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Mathieu Gautier

@mgda76.bsky.social
194 followers 327 following 10 posts

Population Geneticist at INRAE (France)

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Reposted by Mathieu Gautier
Joe Hanly @hanliconius.bsky.social · 22/09/2026
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:
chromosome synteny riparian plot in which every chromosome has crossing lineschromosome synteny plot in which no chromosomes have crossing lines. The underlying structure is identical.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 19/09/2026
This must be the place: deep learning local adaptation www.biorxiv.org/content/10.64898/20…
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Dr. Sarah Signor @signor-molevol.bsky.social · 16/09/2026
Congratulations to @rpianezza.bsky.social @rokofler.bsky.social, Matt Beaumont and Sarah Saadain! We found an endogenous retro virus currently invading D. melanogaster!
nature.com
The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations - Nature Communications
Transposable elements are mobile DNA sequences that can copy themselves and spread between species. This study finds that Kuruka, a retrovirus-like transposon, invaded Drosophila melanogaster within t...
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Robert Kofler @rokofler.bsky.social · 10/09/2026
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
annualreviews.org
The History of Transposable Element Invasions in Drosophila melanogaster
As a fundamental biological principle, genomic information is typically transmitted vertically from parent to offspring. Occasionally, however, genetic material is transferred horizontally between spe...
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Aki Vehtari @avehtari.bsky.social · 13/08/2026
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!)
avehtari.github.io
Bayesian Workflow book: Website – Bayesian Workflow book
Website for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
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Leeban Yusuf @leebanhy.bsky.social · 20/08/2026
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...
github.com
GitHub - LeebanY/DemogFit: Have minimal genomic samples from two species and want to infer their demographic history? DemogFit is an R package for fitting four simple likelihood-based demographic mode...
Have minimal genomic samples from two species and want to infer their demographic history? DemogFit is an R package for fitting four simple likelihood-based demographic models using the distributio...
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Yann Bourgeois @bourgeoisyann.bsky.social · 17/08/2026
Nice. watchgen.readthedocs.io/en/latest/ph...
watchgen.readthedocs.io
The Watchmaker’s Philosophy — The Watchmaker's Guide to Population Genetics
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Mathieu Gautier @mgda76.bsky.social · 09/07/2026
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...
sciencedirect.com
Can habitat modification in the native range promote invasion?
The anthropogenically induced adaptation to invade (AIAI) hypothesis posits that selection in human-modified habitats within native ranges can adapt p…
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jasserole @jasserole.blacksky.app · 04/07/2026
I'm not sure if video is your thing, but this really helped me get a sense of it youtu.be/z64a7USuGX0?...
youtu.be
What the Books Get Wrong about AI [Double Descent]
YouTube video by Welch Labs
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Andrew Carroll @acarroll.bsky.social · 01/07/2026
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...
andrewcarroll.github.io
The Best of Both Worlds - Assessing MiniBWA
Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...
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brunolemaitre.bsky.social @brunolemaitre.bsky.social · 17/06/2026
A short, informal intro to Drosophila genetics (with a French accent 🇫🇷): key concepts & techniques for new lab members. www.epfl.ch/labs/lemaitr...
epfl.ch
Short Introduction to Drosophila_Engl
If you like French accent:A short and informal introduction to Drosophila genetics, covering the basic knowledge and techniques that may be helpful when working with Drosophila. This series of short l...
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Heng Li @lh3lh3.bsky.social · 16/06/2026
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...
github.com
GitHub - lh3/minibwa: Successor of bwa-mem for short-read alignment
Successor of bwa-mem for short-read alignment. Contribute to lh3/minibwa development by creating an account on GitHub.
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Heng Li @lh3lh3.bsky.social · 16/06/2026
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
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Benoit Nabholz @benoitevol.bsky.social · 15/06/2026
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/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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Charles Perrier @charles-perrier.bsky.social · 11/06/2026
Pine Processionary Moth chromosome-level #genome Assembly by @mgda76.bsky.social, @prrnhd.bsky.social et al. in Journal of Heredity @theaga.bsky.social. 615.9 Mb 50 pseudochromosomes 12,898 annotated genes @cbgpmontpellier.bsky.social academic.oup.com/jhered/artic...
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Andrej Spiridonov @andrejpaleo.bsky.social · 05/06/2026
The concise history of modeling character evolution. Handy timeline. academic.oup.com/sysbio/advan... 🧪 #EvoBio #Paleobio
Timeline of select major events in the development of phylogenetic comparative methods, sorted by discrete trait models, continuous trait models, and tree models. We elaborate on some of these methods in the main text.
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DrosEU @droseu.bsky.social · 01/06/2026
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
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Heng Li @lh3lh3.bsky.social · 30/05/2026
Rammap: github.com/jwanglab/ram... Minimap2 v2.31: github.com/lh3/minimap2...
github.com
GitHub - jwanglab/rammap: An extensible and performant aligner and read mapper
An extensible and performant aligner and read mapper - jwanglab/rammap
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 30/05/2026
The Drosophila melanogaster Genetic Reference Panel, Version 3 (DGRP3) www.biorxiv.org/content/10.64898/20…
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Dwarkesh Podcast @dwarkesh.skystack.xyz · 08/05/2026
David Reich – Why the Bronze Age was an inflection point in human evolution • "Instead of being quiescent, natural selection is everywhere."
dwarkesh.com
David Reich – Why the Bronze Age was an inflection point in human evolution
"Instead of being quiescent, natural selection is everywhere."
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Tyler Morgan-Wall @tylermw.com · 23/04/2026
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
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Genome Biology and Evolution @genomebiolevol.bsky.social · 22/04/2026
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
doi.org
Genetic Footprints of Seasonal Fluctuating Selection: A Comparison With Established Selection Forms
Abstract. Fluctuating selection is frequently studied in natural populations by observing allele frequency trajectories over evolutionarily brief timeframe
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Graham Coop @gcbias.bsky.social · 17/04/2026
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.
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Mathieu Gautier @mgda76.bsky.social · 11/04/2026
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
droseusuz.sciencesconf.org
16th DrosEU meeting and satellite Drosophila suzukii International conference - Sciencesconf.org
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DrosEU @droseu.bsky.social · 31/10/2025
🪰 🧬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
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Daniel E. Weeks @statgendan.bsky.social · 10/04/2026
“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
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Dmitri Petrov @petrovadmitri.bsky.social · 27/03/2026
I think this is our lab's first paper in a proper ecology journal. We are now card carrying ecologists!
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Olivier Gimenez 🦦 @oaggimenez.bsky.social · 05/03/2026
📘 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
couverture du livre introduction à la statistique bayésienne avec R
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Victor Pereira @victorpereira.bsky.social · 05/03/2026
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...
lusa.pt
Escritor António Lobo Antunes morre aos 83 anos
O escritor António Lobo Antunes, um dos maiores nomes da literatura portuguesa desde a segunda metade do século XX, morreu hoje aos 83 anos.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 27/02/2026
Phenotypic and Genomic Evidence of Adaptive Tracking in Thermal Tolerance of Wild Populations of an Invasive Drosophila. www.biorxiv.org/content/10.64898/20…
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Mathieu Gautier @mgda76.bsky.social · 25/02/2026
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. [cran.r-project.org/web/packages/poo…...)
cran.r-project.org
poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-S...
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PLOS Biology @plosbiology.org · 19/02/2026
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
Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.
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France Culture @franceculture.fr · 15/02/2026
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 l.franceculture.fr/uXP
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Cedric Boeckx @cedricboeckx.bsky.social · 14/02/2026
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...
nature.com
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations - Nature Communications
Most GWAS have focused on common variants or rare protein coding variants. Here, the authors interrogate the contribution of rare non-coding variants for anthropometric traits, identifying new genes a...
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Science Magazine @science.org · 22/01/2026
No bull: This Austrian cow has learned to use tools. Learn more: scim.ag/3LYTXNd
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/01/2026
Ancestral sequence reconstruction using generative models www.biorxiv.org/content/10.64898/20…
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Nina Willburger @drnwillburger.bsky.social · 11/01/2026
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
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.
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Molecular Biology and Evolution @molbioevol.bsky.social · 05/01/2026
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
MBE | SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes
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Joaquin Nunez @jcbnunez.bsky.social · 08/01/2026
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.org
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...
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Heng Li @lh3lh3.bsky.social · 06/01/2026
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.
academic.oup.com
Validate User
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Heng Li @lh3lh3.bsky.social · 06/01/2026
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.
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Arthur Charpentier @freakonometrics.bsky.social · 01/01/2026
"The era of the business idiot" freakonometrics.hypotheses.org/87139
freakonometrics.hypotheses.org
“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...
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anthrofuentes.bsky.social @anthrofuentes.bsky.social · 30/12/2025
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-...
prosocial.world
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.
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Johann Confais @johannconfais.bsky.social · 29/12/2025
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
doi.org
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Christopher Witt @msbbirds.bsky.social · 13/12/2025
Now TWO great new papers on why frequencies of disease genes rarely match expectations Here was the first: www.nature.com/articles/s41...
nature.com
Hotspots of human mutation point to clonal expansions in spermatogonia - Nature
A systematic statistical genetics approach discovers CES drivers as hotspots of human de novo mutation and shows that clonal expansions in germline may both modulate the prevalence of disorders and le...
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Jonathan Pritchard @jkpritch.bsky.social · 11/12/2025
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🧵:
nature.com
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.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/11/2025
RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions www.biorxiv.org/content/10.1101/202…
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Thibault (Tibo) Leroy @tiboleroyinen.bsky.social · 28/11/2025
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...
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Science Magazine @science.org · 27/11/2025
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: scim.ag/44kov1S
A shorthair domestic cat gazes upward.
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Alan Rogers @alanrogers.bsky.social · 27/11/2025
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.com
GitHub - alanrogers/popgen: A course on population genetics
A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.
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