Mathieu Gautier
@mgda76.bsky.social
Population Geneticist at INRAE (France)
Reposted by Mathieu Gautier
January 22, 2026 at 5:32 PM
Reposted by Mathieu Gautier
Ancestral sequence reconstruction using generative models https://www.biorxiv.org/content/10.64898/2026.01.18.700141v1
January 22, 2026 at 1:48 AM
Ancestral sequence reconstruction using generative models https://www.biorxiv.org/content/10.64898/2026.01.18.700141v1
Reposted by Mathieu Gautier
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
🏺 #archaeology
📷 me
January 11, 2026 at 8:14 AM
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
🏺 #archaeology
📷 me
Reposted by Mathieu Gautier
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
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
January 5, 2026 at 8:53 AM
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
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
Reposted by Mathieu Gautier
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/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
January 8, 2026 at 8:57 PM
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/...
Reposted by Mathieu Gautier
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.
January 6, 2026 at 10:55 PM
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.
Reposted by Mathieu Gautier
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.
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
arxiv.org/abs/2506.12986
January 6, 2026 at 11:02 PM
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.
Reposted by Mathieu Gautier
"The era of the business idiot" freakonometrics.hypotheses.org/87139
“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...
freakonometrics.hypotheses.org
January 1, 2026 at 5:23 AM
"The era of the business idiot" freakonometrics.hypotheses.org/87139
Reposted by Mathieu Gautier
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-...
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.
www.prosocial.world
December 30, 2025 at 8:31 PM
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-...
Reposted by Mathieu Gautier
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 #transposon
doi.org
December 29, 2025 at 5:42 PM
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 #transposon
Reposted by Mathieu Gautier
Now TWO great new papers on why frequencies of disease genes rarely match expectations
Here was the first: www.nature.com/articles/s41...
Here was the first: www.nature.com/articles/s41...
December 13, 2025 at 5:44 PM
Now TWO great new papers on why frequencies of disease genes rarely match expectations
Here was the first: www.nature.com/articles/s41...
Here was the first: www.nature.com/articles/s41...
Reposted by Mathieu Gautier
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
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.
www.nature.com
December 11, 2025 at 5:54 PM
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by 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
November 30, 2025 at 1:31 AM
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
Reposted by Mathieu Gautier
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...
@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...
November 28, 2025 at 5:14 AM
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...
@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...
Reposted by Mathieu Gautier
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
Learn more: https://scim.ag/44kov1S
November 27, 2025 at 7:05 PM
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
Learn more: https://scim.ag/44kov1S
Reposted by Mathieu Gautier
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
GitHub - alanrogers/popgen: A course on population genetics
A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.
github.com
November 27, 2025 at 7:10 PM
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
Reposted by Mathieu Gautier
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
A major selective sweep likely linked to insecticide resistance identified along altitudinal gradients in the pine processionary moth https://www.biorxiv.org/content/10.1101/2025.11.24.690095v1
November 26, 2025 at 8:34 PM
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
Reposted by Mathieu Gautier
An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...
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...
www.nature.com
November 26, 2025 at 6:56 AM
An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...
Reposted by Mathieu Gautier
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.
Amsterdam, l’île confetti aux avant-postes de la recherche
lejournal.cnrs.fr
November 18, 2025 at 6:48 PM
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.
Reposted by Mathieu Gautier
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...
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 ...
doi.org
November 18, 2025 at 12:15 AM
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...
Reposted by Mathieu Gautier
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
Science publication is Darwinian: a survival pressure to publish.
royalsocietypublishing.org/doi/full/10....
#IRICSydney
November 16, 2025 at 10:02 PM
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
Science publication is Darwinian: a survival pressure to publish.
royalsocietypublishing.org/doi/full/10....
#IRICSydney
Reposted by Mathieu Gautier
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
Les salariés craignent de voir leur indépendance s'envoler.
Lire l'article ➡️ https://l.reporterre.net/S0B
November 11, 2025 at 3:12 PM
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
Les salariés craignent de voir leur indépendance s'envoler.
Lire l'article ➡️ https://l.reporterre.net/S0B
Reposted by Mathieu Gautier
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.
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.
November 10, 2025 at 4:24 PM
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.
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.
Reposted by Mathieu Gautier
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)
October 19, 2025 at 9:35 AM
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)
Reposted by Mathieu Gautier
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
October 14, 2025 at 12:58 PM
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