David Enard

That looks great! To avoid errors due to starting with spotty gene annotations (gene loss vs. not annotated), I would suggest re-annotating every genome used with TOGA2 from the Hiller lab:
github.com/hillerlab/TO...
Many annotations out there are not optimal and TOGA2 has great power and accuracy.

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

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📣 *Abstract submission by January 31st*

"Host adaptations to viral infections” International Meeting
May 10th-13th 2026
@cnrs.fr Station Biologique Roscoff, Brittany, France

Register & Join us +amazing international speakers!
#CNRS @cnrsbiologie.bsky.social #IRP

www.insb.cnrs.fr/fr/evenement...

Homepage - 2026 Population, Evolutionary, and Quantitative Genetics Conference Visit our website to learn more.

PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5!

*Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.

This is shaping up to be a great workshop. There is still time to register before the deadline! Please RT! #evolution #viruses #pathogens

Funny since Judo is in fact a LOT about sweeps and disequilibrium!

I forgot using tags again: #evolution #genomics #machinelearning #CNNs

Patterns of shared signatures of recent positive selection across human populations Signatures of recent positive selection often overlap across human populations, but the question of how often these overlaps represent a single ancestral event remains unresolved. If a single selective event spread across many populations, the same ...

5/5) To learn about normalizing sweeps stats by recombination bins, below is a great paper:
pmc.ncbi.nlm.nih.gov/articles/PMC...

Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data Author summary Population genetic simulation is a powerful tool in the study of evolution. A number of supervised machine learning methods have been developed that take advantage of inexpensive simula...

4/5) We also find in preliminary tests that DANN form the Siepel lab really helps mitigating these issues:
journals.plos.org/plosgenetics...

3/5) real genome. A stat like iHS for example, or anything haplotype-based really. We are working on adding this to Flexsweep and preparing a manuscript, but even before that anyone using CNNs for sweep analysis should be very careful about recombination.

2/5) , and/or normalizing statistics by local recombination rate is really important. This is because many sweep stats values depend on local recombination rate, and thus normalization based on genome-wide variants will be heavily dependent on the recombination simulated in the training vs. in the

1/5) After months scratching our heads (Is this why I am bald?) when analyzing the performance of CNNs to find sweeps in real genomes, postdoc Jesus Murga Moreno figured out that training with simulations with recombination that closely reflects the distribution of recombination in the real genome

Very interesting alternative to maximum likelihood to reconstruct ancestral sequences.

Interesting to think about in the context of mass extinctions. Is there evidence of very large but phenotypically homogenous species having greater extinction probability?

Indeed!

Rare variation in malaria parasites biases population-genetic inference Understanding how pathogens evolve is fundamental to disease control and is a basic question in evolutionary biology, yet pathogens with complex life cycles violate assumptions of classic evolutionary...

New preprint! and my first single-author paper, so bear with me.
www.biorxiv.org/content/10.6...

Malaria population genetic studies have found some puzzling patterns: Ne estimates spanning orders of magnitude, genome-wide negative Tajima's D, and over a quarter of genes with πN/πS >1

1/n

Registration deadline is fast approaching for the "Host adaptations to viral infections” Meeting May 10th-13th, 2026, at the CNRS Station Biologique de Roscoff, Brittany, France! JOIN US and the many amazing speakers! JOIN US!

sites.google.com/berkeley.edu...

GitHub - ranwez-search/SeqTUI: A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all ... A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all from the terminal. - ranwez-...

Just sharing new tool written by Vincent Ranwez to view and manipulate sequences and alignments directly in your terminal
github.com/ranwez-searc...
Pretty convenient!

I use it every year at the start of my popgen course, asking the students to think about how they can explain what they see.

GHIST logo

Congratulations to the winners of the 2025 Genomic History Inference Strategies Tournament challenges!

Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social

Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!

academic.oup.com/genetics/art...

The collision of two genomes threatens global food security Human activity alters selection pressures and species' ranges, creating opportunities for hybridisation through secondary contact. Ancient hybridization has enabled adaptive radiation, but its role in...

Excited about our new preprint showing bidirectional adaptive introgression between invasive and native crop pests over ecological timescales www.biorxiv.org/content/10.6...

Si c'est pour des fruits de mer ou des asperges c'est inexcusable.

Genes don’t explain what made humans different Tiny genetic variations between humans, Neanderthals and Denisovans might not be all they were cracked up to be.

This headline is wrong and misleading, and the brief text below it is not much better. Whatever might constitute a full explanation of the differences between sapiens and other hominins, we remain confident that 'genes' will be central to it.

www.nature.com/articles/d41...

Check the latest preprint from the lab, #Virus, #evolution, #VirusEvolution, armchair #virology

Ha, noob mistake then, I was not aware they are so important on this platform! Thank you for the tip!

Hopefully that will turn out to be true :)

I am mostly disappointed for the student, they put a lot of effort in it.

The number of RTs for this preprint that took an absolutely massive amount of work and conceptual effort is interesting to say the least. Probably time to try other avenues of dissemination.