I have started updating my website because I am no longer at San Francisco State. I also wrote on my website landing page that I am writing a book about my favorite topic: evolution of drug resistance. That's my biggest goal for the year! pleunipennings.wordpress.com

wow — the preprint host, arxiv, is banning authors for a year if they submit papers with hallucinated citations 🤖

Help needed! Does anyone have experience extracting nuclei from flash frozen tissue? Especially helpful if it is fish skin or tail tissue! We are trying to get some precious melanoma samples processed for snRNAseq but are having issues with either nuclei number and/or quality

Excited to share this new pre-print from the fantastic @kelsiehunnicutt.bsky.social! Kelsie put together a thoughtful and thorough review on hybridization in animal evolution: ecoevorxiv.org/repository/v.... She tracks notable shifts in perspectives on the study of hybridization through time.

Do you know any students who are planning to apply to graduate school this cycle? Encourage them to apply to the Biology Preview Program! We provide intensive workshops to help students w/ their applications + 1:1 mentorship.

Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS! www.pnas.org/doi/abs/10.1.... A really fun and informative collaboration with @mharris.bsky.social, Ziyi Mo and Adam Siepel. (1/n)

Simons Graduate Fellowships in #Ecology and #Evolution #science #scienceSky #evoSky www.simonsfoundation.org/grant/simons...

Please share widely! We will imminently be posting a technician position in our lab group since @rheasood.bsky.social is off to grad school 🙌! If you know of anyone excited about molecular biology, evolution, and functional genomics please have them reach out (schumer at stanford). Start date ~June

I agree with your framing... We have an example of this in a wild plant species for a strong-effect phytochemistry QTL: www.nature.com/articles/s41... Granted it's just 1 locus but maybe a useful proof of concept. Were the reviewers arguing balancing sel = heterozygote advantage?

I am hiring a popgen postdoc! Looking for a creative scientist to join us at USC to investigate recessive variation and complex traits in model or non-model species. The project is funded by a multi-year NIH grant, contract can be renewed. Job add & details 👇🏽 usccareers.usc.edu/job/los-ange...

We are revising this ms www.biorxiv.org/content/10.1... and responding to reviewers who liked the paper but had issues with how we thought of balancing selection and its relationship to ecological, local adaptation 1/n

Our PhD student Kennedy Orwa, who studies applications of AI to health care, was hastily deported today to Kenya along with his 13-year-old son without opportunity to speak to legal counsel. King 5 reports that he held a valid visa that was rescinded without explanation.

The two papers: www.science.org/doi/10.1126/... and www.science.org/doi/10.1126/...

We’ve been talking in our lab meetings about sexual conflict and sexual dimorphism, and have some thoughts. What if animal genomes are far more sex-specific and less cosntrained than we assume? @linley-sherin.bsky.social pulled it all together here www.zoology.ubc.ca/mank-lab/pdf... 1/n

Very excited about this paper. Olivia did such a beautiful job and in particular tackled an analytically very hard question of whether different environments are limited by the same of distinct functions. Very curious what people think! 1/2

Gonna be some rad science -- @mollyschumer.bsky.social keynote and a bunch of good talks and posters. And I'll personally pay the registration of anyone who wants to come (it's free).

Jeff is way too generous. He and I will split it!

Coming up soon! Check out the excellent line up of talks! @jrossibarra.bsky.social bapg-conference.github.io

Some work from our lab by @grantkinsler.bsky.social , @kgslab.bsky.social and @petrovadmitri.bsky.social pioneered a new way to investigate these genotype-phenotype-fitness maps in microbes, using a top-down approach elifesciences.org/articles/61271. (4/n)

Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...

Really neat piece of work in @plosbiology.org, inferring the hidden layer of "fitnotypes" that link genotypes to fitness, and finding surprisingly low dimensionality. From @oliviamghosh.bsky.social @grantkinsler.bsky.social @benjaminhgood.bsky.social & @petrovadmitri.bsky.social

Happy to share the final version of @oliviamghosh.bsky.social's paper on inferring low dimensional phenotype-fitness maps from high-throughput fitness measurements across environments. Fun collaboration with @oliviamghosh.bsky.social, @grantkinsler.bsky.social, & @petrovadmitri.bsky.social

Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez

Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez

I think this is our lab's first paper in a proper ecology journal. We are now card carrying ecologists!

Really excited to see this work out now in Ecology Letters! May be particularly interesting to those thinking about life-history trade-offs and eco-evolutionary feedbacks, and how those may interact to maintain variation within natural populations. onlinelibrary.wiley.com/doi/10.1111/...

The conference is quickly filling up! Don't wait to sign up. We also received some funding and can offer fellowships to graduate students and postdocs. Won't cover the whole cost but will certainly make it much easier!

A question for biologists: we often talk about evolutionary novelty. What does “novelty” mean for you? What’s your favorite definition if any? Or just a rule of thumb for what is and isn’t novel.

David Botstein was one of the giants of genetics and genomics, and my mentor, colleague and friend for more than 40 years. I’m sad that he is gone, but his larger-than-life persona comes through here. www.nytimes.com/2026/03/20/s...

Really impressive study with a clear and very interesting conclusion. As @plantevolution.bsky.social says - scale matters - I wonder what the results would show if the sampling continued across more sites, and across more abiotic and biotic esp. disease states?

Very proud of this contribution. Beautiful and hyper careful work by @jahemker.bsky.social showing that not all long read assembles are created equal and at times it really does matter to have enough not just long but very long reads. Curious what you all think!

Proud that this work is now published! We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community! doi.org/10.1093/g3jo...

Very proud of this paper, now officially out at PRX LIFE journals.aps.org/prxlife/abst.... Here @mrazo.bsky.social shows that geometry-aware autoencoder architecture can discover low dimensional phenotypic spaces traversed by evolution. 1/2

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

Bay Area Popgen. FREE awesome popgen conference. Registration and application for talks now live on our website!

The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io

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

With @litinice.bsky.social, we built a haploid resource from 33 wild Taiwanese Saccharomyces cerevisiae strains — including some of the most genetically divergent Asian lineages — to bring natural yeast diversity into a genetically tractable framework. www.biorxiv.org/content/10.6...

Exciting to see that the conference is filling up fast! Don't dawdle and apply soon!

and 2024

Based on these threads, 2024 papers (latter half of the thread) surprised me more. In general, the synteny phylogenomics papers in recent years have perhaps been a really new contribution

I have particularly enjoyed recent papers that show how expression levels affect protein evolution in various ways. One of them www.nature.com/articles/s41...

This one is super cool www.nature.com/articles/s41...

The program for the 2026 New York Population Genetics meeting, hosted by at the @simonsfoundation.org on March 9th 2026, is now up: events.simonsfoundation.org/event/7c91dd....

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Happy Darwin Day to all! To celebrate can you comment with your favorite paper on evolutionary biology from the last few years? Whatever comes to mind and whichever paper that really changed your view of evolution.

Interested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages?? Check out our latest preprint, now up on BioRxiv! biorxiv.org/content/10.6... For a quick summary, peep the thread below...🧵 (1/10)

How does population density affect evolutionary trajectory? Microbes construct their own niche which in turn reshapes their evolution. Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!

Slim 5 can now simulate genomes with multiple chromosomes like autosomes, sex chromosomes, mitochondria and chloroplast dna academic.oup.com/mbe/article/...