🚨 New offer in our lab: 🐝🧬22-month postdoc or engineer position to estimate the effectiveness of the genetic queen fertilisation control in honey bees through large-scale sequencing and genomic analysis Location: Toulouse, France 😍 More information: thibaultleroyfr.github.io/pdf/Annonce_... Reposts🙏

PCA is one of those techniques that sounds unreasonable (yeah sure we all want to fit a p-dimensional ellipsoid to our data) but turns out to be a reasonable solution to a wide range of problems. Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria

POSTDOC recruitment! We’re looking for a post-doc to join us to work on the (epi)genetic basis of inbreeding depression as part of the ANR-funded project FRIDA macrostomum.wordpress.com/the-genetic-... Please share!

Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti... Thanks to those who already shared the link!

A nice opinion paper (doi.org/10.1016/j.pb... ) from @anneroulin.bsky.social that highlights the need for caution when generalizing about the importance of TEs in local plant adaptation. #TEsky #transposon

#TEsky Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics doi.org/10.1016/j.pb...

A nice work, I think. doi.org/10.1111/mec....

From experience, using whatshap to build small blocks then phasing with those as priors usually seems to work well. + sanity check with phase-insensitive methods like SMC++

Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors https://www.biorxiv.org/content/10.1101/2025.11.24.690249v1

doi.org/10.1038/s414... and onlinelibrary.wiley.com/doi/full/10....

Our paper on the temporal genomics of Ethiopian birds has been highlighted (and gotten the cover) in @genomebiolevol.bsky.social Article: doi.org/10.1093/gbe/evaf163 Highlight: doi.org/10.1093/gbe/evaf175 w/ @bourgeoisyann.bsky.social, @lcampillo.bsky.social, and others not on bsky

Really cool www.biorxiv.org/content/10.1...

Cool. www.science.org/doi/10.1126/...

Cool news from the former lab. www.pnas.org/doi/10.1073/...

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...

Nice!

Wondering whether there is work about the role of polymorphic, possibly long indels in explaining Lewontin's paradox? Wouldn't one expect reduction in Ne proportional to the frequency of the deletion? Possibly in combination with interference process?

The latest paper on Ethiopian birds, led by @jdmanthey.bsky.social doi.org/10.1093/gbe/...

Cool! doi.org/10.1093/molb...

For whoever interrested in, Pascaline Salvado will eventually present her ongoing work on Ophrys orchids today on spot 359 at #ESEB2025. Do not hesitate to come and discuss about science and/or post-doc opportunities with us!

If you like evolutionary constraints, serial homology, teeth, bats or all of the above, come and see our talk and posters! 👇🏼 At 3:30 I will talk about the genomic and developmental foundation of adaptive tooth shape evolution in bats Room S09 rm 118-119 #ESEB2025

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies academic.oup.com/mbe/article/...

*ALERT! GLOBAL GENETIC DIVERSITY TREND RE-ANALYSIS* "Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis" doi.org/10.1101/2025...

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1

A couple of things: I have a new website: yannbourgeois.github.io The url www.methodspopgen.com now redirects to a dedicated methods section on the new website. As a complement, note that we have developed Physalia workshops that may be useful to newcomers in the field: github.com/PhysaliaIntr...

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

Where we look at anoles in the city doi.org/10.1111/mec....

I just concluded two weeks of very productive work with my Argentinian colleagues at CEPAVE in La Plata. Thanks to them all! Great to see that people remain highly motivated to do science, despite the government de-funding, and expecting interesting results! Project with @cbgpmontpellier.bsky.social

Interested to know more about a new theory relating the #evolution of #sexchromosomes to the rules of #speciation? Check out this paper that we published with Denis Roze in the last issue of #Science. PDF here: www.science.org/stoken/autho...

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

The evolution of tandem repeat sequences under partial selfing and different modes of selection https://www.biorxiv.org/content/10.1101/2025.07.04.663195v1

Cool! doi.org/10.1038/s414...

Our proposal on the evolution of bee orchids will be funded by an #ANR project! With @bourgeoisyann.bsky.social, we will be recruiting two people to work on: 🌸 innovative/AI-powered phenotyping 🧬 genomic architecture of adaptive radiations Get in touch and meet up at @eseb2025.bsky.social!

"A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools" - a new PCI Genomics recommendation from Raúl Castanera: tinyurl.com/mr2ac84m

PhaseGen: Exact Solutions for Time-Inhomogenous Multivariate Coalescent Distributions under Diverse Demographies https://www.biorxiv.org/content/10.1101/2025.05.13.653888v1

📣📣📣 PCI Plants @pciplants.bsky.social has been launched!!! @bourgeoisyann.bsky.social @mangolab.bsky.social @francoissabot.bsky.social @jorisbertrand.bsky.social

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals https://www.biorxiv.org/content/10.1101/2025.02.07.637047v1