Here’s a paper by an undergrad(!) that I’m very proud of: academic.oup.com/evlett/artic... What happens when a susceptible host founds a new population exposed to a parasite? In 50 years they go from highly infected to immune.

ARGs are good. Inferring ARGs from real data hard. Analyzing ARGs from real data hard. ...check your missing data; test your inference doesn't screw up with masked/missing data. ...check your polarization. SINGER prior for example doesn't work as expected if you give it a vcf with ref/alt

Postdoc J. M. Moreno is very close to release Flex-sweep v2 to make users' life easier. v2 is entirely recoded, faster and uses much less RAM. Robustness is up thanks to adding Siepel's lab domain adaptive step. Available soon at pypi.org/project/flex... flexsweep.readthedocs.io/en/latest/

Lab member Jesus Murga Moreno got a much faster and user-friendly version of Flex-sweep up and running. Among other improvements, it requires much less RAM thanks to a new version of discoal provided by Andy Kern: github.com/jmurga/flexs... flexsweep.readthedocs.io/en/latest/

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

In the earliest stages of adaptive introgression, beneficial immigration can drive genome-wide changes. In a new preprint www.biorxiv.org/content/10.1... colleagues & I document exceptionally rapid genomic introgression in a lake population of stickleback.

Does anyone know if the current Alphafold EBI database is still made of Alphafold2 models, or has it been updated with Alphafold3? I cannot find the Alphafold version used to generate specific models.

A simple place to start changing things is to stop systematically distributing conference awards among students from big famous labs.

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.

This sounds incredibly important.

The preliminary program of ProbGen 2026, which will be held at UC Berkeley, is now up: probgen2026.github.io Sharing on behalf of Rasmus Nielsen who is not on this site. For more see his thread on that other site: x.com/ras_nielsen/...

The lab has started using CatBoost to predict selective constraint in mammalian coding sequences, and it is shocking how good it is. It could make it possible to test adaptation accounting for constraint as McDonald-Kreitman does, but without having to do a lot of resequencing to get PN/PS.

As I am preparing my MIRA renewal submission, I have been wondering, should I count in the progress report the publications that were not on the main topic of my initial proposal, but were made possible by the methods that we developed for the proposal?

Fun collaboration with Mélodie Bastian and Nicolas Lartillot. Pi_S and Pi_N/Pi_S extracted from genome assemblies follow nearly neutral predictions across 150 mammals. Getting closer to getting the constraint controls needed to detect ancient epidemics mammals-wide. www.biorxiv.org/content/10.1...

This excellent preprint makes me wonder how frequent reversion of adaptive substitutions is (that are deleterious when the selective pressure is gone), and how much of of the true extent of adaptation we might miss looking at divergence after the fact as result. www.biorxiv.org/content/10.1...

Our latest paper revisits Haldane 1957 on speed limits to adaptation, the paper that triggered neutral theory. We clarify and then significantly extend the theory, and apply the resulting model to @mexpositoalonso.bsky.social's data doi.org/10.1093/gene... 1/14

Shameless self promotion of an excellent article on #EvMed #PetosParadox by @vcallier.bsky.social heads up @ubuffalo.bsky.social 🧪 🐘 🦇🐋🧫🧬

The question of selection during the Black Death will likely require a Yersinia pestis-human-host interactome. Looking at selection at human YIPs (Yersinia-interacting proteins) should be more specific and powerful than immune genes in general. Population genetics in a silo can only go so far.

Following criticisms raised concerning our article www.nature.com/articles/s41..., we just confirmed our original conclusions, demonstrating that the rs2549794 variant near the ERAP2 locus displays a strong positive selection signal associated with the Black Death ☠️ www.nature.com/articles/s41...

I am a bit surprised to see many posts on the response to the selection during Black Death paper without also a link to the response to the response, as it has been out for a long while now: www.nature.com/articles/s41... www.biorxiv.org/content/10.1...

A few macro shots of flying bees I took recently in Tucson. Winter is a bit different here.

1/2) You cannot look for a general sweep signature in humans without carefully controlling for functional density and background selection, i.e. trying to make other things equal. The persistent lack of consideration for such as basic control has been a bizarre thing to witness.

Was just discussing evidence of positive natural selection in humans with a colleague who cited Hernandez 2011 paper for the lack of selective sweeps pubmed.ncbi.nlm.nih.gov/21330547/ and his firm belief that this showed that studies showing natural selection in humans are mostly false positives 1/n

C'est tres simple. Jayce et les Conquérants de la Lumiere ne sont pas venus, et les Monstroplantes ont gagné.

New paper with @lucievirevolte.bsky.social and @psudmant.bsky.social, led by Lucie Etienne and Amandine Le Corf. The sub-cellular localization of important innate antiviral factor GBP5 has evolved multiple times during bat evolution, with consequences for activity. www.biorxiv.org/content/10.1...

Such a blast to collaborate w. Enard & Sudmant Labs: #IRP #IRC @cnrsbiologie.bsky.social @cnrswashington.bsky.social @ucberkeleyofficial.bsky.social @uarizona.bsky.social partnership! Special thanks to Elise Lauterbur @lauterbur.bsky.social & Manny Vazquez⭐ @denard.bsky.social @psudmant.bsky.social

👀Our latest work, led by Amandine Le Corf fantastic PhD student alumni @biorxivpreprint.bsky.social . Great collab @denard.bsky.social @psudmant.bsky.social Genomic and functional #adaptations in #GBP5 highlight specificities of #bat antiviral innate #immunity 🦇🦠 www.biorxiv.org/content/10.1...

Macro shot of bees mid-flight around poppies at the Tucson Botanical Gardens.

#a7rv macro shots with a cheap Tamron travel zoom lens. Can't wait to see what comes out of a proper macro lens.

A crop of ~8% of the original raw, not even with a prime lens. The new camera is a beast.

An excellent article by B. Charlesworth. I would add a potential "exctinction bias" (those populations we are seeing have higher diversity given their),hybridization processes homogenizing diversity, and epistasis at very large population sizes. academic.oup.com/gbe/article/...

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

Based on struggles with specific CNN training sets, we have started considering the idea of finding a limit recombination rate below which it becomes very hard to distinguish real sweeps from false +. Demography-dependent, and there may be regions of the genome where the issue just cannot be solved.

A very interesting preprint. The same is likely true for closely related bat species with great phenotypic differences maintained in the presence of massive gene flow. www.biorxiv.org/content/10.1...

Spread the word that I have a postdoc opening right now, and am also open to PhD applications evol.mcmaster.ca/brian/evoldi.... We have lots of follow up ideas! 15/15

Photography has become a lot easier than it used to. Shot this today without a tripod, no macro lens, and windy conditions. Unthinkable without insane pro skills with good gear even from just 15 years ago.

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

An interesting question that came up going over a comps proposal: do sweeps without introgression bias ABBA-BABA based D or F statistics?

Check it out - PhD student @maggiesteiner.bsky.social's nice thread and link to our new preprint on how sample design, in terms of how geographically narrow vs broad a sample is, impacts the discovery/SFS of deleterious variants.

Your SNPs aren't where you think they are. ~10% of SNPs in maize aren't where the vcf says they are. Work by Edwin Solares when he was a pdoc in the lab. With a doi as a couple folks have asked for something they could cite (hopefully a paper someday). 🖥️🧬 figshare.com/articles/fig...

As we approach mid-winter, an illustration of cave art showing two Reindeer; from Font de Gaume cave, France. One is licking or smelling the other who appears to be sleeping? giving birth? dead or dying?. Originally rendered by someone of the Magdalenian culture, 16,000 years ago. #AncientSky 🦣🏺

🧪 Join us in Tucson! We will begin reviewing applications on December 9 for our tenure track faculty position on the genomics of resilience @uofa-eeb.bsky.social! Apply here: arizona.csod.com/ux/ats/caree...

Germany has been a head scratcher for me. It is persisting with irrational energy policies driven by science-denying ideology, that they have the audacity to still try to force on the rest of Europe. The inability of the country to get in order and be a leader is telling.

Nice to see more work on this topic. The agent-based modelling here (using SLiM 4.0) complements the mathematical and agent-based approaches we took in our preprint (www.biorxiv.org/content/10.1...; v1 posted a year ago). It's reassuring that the results are generally consistent. #mathonco #evobio

That feeling as an AE when you have already invited a dozen reviewers, and the latest decliners start suggesting the previous decliners as alternatives...

Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience @uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...

We found high levels of adaptive evolution in genes expressed in barrier tissue immune cells including 🫁, and/or expressed early during immune responses --> host adaptation likely works best when it cuts infections short early, before pathogens reach high numbers. www.nature.com/articles/s41...

Looking forward to the 2025 Ecological and Evolutionary Genomics Gordon Conference in Italy this summer! This meeting was fantastic in 2023 and promises to be outstanding again! Get more info and register here: www.grc.org/ecological-a... @samyeaman.bsky.social @chicascientifica.bsky.social

Ahem, I don't think "Catch the Bat" would fly as well... It might become "Catch the Rabies" too often...