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Bertrand Servin

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Reposted by: Bertrand Servin

popgroup2026.bsky.social
Exciting news!
The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris.

This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics.

More info: populationgeneticsgroup.org.uk

See you there !
Population Genetics group 59
populationgeneticsgroup.org.uk
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Reposted by: Bertrand Servin, Philip Nel

runrichrun.mastodon.social.ap.brid.gy
It's Signal. It's worth using. Good interview with @Mer__edith
https://english.elpais.com/technology/2025-09-14/signal-president-meredith-whittaker-in-technology-its-way-too-easy-for-marketing-to-replace-substance-thats-whats-happened-with-telegram.html
h/t

#signal
Signal president Meredith Whittaker: ‘In technology, it’s way too easy for marketing to replace substance. That’s what’s happened with Telegram’
The app best known for respecting privacy looks to grow, despite anti-privacy efforts
english.elpais.com
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Reposted by: Bertrand Servin, Brian J. Enquist, John Wilkins , and 1 more

crouxevo.bsky.social
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
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Reposted by: Bertrand Servin, Jason Stajich

arunsethuraman.bsky.social
Excited for this to finally see the light of day - new preprint from my lab, where we present a fast, accurate maximum likelihood tool to estimate population structure, called MULTICLUST. We extend the model of Alexander et al 2009 (ADMIXTURE) to multiallelic data. www.biorxiv.org/content/10.1...
MULTICLUST - Fast multinomial clustering of multiallelic genotypes to infer genetic population structure
Identifying population structure from multilocus genotype data is key to downstream population genetic analyses in a variety of fields, including conservation, evolutionary genetics, Genome-Wide Assoc...
www.biorxiv.org
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Reposted by: Bertrand Servin

sagitaninta.bsky.social
Just want to share this wild revision history of the Wikipedia page on Linkage Disequilibrium where Felsenstein himself debated people on the correct use of notations & definitions.

After 100 years of #popgen people does not seem to be totally agree on what LD is?

en.wikipedia.org/wiki/Talk:Li...
Talk:Linkage disequilibrium - Wikipedia
en.wikipedia.org
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by Bertrand Servin

bertrandservin.bsky.social
I'd like to advertise a PhD Position opened in our INRAE lab in Toulouse with Pierre Faux and myself to work on evaluating methods to infer demography of livestock populations 🐐 🐏 ...

More details here : jobs.inrae.fr/en/ot-25908 and even more after contacting us :) Applications are open !
Integration of pedigrees and methods for demographic inference in livestock population genomics
Demographic inference is a central tool for reconstructing the genetic history of a population. Recently, several new approaches have brought this tool into a new era, that of the exhaustive use of whole-genome sequence. These approaches can be divided into two categories: demographic inference based on ancestral recombination graphs (ARGs1) and deep learning based inference2,3. However, without any other source of information, it is difficult to assess the actual degree of accuracy of these methods. In the case of livestock species, we usually have access to an additional information, rather unique and valuable, the pedigree over several generations. This set of relationships makes it possible to compare inferred demographic histories with the exact, albeit incomplete, history of the population.In this thesis project, we aim to use the pedigree information on the one hand, to assess the results obtained with the new approaches of demographic inference, and, on the other hand, to refine methods for ARG estimation. Therefore, we propose a research program divided into three main tasks: (i) to appropriate new approaches (ARG, deep learning) in demographic inference on goat and sheep datasets, (ii) to compare these approaches together, in particular to evaluate their inference of the effective size of a population in the light of genealogical information, and (iii) to integrate this information into the inference of ARGs.Kelleher, J. et al. Inferring whole-genome histories in large population datasets. Nature Genetics 51, 1330–1338 (2019).Schrider, D. R. & Kern, A. D. Supervised Machine Learning for Population Genetics: A New Paradigm. Trends in Genetics 34, 301–312 (2018).Korfmann, K., Gaggiotti, O. E. & Fumagalli, M. Deep learning in population genetics. Genome Biology and Evolution 15, evad008 (2023).You will be welcomed in the CHAMADE team (“CHAracterization and MAnagement of Diversity”) of the GenPhySE research unit (https://genphyse.inrae.fr/), located in the Occitanie-Toulouse research centre (31320, Castanet-Tolosan). The CHAMADE team is part of the “Diversity and Selection” scientific division of the research unit. The team is interested in methodological issues in the field of population genomics, genetic evaluation of livestock species and quantitative and evolutionary genetics. On deep learning approaches for demographic inference, collaboration is also planned with the BioInfo team from the Laboratoire Interdisciplinaire des Sciences du Numérique (LISN, Paris-Saclay University).
jobs.inrae.fr
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Reposted by: Bertrand Servin

simorasmu.bsky.social
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Out now in Cell: Our new study uncovers the ancient origins of a genetic mutation that protects against HIV — and rewrites the story of its surprising high frequency in Europe.

Link: doi.org/10.1016/j.ce...
Let’s dig in (popular science first, jump to 16 for technical details)
Redirecting
doi.org
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Reposted by: Bertrand Servin

carlzimmer.com
Denisovans in Taiwan! Here’s my story (gift link) nyti.ms/3RHlz8G
Denisovans Extend Their Range to Asia’s Pacific Coast (Gift Article)
A bone discovered in Taiwan turns out to have belonged to a Denisovan, a lineage previously identified only thousands of miles away.
nyti.ms
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Reposted by: Bertrand Servin, Jillian M. Buriak, Jason M. Fletcher , and 3 more

jeremymberg.bsky.social
Bluetorial-A dream and a bit of a nightmare

Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
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Reposted by: Bertrand Servin

pdevillemereuil.bsky.social
Excited to share the news that our article on the partition of variance of reaction norm with @lmchev.bsky.social has been recommended by @peercommunityin.bsky.social Evolutionary Biology: 👇🧵
ecoevorxiv.org/repository/v...
evolbiol.peercommunityin.org/articles/rec...

#phenplas #quantgen
Partitioning the phenotypic and genetic variances of reaction norms
ecoevorxiv.org
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Reposted by: Bertrand Servin

gcbias.bsky.social
Thoughtful piece by Greg Gibson pushing strongly back on the "Heritable polygenic editing" article
genomestake.substack.com/p/genome-edi...
Genome Editing and Eugenics
The one hundred and third Take:
genomestake.substack.com
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Reposted by: Bertrand Servin

nicolasgaltier.bsky.social
In 2010 (SMBE Lyon) I gave a talk about the impact of GC-biased gene conversion (gBGC) on functional sequence evolution. I argued that, because gBGC promotes G and C alleles irrespective of their fitness effect, it should generate some genetic load. 1/5
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Reposted by: Bertrand Servin

solidevidence.bsky.social
I’m pleased to share that we FINALLY submitted our latest manuscript on SARS-CoV-2 cryptic lineages and what they tell us about the origins of COVID-19.
This was a ton of work.
medrxiv.org/cgi/content/...
1/
Detecting SARS-CoV-2 Cryptic Lineages using Publicly Available Whole Genome Wastewater Sequencing Data
Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on the most mutagenic region of SARS-Co...
medrxiv.org
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Reposted by: Bertrand Servin, Paul Ekblom

catsforpeace2.bsky.social
We MUST keep vaccines.
have you written your Senator to let them know?
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Reposted by: Bertrand Servin, Victor A. Albert

elliescerri.bsky.social
A little bomb. They're not saying hybridization didn't happen, they're arguing that it hasn't been conclusively shown, as the same patterns can be produced in other ways without Neanderthal admixture. An interesting read. Thoughts?
www.nature.com/articles/s41...
Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events - Nature Ecology & Evolution
Simulating a metapopulation of human evolution without Neanderthal introgression into Homo sapiens still identifies Neanderthal fragments in simulated genomes, and an admixture event that never took p...
www.nature.com
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Reposted by: Bertrand Servin

steamtraen.eu
Yup
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Reposted by: Bertrand Servin

betanalpha.bsky.social
“Null hypotheses are usually known in advance to be false, and the point of significance tests is usually to find out wether they are nevertheless approximately true.”
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Reposted by: Bertrand Servin

betanalpha.bsky.social
Today I.J. Good is getting spicy about hypothesis testing.

All quotes are from "Good Thinking", store.doverpublications.com/products/978....
store.doverpublications.com
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Reposted by: Bertrand Servin

austintwang.bsky.social
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
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Reposted by: Bertrand Servin

krynadachowska.bsky.social
I am looking for a postdoc! Pls share
#postdoc #genomics #insects #inversions
genomicsofoutbreaks.com/?page_id=141
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Reposted by: Bertrand Servin

gregorgorjanc.bsky.social
A new pre-print “Robust Optimal Contribution Selection” led by Josh Fogg. We show how to account for the uncertainty and correlation of estimated breeding values in the optimal contribution selection problem: arxiv.org/abs/2412.02888
Robust Optimal Contribution Selection
Optimal contribution selection (OCS) is a selective breeding method that manages the conversion of genetic variation into genetic gain to facilitate short-term competitiveness and long-term sustainabi...
arxiv.org
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Reposted by: Bertrand Servin

fablin.bsky.social
Ce n'est pas parce qu'on manifeste contre un président accusé de haute trahison qu'on ne peut pas le faire avec le sens de l'humour : au cours de la semaine passée, plusieurs drapeaux de manifestants ont attiré l’attention pour leur côté décalé. Traditionnellement, ces drapeaux étaient là pour
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Reposted by: Bertrand Servin, Greg Barton

charleslister1.bsky.social
Having worked on #Syria full-time since the crisis began nearly 14yrs ago, there really is no understating how remarkable the losses imposed on #Assad's regime have been over the past week.

A large reason for this lies with #HTS — a 🧵:
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Reposted by: Bertrand Servin

michelnivard.bsky.social
🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.
GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics.
A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics
github.com
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by Katharine Hayhoe — Reposted by: Bertrand Servin, Dan Brockington, Gunnar Luderer , and 7 more

hansonmark.bsky.social
The strain on scientific publishing: we set out to characterise the remarkable growth of the scientific literature in the last few years, in spite of declining growth in total scientists. What is going on?

direct.mit.edu/qss/article/...

A 🧵 1/n
#AcademicSky #PhDchat #ScientificPublishing #SciPub
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Reposted by: Bertrand Servin

yun-s-song.bsky.social
Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task.
1/7
openreview.net/forum?id=H7m...
Ultrafast classical phylogenetic method beats large protein...
Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...
openreview.net
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Reposted by: Bertrand Servin

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Reposted by: Bertrand Servin

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Reposted by: Bertrand Servin

nikhilmilind.dev
For many traits there is a correlation between the number of duplications or loss-of-function (LoF) mutations someone carries, and their phenotype. Curiously, for most traits, these effects are aligned in the SAME direction. Why?
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Reposted by: Bertrand Servin

wonderofscience.bsky.social
This is what a rocket launch looks like from space.
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