I just posted a large update of methodspopgen.com / yannbourgeois.github.io/projects/4_p.... It should now list most of the more recent advances in deep learning, scans for introgression and ARG inference. Work on the page still in progress, but it may already give a few pointers.

I’m getting tired of mis-citations, especially in reviews (1/2) www.sciencedirect.com/science/arti... sates "[...] the increased TE load coinciding with the expansion on of A. thaliana popu- lations, further underscoring the involvement of TEs in population evolution and expansion [36]"

Ever wondered what makes some alleles dominant (A) and others recessive (a) ? In our new paper, we explored how a series of recently discovered "dominance modifiers", genetic elements that have long remained elusive, achieve their regulatory function. journals.plos.org/plosgenetics...

To test. doi.org/10.1101/2025...

New preprint! We sequenced 175 'Alalā (Hawaiian crow) genomes to understand why >50% of eggs fail to hatch in a species recovered from just 9 individuals. What we found was a both exciting and surprising. www.biorxiv.org/content/10.6...

ATHILAfinder: a tool to detect ATHILA LTR retrotransposons in plant genomes https://www.biorxiv.org/content/10.64898/2026.03.20.713144v1

Cool!

With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz

Popformer: Learning general signatures of positive selection with a self-supervised transformer https://www.biorxiv.org/content/10.64898/2026.03.06.710163v1

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

The B-value calculator: expected diversity under background selection https://www.biorxiv.org/content/10.64898/2026.03.04.709642v1

Hello Bluesky! Does Nₑ really explain mutation rate (μ) or genome size (GS) in vertebrates? We find the apparent Nₑ–μ link in Bergeron et al. (2023) is a “back-door” path via generation time, and GS is decoupled from both Nₑ and life-history traits. www.pnas.org/doi/10.1073/... #evobio #PNAS

In addition to the post-doc advertised by Joris, note the opening of the other post-doc position in population genomics, located in Montpellier (IRD). yannbourgeois.github.io/blog/2026/po... You can apply at this link: emploi-recrutement.ird.fr/offre-de-emp... bsky.app/profile/jori...

With @bourgeoisyann.bsky.social and @anaisgibert.bsky.social we are recruiting a post-doc to integrate multi-omic data to investigate the links between genotype, phenotype and fitness in Ophrys orchids evolutionary divergence. Feel free to contact us or share! www.jorisbertrand.com/wp-content/u...

Meiotic drive has long been considered as a genetic curiosity. Genomic "footprints" suggest otherwise. Check out our new review doi.org/10.1093/molb..., a cross-taxa synthesis arguing that recurrent drive is a pervasive and underappreciated force in genome evolution.

🚨 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...