post, we’re checking our calendars and addressing how climate change is causing shifts in breeding dates for reptiles! Discussing the article “A multi-trait evaluation of patter…

👀Behind the paper!👀

🌙Théo Bodineau discusses the impact of nocturnal warming on breeding and gestation in lizards, the challenges of caring for them, and transitioning from medical school to ecology🦎

Read it here👇
functionalecologists.com/2025/06/26/i...

🧪🌍

Really happy to share our new paper ! We characterized the Morpho butterfly visual system, and found a link between opsin evolution, wing coloration and light habitat. We also highlight correlated evolution between amino acids from different opsin genes at a molecular scale !

In 2024, Infant and Child Development (ICD) withdrew as a PCI RR-friendly journal and reneged on three Stage 1 recommendations issued by PCI RR. In addition, Wiley – the publisher of ICD – notified PCI RR and the PCI core team of its decision to withdraw all Wiley journals from PCI and PCI RR, including an additional 9 PCI-friendly journals. Finally, Wiley appears to have banned all of its ~1600 journals from considering submissions that have been previously reviewed by PCI or PCI RR. This statement explains the history of ICD joining PCI RR and developments that led to the current outcome. The PCI RR Managing Board believes that this shift in policy to become “PCI-hostile” renders Wiley journals incompatible not only with community-based preprint review but with preprint archiving in general.

NEW: Statement from the PCI RR Managing Board on the withdrawal of Infant and Child Development as a PCI RR-friendly journal, and the decision by Wiley to refuse preprints that have been peer-reviewed by @peercommunityin.bsky.social / @pci-regreports.bsky.social

Read here ➡️ osf.io/tn8mh

Protocalliphora larvae: moderate but lasting carry-over effects on yearling and mother coloration Raising parasite-infected chicks and being parasitized as a chick can dull your shine. Using a long-term dataset on blue tit, we showed a negative relation

Here a nice paper from Christian Tchana and al on our corsican blue tits!
Protocalliphora larvae: moderate but lasting carry-over
effects on yearling and mother coloration
doi.org/10.1093/behe...
in Behaviroural Ecology

A great work from Erwan on weaver birds in PCI!!
doi.org/10.24072/pcj...

Peer Community In - free peer review & validation of preprints of articles PCI is a non-profit open science organization of scientists to evaluate, recommend and publish research preprints in free open access

Don’t know where to submit your latest research in evolutionary biology? Don’t want to spend research (i.e., taxpayer/public) money enriching major publishers’ shareholders?

Consider Peer Community in : peercommunityin.org

Lastest recommendation in PCI Evol Biol : evolbiol.peercommunityin.org

Evolution of plasticity and character displacement in a fluctuating environment

Our paper on evolution of plasticity and character displacement in a fluctuating environment is now published as early view in Evolution. Check it out if you're interested in eco-evolutionary dynamics, coevolution... and plasticity of course!
academic.oup.com/evolut/advan...

Less than 2 weeks left to apply for this! Come join us in @crab-exeter.bsky.social and as part of team MacaqueNet, to do some comparative social network and life-history research 🤩

La Korrigane, le nouveau bateau du @mnhn.fr est à Paris…

La Korrigane, le navire de recherche bas-carbone du Muséum © C. Guillou

La Korrigane, le navire de recherche bas-carbone du Muséum © C. Guillou

La Korrigane, le navire de recherche bas-carbone du Muséum © C. Guillou

La Korrigane, le navire de recherche bas-carbone du Muséum © C. Guillou

🌊🚢 Le Muséum présente son nouveau navire de recherche bas carbone : la Korrigane !

Du 12 au 14 mai, le navire s’amarre sur la Seine, près du @museedelhomme.fr, pour porter la voix du Muséum en faveur de l’Océan. 👉 www.mnhn.fr/fr/actualite...

#AnnéeDeLaMer #UNOC2025

RUG ondersteunt Peer Community In Sinds april 2025 is de RUG sponsorlid van Peer Community In (PCI). PCI is een non-profitorganisatie onder leiding van wetenschappers die gratis...

A heartfelt thank you to the University of Groningen, which is now a supporter of PCI 🙏 ! You can find more details at
www.rug.nl/library/open...

Une station de recherche en Ariège pour étudier les effets du changement climatique sur la faune

En Ariège, la Station d'écologie théorique et expérimentale (SETE) offre un laboratoire unique en Europe : grottes instrumentées, volières, metatrons... Pour étudier les interactions entre espèces, climat et environnement en conditions contrôlées. 🦌🐛

There is still a few days to apply to this PhD offer! Come enjoy Paris and the "Jardin des Plantes" at the heart of it, while working on exciting science!