Mathieu Gautier
@mgda76.bsky.social
Population Geneticist at INRAE (France)
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
Reposted by Mathieu Gautier
7 reasons to use Bayesian inference!
statmodeling.stat.columbia.edu/2025/10/11/7...
statmodeling.stat.columbia.edu/2025/10/11/7...
7 reasons to use Bayesian inference! | Statistical Modeling, Causal Inference, and Social Science
statmodeling.stat.columbia.edu
October 11, 2025 at 1:54 PM
7 reasons to use Bayesian inference!
statmodeling.stat.columbia.edu/2025/10/11/7...
statmodeling.stat.columbia.edu/2025/10/11/7...
Reposted by Mathieu Gautier
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Mathieu Gautier
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...
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...
link.springer.com
September 6, 2025 at 4:12 PM
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...
Reposted by Mathieu Gautier
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
🔗 doi.org/10.1093/molbev/msaf206
#evobio #molbio #TEsky
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
doi.org
September 5, 2025 at 2:52 PM
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
🔗 doi.org/10.1093/molbev/msaf206
#evobio #molbio #TEsky
Reposted by Mathieu Gautier
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?...
(video in French with English subtitles available)
youtu.be/2u_qckfAQa4?...
La dengue aux commandes
YouTube video by Institut Pasteur
youtu.be
August 28, 2025 at 11:42 AM
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?...
(video in French with English subtitles available)
youtu.be/2u_qckfAQa4?...
Reposted by Mathieu Gautier
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
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
August 26, 2025 at 1:07 PM
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
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
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...
🔹 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...
GAUTIER Mathieu / baypass public · GitLab
GitLab Community Edition
forge.inrae.fr
August 26, 2025 at 2:48 PM
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...
🔹 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...
Reposted by Mathieu Gautier
interesting pre-print arxiv.org/abs/2408.07300
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. ...
arxiv.org
August 23, 2025 at 5:31 PM
interesting pre-print arxiv.org/abs/2408.07300
Reposted by Mathieu Gautier
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
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
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
August 19, 2025 at 1:34 AM
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
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
Reposted by Mathieu Gautier
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. 🧪👇
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.
www.cell.com
August 7, 2025 at 11:10 AM
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. 🧪👇
Reposted by Mathieu Gautier
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
buff.ly/SaZP3CA
July 25, 2025 at 6:03 PM
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
buff.ly/SaZP3CA
Reposted by Mathieu Gautier
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...
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.
doi.org
July 19, 2025 at 5:50 AM
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...
Reposted by Mathieu Gautier
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...
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.
elevanth.org
July 9, 2025 at 1:40 PM
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...
Reposted by Mathieu Gautier
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...
www.nature.com/articles/s41...
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...
www.nature.com
June 30, 2025 at 1:12 PM
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...
www.nature.com/articles/s41...
Reposted by Mathieu Gautier
Thanks Kew!
The paper itself can be found here: www.science.org/doi/10.1126/...
The paper itself can be found here: www.science.org/doi/10.1126/...
BIG NEWS! We’ve found that ash trees are fighting back against ash dieback disease! 🌳💪
Scientists at Kew & QMUL @qmul.bsky.social have discovered that young ash trees are evolving resistance to this devastating fungus - & fast 🌍
Read the story👉 www.kew.org/read-and-wat...
#PlantScience #SciNews
Scientists at Kew & QMUL @qmul.bsky.social have discovered that young ash trees are evolving resistance to this devastating fungus - & fast 🌍
Read the story👉 www.kew.org/read-and-wat...
#PlantScience #SciNews
June 27, 2025 at 10:43 PM
Thanks Kew!
The paper itself can be found here: www.science.org/doi/10.1126/...
The paper itself can be found here: www.science.org/doi/10.1126/...
Reposted by Mathieu Gautier
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...
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...
June 19, 2025 at 10:15 AM