Mathieu Gautier

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

A stone sculpture displayed in a museum gallery, carved from rough brown rock.The figure is front-facing and stylized, with a rounded top, deeply incised facial features, and symmetrical patterns resembling eyes, nose, hands, and legs. Lines on the cheeks can be seen, as well as a pendant and a belt.. The surface is textured and weathered.

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

MBE | SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes

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” Au printemps dernier, Ed Zitron publiait un texte passionnant, et certes, un peu long, The Era Of The Business Idiot, que j’ai découvert seulement au début des fêtes (désolé). Il ne se contente pas de...

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

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.

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...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions https://www.biorxiv.org/content/10.1101/2025.11.26.690685v1

Excited to share our latest preprint!
@mheuertz.bsky.social & I just completed a review covering methods and empirical studies on adaptive introgression in a climate context.
We likely missed a few refs & ideas, so your feedback is highly welcome (ideally by email)!
Preprint➡️ doi.org/10.32942/X2B...

A shorthair domestic cat gazes upward.

The domestic cat may be a far more recent arrival to Europe than previously thought, a new Science study. finds. The results offer new insight into one of humanity’s most enigmatic animal companions and identify North Africa as the cradle of the modern housecat.

Learn more: https://scim.ag/44kov1S

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

We set out to investigate polygenic footprints of altitude adaptation in a moth species, but instead we uncovered a major selective sweep at genes often associated with insecticide resistance @prrnhd.bsky.social @schifanoalexandre.bsky.social @mgda76.bsky.social @cbgpmontpellier.bsky.social

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...

Amsterdam, l’île confetti aux avant-postes de la recherche

Début 2025, un gigantesque incendie a ravagé plus de la moitié de l’île Amsterdam. De retour sur place plusieurs mois après, des scientifiques tentent d’en estimer les conséquences sur ce havre de biodiversité à la croisée de l’océan Indien et de l’Antarctique.

High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...

Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...

Slide showing the forgotten curve Goodman 1992: https://onlinelibrary.wiley.com/doi/abs/10.1002/sim.4780110705 Curran-Everett 2017:

SG: The 'forgotten' curve - the problem of p values. The chance that your replicate experiment of an experiment with p=0.05 will be reproducible is only 0.5 - it's a toss up!

Science publication is Darwinian: a survival pressure to publish.
royalsocietypublishing.org/doi/full/10....
#IRICSydney

Le groupe LVMH de Bernard Arnault va devenir entièrement propriétaire du magazine économique « Challenges » et des revues « Sciences et Avenir » et « La Recherche ».

Les salariés craignent de voir leur indépendance s'envoler.

Lire l'article ➡️ https://l.reporterre.net/S0B

This is out now:

www.sciencedirect.com/science/arti...

Association between lactase persistence and height in the past (indicating people with the persistence allele were better nourished by drinking milk than those without it) provides a potential explanation for why it was under strong selection.

We are in Bluesky and we are happy to share our two last consortium publications: the DrosEU expanded DEST dataset and a Continent-wide study of phenotypic differentiation among European #Drosophila melanogaster populations (1/7)

Heritability and target size underlie differences between trait architectures: examples for three traits. Top: Height (blue) and platelet crit (red) have the same heritability per site h2/L, but height has a much higher mutational target size L. This results in many more hits for height (1533) than for platelet crit (648) (2 left panels). However, the marginal distributions of effect sizes, MAFs, and z-scores of hits are nearly identical for the two traits (3 right panels). Middle: Height (blue) and FEV1 (gold) differ in h2/L, but have similar L. Consequently, the joint distribution of z-scores and MAFs of their hits are markedly different (2 left panels), as are the marginal distributions of hit effect sizes, MAFs and z-scores (right). Bottom: After scaling by their respective , and imposing the more stringent scaled significance threshold (corresponding to FEV1) for both traits, the joint distribution of z-scores and MAFs of their hits (2 left panels) and the corresponding marginal distributions (3 right panels) are highly similar.

Genetic architectures of #ComplexTraits vary widely. @yuvalsim.bsky.social @jkpritch.bsky.social @gs2747.bsky.social &co show these diffs arise from mutational target size & heritability per site; when controlled for, all tested traits have similar architectures @plosbiology.org 🧪 plos.io/47mZXqT

7 reasons to use Bayesian inference!
statmodeling.stat.columbia.edu/2025/10/11/7...

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory - BMC Biology Background Dietary shifts are major evolutionary steps that shape ecological niches and biodiversity. The beetle family Coccinellidae, commonly known as ladybirds, first transitioned from a fungivorou...

Molecular evolution of dietary shifts in ladybirds 🐞 expansions of digestive & detoxifying #gene families in the herbivorous ladybirds, & absence of most plant cell wall-degrading enzymes in the ladybirds from the transition to carnivory link.springer.com/article/10.1...