Yann Bourgeois

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...

The Evolutionary Genomics of Meiotic Drive Abstract. Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologist

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.

It is becoming increasingly obvious that it is all a simulation...

🚨 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

A cartoon Macrostomum flatworm

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!

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

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....

Masking correctly and assembly fragmentation is more critical I suspect.

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

Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress - Nature Communications Genomic coupling theory predicts that speciation progress involves the buildup of genomic associations that manifest in aggregate barriers to gene flow. This study develops approaches to quantify geno...

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

RDAforest: Identifying Environmental Drivers of Polygenic Adaptation Identifying environmental gradients driving genetic adaptation is one of the major goals of ecological genomics. We present RDAforest, a methodology that leverages the predominantly polygenic nature ....

doi.org/10.1111/1755...

Highlight: A Century of Genomic Data Preserved in Museums Illuminates Bird Conservation in Ethiopia Dawn in the Ethiopian Highlands is filled with a rich and unique chorus of bird songs. This mountainous region (Fig. 1a) comprises a significant portion of

doi.org/10.1093/gbe/...

Genome Biology and Evolution October 2025 cover image with a photo of an Ethiopian White-eye.

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...

Rapid establishment of species barriers in plants compared with that in animals Speciation, the process by which new reproductively isolated species emerge from ancestral populations, results from the gradual accumulation of barriers to gene flow within genomes. To date, the noti...

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

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

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...

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?