A first attempt at deep learning, ABC, and moments to estimate parameters about the pop dynamics of transposons. I will soon post a post-doc offer to work on TEs in palms, and I hope these resources may be helpful. Feel free to comment. I need feedback. yannbourgeois.github.io/projects/1_p...

Estimation of Contemporary and Recent Effective Population Size from Genomic Data www.annualreviews.org/content/jour...

Estimation of Contemporary and Recent Effective Population Size from Genomic Data

Effective population size (Ne) is a crucial parameter in the fields of evolutionary biology, conservation biology of endangered species, and selective breeding of domestic animals and crops, as it qua...

annualreviews.org

Multispecies pangenomes reveal a pervasive influence of population size on structural variation | Science www.science.org/doi/10.1126/...

Multispecies pangenomes reveal a pervasive influence of population size on structural variation

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze S...

science.org

My first first-author paper from my PhD is out! Check it out in @plosbiology.org

PLOS Biology@plosbiology.org · 3w ago

Reproductive organs from different species contain conserved cell types. This study compares single-cell data of two Drosophila species, showing that some testis cell types are hotspots for gene expression #evolution, while ovarian cells are more conserved. 🧪 #AcademicSky plos.io/4hqIkMd

Clean and clear academic.oup.com/gbe/article/...

A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them

Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi

academic.oup.com

New review doi.org/10.1111/nph....

Linum bienne is the wild ancestor of a fiber crop, flax, and the threads of its evolutionary history are as entangled as it can get! 🪡🌱 We used (phylo)genomics to untangle how secondary contact and climatic shifts shaped this complex species across taxonomic scales. @rorrodew.bsky.social

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 2mo ago

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne https://www.biorxiv.org/content/10.64898/2026.06.17.732954v1

New work led by Beatrice Landoni: doi.org/10.64898/202...

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne

Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We inv...

doi.org

We are actively searching for a postdoc to join the lab! Details provided here - johrilab.org/join Please share. I will be at PEQG and will be happy to chat if you're interested!

Our contribution to the conservation genomics of a rare Pyrenean endemic monotypic species is online: Life-history traits may buffer genetic erosion under isolation in mountain sky-island systems www.biorxiv.org/content/10.6... @upvd.bsky.social @anaisgibert.bsky.social @pascaline27.bsky.social

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]"

Deflecting the parasitic paradigm: new insights into mutualistic transposons in plant genomes

Inherited transposable elements (TEs) embedded in genomes have an incomparable potential for large-effect mutagenesis. Notwithstanding that transposab…

sciencedirect.com

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...

Dominance modifiers at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical pathways

Author summary Many plants avoid self-fertilization through a system of self-incompatibility, which allows them to recognize and reject their own pollen. In plants like those in the Arabidopsis family...

journals.plos.org

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!

PLOS Biology@plosbiology.org · 5mo ago

In a new study, Sarah Marion &co use genetic mapping and whole genome sequencing in wild #Drosophila to reveal the genetic basis of naturally occurring lethal mutations and introduce a new model that could explain their frequencies in natural populations. 🧪 #genetics

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...

Joris Bertrand@jorisbertrand.bsky.social · 6mo ago

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...

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.

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

doi.org

🚨 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

Eric Leung@erictleung.bsky.social · 7mo ago

still one of the best explanations of principal component analysis (pca), explained at different levels from layman to the more math inclined stats.stackexchange.com/a/140579/132...

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!

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…

sciencedirect.com

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