Mathieu Gautier

It's been 30 years (!!!) since the conceptualization of GWAS. GWAS has driven tons of discoveries, but with recent experimental developments (CRISPR, single-cell omics), we thought it was time to think about how to drive the next 30 years of human genetics. doi.org/10.5281/zeno...

I've complained on here a few times about synteny plots that are harder to read than they need to be. I decided it was time to actaully do something about it: introducing SynTangle, a tool for untangling whole-genome synteny plots github.com/Hanliconius/... 1/

Christian Robert reviews Bayesian Workflow, suggests the abbreviation BaWoFlow. xianblog.fr/2026/10/08/b...

A population genetics study investigates how genetic variation is maintained in a polygenic trait under stabilizing selection in a subdivided population. Learn more in #GENETICS 🔗 buff.ly/cDuTqm4

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

This must be the place: deep learning local adaptation https://www.biorxiv.org/content/10.64898/2026.09.16.752190v1

super proud - my very first review is online www.annualreviews.org/content/jour... many thanks to @signor-molevol.bsky.social @rpianezza.bsky.social @almoroscarpa.bsky.social for the fun collaboration

All four books I've co-authored are freely available online for non-commercial use: - Bayesian Workflow at avehtari.github.io/Bayesian-Wor... Links to other three books are in the quoted post 👇 (too many books to fit in one post!)

Working with minimal genomic samples from two species? I’ve put together DemogFit, a small R package for fitting IM models and estimating gene flow parameters from a single whole-genome sample per species, plus a Snakemake pipeline to generate the input files. github.com/LeebanY/Demo...

Nice. watchgen.readthedocs.io/en/latest/ph...

For those interested in invasion biology, this review discusses new approaches for testing the Anthropogenically Induced Adaptation to Invade (AIAI) hypothesis using population genomics and environmental genomic analyses. doi.org/10.1016/j.tr...

I'm not sure if video is your thing, but this really helped me get a sense of it youtu.be/z64a7USuGX0?...

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

A short, informal intro to Drosophila genetics (with a French accent 🇫🇷): key concepts & techniques for new lab members. www.epfl.ch/labs/lemaitr...

Current bwa-mem users are encouraged to try minibwa as minibwa is planned to replace bwa-mem (but not minimap2). Source code: * minibwa in C: github.com/lh3/minibwa * minibwa-rs (Rust rewrite by AI): github.com/henriksson-l...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them academic.oup.com/gbe/article/...

The concise history of modeling character evolution. Handy timeline. academic.oup.com/sysbio/advan... 🧪 #EvoBio #Paleobio

Save the date! The 17th DrosEU workshop will be held in České Budějovice on the 24th to 26th May 2027. Thanks to @janhreck.bsky.social for hosting us! #Drosophila #genomics

Rammap: github.com/jwanglab/ram... Minimap2 v2.31: github.com/lh3/minimap2...

The Drosophila melanogaster Genetic Reference Panel, Version 3 (DGRP3) https://www.biorxiv.org/content/10.64898/2026.05.29.728783v1

David Reich – Why the Bronze Age was an inflection point in human evolution • "Instead of being quiescent, natural selection is everywhere."

This is really big (if it works!)—a big limitation for the use of R in simulation up to this point has been memory bloat. I’ve had to turn off parallel processing/reduce the number of workers many times in my {targets} workflows due to OOM errors. Hopefully this will solve that problem #RStats

Johnson et al. analyse the genomic signatures of fluctuating selection and introduce statistical strategies for distinguishing it from other modes of selection in population genetic studies. 🔗 doi.org/10.1093/gbe/evag082 #genome #evolution

Reposting this old thread on the "Pervasive findings of directional selection" from ancient DNA. While the authors extended their results in various ways, I think many of these points still stand.

The 16th DrosEU Meeting kicks off this Monday, April 13! 🧬 A great scientific program and discussions await: droseusuz.sciencesconf.org #DrosEU2026 @droseu.bsky.social With support from @occitanie.bsky.social, @umontpellier.bsky.social, GIS Fruit, IGH, GenoPolys, and @sfgenetique.bsky.social

🪰 🧬16th #DrosEU2026 Workshop & Satellite #DrosophilaSuzukii Meeting Conference will take place 13–17 April 2026 in #Montpellier, France 🇫🇷. We look forward to connecting with colleagues across Europe to discuss new research in #Drosophila #genomics #evolution & #CitizenScience +info 👉 droseu.net

“Looking is not the same as seeing, after all, and this may be why some of us may stumble upon discoveries in data that others have already analyzed.” #stats #statistics #DataExploration

I think this is our lab's first paper in a proper ecology journal. We are now card carrying ecologists!

📘 Nouveau livre ! Introduction à la statistique bayésienne avec le logiciel R Découvrez pas à pas la statistique bayésienne et sa mise en œuvre dans R : théorème de Bayes, MCMC, priors, régression, GLM/GLMM et comparaison/validation de modèles. Aux éditions Quae 🙏 📷 Crédit photo : Yann Raulet

Médecin de formation, António Lobo Antunes avait vécu de près les horreurs de la guerre coloniale en Angola. Il en tire un livre coup de poing : le cul de judas. Suivront des dizaines d’autres ouvrages décortiquant le Portugal. Il décède à l’âge de 83 ans. www.lusa.pt/article/4669...

Phenotypic and Genomic Evidence of Adaptive Tracking in Thermal Tolerance of Wild Populations of an Invasive Drosophila. https://www.biorxiv.org/content/10.64898/2026.02.26.708249v1

For those interested, a new version (v3.1.0) of poolfstat is now on CRAN, including new functions and updates, new stats (Fh, Fd, FdM) implemented in sliding.windows.fstat; and a revised vignette. [https://cran.r-project.org/web/packages/poolfstat/index.html](cran.r-project.org/web/packages...)

The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI

Michel Portal est mort. Il avait 90 ans. Avec lui disparaît l’un des musiciens français les plus singuliers de ces cinquante dernières années, un artiste qui n’a jamais accepté de choisir entre Mozart et Charlie Parker. Entretien de 2015 avec ce musicien inclassable https://l.franceculture.fr/uXP

Very nice work led @drghawkes.bsky.social, showing convergence between rare and common genetic associations, using whole-genome sequencing data to evaluate the contribution of rare non-coding variants for commonly studied anthropometric traits 🧪🧬 www.nature.com/articles/s41...

No bull: This Austrian cow has learned to use tools. Learn more: https://scim.ag/3LYTXNd

Ancestral sequence reconstruction using generative models https://www.biorxiv.org/content/10.64898/2026.01.18.700141v1

For #StandingStoneSunday a #Neolithic human-shaped stela with a necklace and a belt, found in La Serre, Aveyron (#France). The lines on the cheeks are interpreted as facial #tattoos or scars. Dating 3000-2500 BC. In the late neolithic period several cultures living....🧵 1/2 🏺 #archaeology 📷 me

Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations. 🔗 doi.org/10.1093/molbev/msaf313 #evobio #molbio #compbio

New paper out in the Proceedings of the National Academy of Sciences. We identify regulatory variants shaping embryonic heat tolerance in Drosophila, linking lab selection to clinal and seasonal patterns in wild populations. Link: www.pnas.org/doi/10.1073/...

Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

"The era of the business idiot" freakonometrics.hypotheses.org/87139

this is how you science: "What’s True About the Evolution of Men’s Greater Average Height?- Why men are taller than women may have nothing to do with testosterone—or sexual selection." from @dunsworth.bsky.social and @prosocialworld.bsky.social www.prosocial.world/posts/whats-...

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

Now TWO great new papers on why frequencies of disease genes rarely match expectations Here was the first: www.nature.com/articles/s41...