First day of field season, sampling yeast in hickory creek wilderness, Allegheny national forest. www.instagram.com/jfay00/

Super excited to share our lab's work led by PhD student Margot Ruffieux on domestication of Saccharomyces cerevisiae, with a focus on sourdough and baking associated yeast! 🍞

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.

1/🧵 Major milestone unlocked for mycology! 🍄 We just published a massive genomic resource in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐃𝐚𝐭𝐚, releasing 2,695 complete circular mitochondrial species assembled from public data This single dataset nearly 𝐓𝐑𝐈𝐏𝐋𝐄𝐒 📈the known mitochondrial diversity of the Kingdom Fungi rdcu.be/eYZ2h

How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...

How do new centromeres evolve while staying compatible with the division machinery? Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore. 👉 doi.org/10.1038/s41586-025-09779-1

Applications due by Dec. 1

PEQG website live! genetics-gsa.org/peqg-2026/

URochester Biology has a tenure-track position open in evolutionary genetics/genomics, particularly those with mathematical, computational, and/or quantitative approaches. Deadline: Nov 10 apply.interfolio.com/173431 Bio Dept retreat photo for attention

Work is sometimes fun, having fun requires some work. I've found a blend of sampling yeast and riding that is a euphoric mix, and makes me wonder why its taken so many years to find. Route is via the finger lakes national forest, 16 miles round trip, 1hr biking straight out, 5 hours sampling back.

Great to hear back in the day stories, chum with alumns and progeny research at Roc-Fest, a celebration of Orr, Werren, Eickbush, and Jaenike and their contributions to adaptation, speciation, and selfish genetic elements. sites.google.com/view/rocfest... I contributed wine:

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine. 1) MMG (my dept): fundamental research in med micro 2) Peds ID / I4Kids institute 3) Center for Vaccine Research 🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

Very pleased to share this long term (nearly 20 years) study of yeasts isolated from vineyards and forests, now up on biorxiv: www.biorxiv.org/content/10.1...

Ella Al-Shamahi (muslim missionary turned evolutionary biologist, host of BBC human series) opinion piece on why follow the science fails. www.washingtonpost.com/opinions/202...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

What killed the competitive renewal at NIH? drugmonkey.wordpress.com/2025/07/31/w...

Walunjkar, @ghaemmaghamilab.bsky.social @justinfay.bsky.social et al. profiled the proteomes of two yeast species with differences in thermal tolerance, finding a proteome-wide shift in stability, driven by both sequence change and cellular context. 🔗 doi.org/10.1093/molbev/msaf137 #evobio #molbio

New paper w/ @plos.org! @chaochihl.bsky.social identifies a unique mutational pattern among sodium azide-induced mutants. SNPs in 'CC' context and indels. Thanks to @justinfay.bsky.social @lilei0051.bsky.social @giuliafrascarelli.bsky.social @nanoporetech.com et al journals.plos.org/plosgenetics...

"We believe that mapping the damage done and its human costs—and the pushback and resilience work already underway—is necessary groundwork for building and retaining political agency"

Abstract submission and early registration for Evolution and core processes of gene expression www.asbmb.org/meetings-eve... June 26–29, 2025

Hitchhiking in facultative sexuals e.g. baker's yeast: can reduce diversity across the genome and contribute to Lewontin’s paradox. Results relevant to anyone (e.g. me) who has looked but found few if any strong sweeps. www.biorxiv.org/content/10.1...

A model for background selection in non-equilibrium populations https://www.biorxiv.org/content/10.1101/2025.02.19.639084v1

1of3 Our new preprint now online: www.biorxiv.org/content/10.1... Commercial #Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body

All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.

Our work, which shows statistical issues with the previous claim of a severe ancient bottleneck in the ancestry of African populations, has been selected as a Featured article in Genetics. doi.org/10.1093/gene...

And another MIRA from @gutengroup.mcb.arizona.edu ! Please send along successful grant proposals and job apps. Seeing these is enormously helpful to folks applying for grants or jobs the first time!

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3 www.science.org/doi/10.1126/...

Very proud of Nilima Walunjkar’s preprint reporting her work on evolution of protein stability. www.biorxiv.org/content/10.1... This work was very fruitful collaboration with multiple members of the Fay lab, along with the Ghaemmaghami @ghaemmaghamilab.bsky.social and Phizicky labs at U. Rochester.

Great! Loved the preprint 😀, look forward to the final version. 👏 @gsherloc.bsky.social @petrovadmitri.bsky.social

How best to avoid the costs of bearing a #plasmid? Rosanna Wright @brockhurstlab.bsky.social @jpjhall.bsky.social &co find that #bacteria benefit from compensating plasmids by chromosomal (rather than plasmid-borne) mutations @plosbiology.bsky.social plos.io/3ODbXdN

For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...

🤩🦠 A new #preprint #openscience recommendation just out: Yeast consortia for novel wine fermentations by E. Pourcelot, et al. Check here: microbiol.peercommunityin.org/articles/rec... Thanks to @fcocubillosr.bsky.social for handling and @pablo-villa.bsky.social, C. Varela and 3 anonymous reviewers

Thrilled to see this paper out! 🎉 We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.

First post on Bluesky, let’s share some websites offering many free illustrations for scientific figures 🖼️ 🧪 🌍 : scidraw.io bioart.niaid.nih.gov www.phylopic.org More well known but very nice though: www.freepik.com

Here is a great summary of genomic visualization tools: cmdcolin.github.io/awesome-geno...

A valuable and well done community resource following #OpenScience principles academic.oup.com/g3journal/ad...