Dmitri Petrov

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

Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.

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!

I just had the same experience

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

Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability - Nature Ecology & Evolution Directed evolution shows that low expression of the green fluorescent protein facilitates the evolution of cyan fluorescence in E. coli, which can be explained by synergy between the protein’s scarcit...

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...

One mother for two species via obligate cross-species cloning in ants - Nature In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

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: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes Abstract. Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in populat

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

😢

Foreign countries are bribing our president to sell out the American people.
 
Trump family businesses made $187 MILLION from this deal, and just months later he gave the UAE some of our most top-secret AI tech.
 
They are selling our national security to the highest bidder.

I was a White House ethics lawyer.

I used to advise people not to even accept a free cup of coffee from someone who had interests before them. And staff followed those rules.

I can’t even find the words to describe the scale of Trump’s corruption here.

If a university student group had celebrated Charlie Kirk being killed, complete with a graphic made from an actual picture of the killing, the whole lot of them would have been expelled before the ink on the digital story was dry.

Please come join us - so excited for this conference!

Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social

A masked ICE officials with a 5 year old child

This guy went to work today, put a mask on, kidnapped a 5 year old child, and then used him as bait so both he and his father could be sent behind bars

The Norwegian Nobel Prize committee has been forced to make a statement, declaring that the prize cannot be transferred.
It's hard even to comprehend how stupid this has become

Note from a veteran police reporter:

NAMING law officers who use lethal force under any and every circumstance IS NOT doxxing. It is journalism. Officers who invoke lethal force are ID'd publicly as a standard -- or were when we were a republic. Asdress, no. Name, rank, posting, etc. -- yes.

Agreed. The sunken cost fallacy is real. What I tend to do is to put projects on the shelf and once in a while look at them again wondering whether new technology or data would allow us to make progress. Emotionally it feels less like quitting and more as postponement

Endemic and invasion dynamics of wild tomato species on the Galápagos Islands, across two centuries of collection records We aggregated digitized herbarium and other collection records – spanning > 225 yr since 1795 – to assess the biological, geographical, and historical factors shaping distributions of three wild tom...

Endemic and invasion dynamics of wild tomato species on the Galápagos Islands, across two centuries of collection records

Alex D. Kutza, Zoe L. Hert, Leonie C. Moyle

doi.org/10.1111/nph....

Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.

Boring, field-specific answer. This SMART-PTA technology, which allows genotype + phenotype in hundreds of somatic cells, will lead to an expansion of population genetics for somatic cells as a field. www.biorxiv.org/content/10.1...