Mathieu Gautier

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...

How Did Evolution Halve Genome Size During an Oceanic Island Colonization? Abstract. Red devil spiders of the genus Dysdera colonized the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are ne

Red devil spiders from the Canary Islands have a genome half the size of mainland counterparts - Pisarenco, @jrozasub.bsky.social et al. show how purifying selection against slightly deleterious DNA and TE insertions is the primary mechanism.

🔗 doi.org/10.1093/molbev/msaf206

#evobio #molbio #TEsky

YouTube video by Institut Pasteur La dengue aux commandes

Does #dengue virus hijack #mosquitoes' brain? Study led by Felix Hol @pasteur.fr discovered that infected mosquitoes take smaller blood meals. As a result, they bite more often, and potentially infect infect more people.

(video in French with English subtitles available)
youtu.be/2u_qckfAQa4?...

Figure showing ancestry of global dogs.

Dogs are humanity's best friend—but how long has it been that way? 🐕

This Science study investigated ancient dog genomes, revealing a complicated genetic legacy that reflects a long, shared history with humans.

Learn more on #InternationalDogDay: https://scim.ag/41mQvR6

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...

Deeply nested structure of mythological traditions worldwide All human societies present unique narratives that shape their customs and beliefs. Despite cultural differences, some symbolic elements (e.g., heroes and tricksters) are common across many cultures. ...

interesting pre-print arxiv.org/abs/2408.07300

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource Abstract. Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population g

doi.org/10.1093/molb...
Thrilled to share our new paper in MBE! 🎉 Presenting DEST 2.0: 530 pooled Drosophila populations spanning 12 years across 6 continents. We map genomic footprints of adaptation, from pesticide resistance to seasonal changes. #PopulationGenetics #Drosophila #Genomics #Evolution

Notes from Beethoven’s genome Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇

In #GENETICS, Williams et al. present a novel statistics—haplotype score—for summarizing identity-by-descent (IBD) sharing that can distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs and assign individuals to ancestor vs descendant generation.

buff.ly/SaZP3CA

Effective population size does not explain long-term variation in genome size and transposable element content in animals A large-scale survey across animals reveals no general association between genome size expansion and the relaxation of natural selection.

In @elife.bsky.social: Effective population size does not explain long-term variation in genome size and transposable element content in animals doi.org/10.7554/eLif...

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease - Nature Reviews Molecular Cell Biology Transposable elements (TEs) comprise nearly half of the human genome. This Review discusses transcriptional and post-transcriptional mechanisms that repress TE activity, how TEs escape this suppressio...

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease.
www.nature.com/articles/s41...

Thanks Kew!
The paper itself can be found here: www.science.org/doi/10.1126/...

Is a world without #beer, #wine #sake #bread, #cheese livable or even imaginable?

All of these delights & more, we owe to the domestication of one particular kind of #fungi by our ancestors.

Jose Paulo Sampaio & Ana Pontes review the biology of #yeast domestication

www.cell.com/current-biol...

Environmental data provide marginal benefit for predicting climate adaptation Author summary Populations of natural and cultivated plant and animal populations will be affected by more extreme climate events such as drought and flooding in the future. We explore whether charact...

Yay! @genomeofforrest.bsky.social work published today in PLoS Genetics. Forrest took a large maize common garden dataset and asked whether Environmental GWAS was actually useful for predicting which individuals would have highest fitness. Turns out, the answer is no. 1/2