Shreyas Pai

I'm very excited to share something I've been working on off-and-on for a long time now: a new blog about genotype-phenotype landscapes! The first post is a Gödel-Escher-Bach-style dialogue to introduce the topic. If you like it please share/repost! open.substack.com/pub/topossib...

Eco-evolutionary robustness of wild bacterial communities to experimental perturbation Abstract. Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most labo

🚨Fresh out of press!
How do wild bacterial communities respond to environmental perturbations like liming?
We experimentally evolved them to find out!
academic.oup.com/ismej/articl...

New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well

The science was cutting edge, and the company was unparalleled- thank you everyone for such a welcoming and thrilling #GRCMicroPop! Looking forward to cyberstalking all your google scholar profiles ❤️

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC

Had an absolutely fabulous time at the 2025 molecular mechanisms of evolution GRC! Amazing science, amazing people, card games, CanJam, and a lil' EtOH 🥹 - it was a week to remember! Excited to get back into lab this week and put into practice some great suggestions 🤓

the Baym lab 🔜 Molecular Mechanisms GRS! Come talk about the evolution and ecology of MGEs
@fernpizza.bsky.social Multilevel plasmid selection!
@arya (arya.casa) Creation of deletion-born fusion genes (frankenstein genes 🧟)
@theshreyaspai.bsky.social Why sex is so common even though it’s costly

Phage DisCo: targeted discovery of bacteriophages by co-culture | mSystems In this work, we describe a targeted phage discovery method that allows immediate isolation of phages with specific traits. Currently, to find a phage with specific properties, huge libraries of phage...

The latest work from my lab, Phage Disco, a method
@ellie-rand.bsky.social
developed for targeted discovery of bacteriophages based on the bacterial receptor, defense system, or other component they interact with, is now live in mSystems
journals.asm.org/doi/10.1128/...

Disco lights

Phage DisCo! Our targeted phage discovery method in press today: journals.asm.org/doi/10.1128/...

Perfectly timed with our four summer undergrad's first successful phage hunt... disco lights in the lab to mark the occasion 🕺

Prevalence of Group II Introns in Phage Genomes Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!

www.biorxiv.org/content/10.1...

Day 3 of #pint25 is running!!
From the East to the West coast we have so much good science and fun talks! 🤩

Super excited to be talking at Pint of Science next week! Alongside my incredibly talented friend and fellow evolutionary biologist Rishabh Kapoor!

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/

CSHL Yeast Genetics and Genomics was one of the best scientific experiences I've ever had! Incredible instructors, terrific peers, and awesome science!

#mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol

Thanks again to everyone involved in this project! Parris Humphrey, Camille Simonet, Katya Kosheleva, & Anurag Limdi, under the awesome mentorship of Michael Desai. We’d all love to hear your thoughts on the preprint!

Overall, sex decreases the pleiotropic costs of adaptation by purging linked genetic load. Sex thus makes generalism less costly and allows populations to endure environmental change. (10/n)

This crucially depends on the genetic architecture of pleiotropic fitness tradeoffs and local adaptation. In our system, in agreement with most studies of natural populations, local adaptation is generated by ‘mutation accumulation’ rather than ‘antagonistic pleiotropy’. (9/n)

Backcrossing evolved clones to their ancestors suggests that a single round of sex can purge this deleterious load in asexuals. (8/n)

This excess hitchhiking genetic load in asexuals underlies their decreased fitness in alternate environments. (7/n)

By sequencing clones from these populations, we find that sex narrows the outcomes of molecular evolution: sexuals have fewer functional mutations and fewer mutational targets, but a higher proportion of these are ‘multi-hit’ and likely adaptive. (6/n)

Sex increases the rate and repeatability of adaptive evolution locally, while simultaneously alleviating its fitness costs in these alternate environments. (5/n)

Sex speeds adaptation by altering the dynamics of molecular evolution - Nature In a comparison between replicate sexual and asexual populations of Saccharomyces cerevisiae, sexual reproduction increases fitness by reducing clonal interference and alters the type of mutations tha...

We evolved budding yeast populations with or without bouts of sexual recombination in YPD, using a system previously established in the lab (@MikeJayMcD & Dan Rice), and measured their fitness in a variety of ‘away’ environments. (4/n)
doi.org/10.1038/natu...

Sexual recombination does this by decoupling beneficial mutations driving local adaptation from hitchhiking load, which is increasingly costly in alternate environments and generates tradeoffs between environments. (3/n)

Sex provides a key advantage of promoting generalism in changing environments by alleviating pleiotropic costs of local adaptation. This mechanism enables sexual lineages to persist through temporal or spatial environmental shifts over longer evolutionary timescales. (2/n)

Sex decreases the pleiotropic costs of local adaptation Understanding the evolutionary mechanisms that maintain sex throughout nature despite its substantial direct costs is a longstanding challenge in biology. Previous work has shown that sexual recombina...

Link to the preprint: doi.org/10.1101/2025...

Why is sex so common if it's so costly?
Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)

Same!

Bay Area RaMP Mission The Bay Area RaMP Program in Microbiome Sciences exists to increase potential for scientific advances by expanding the microbiome research workforce with well-trained, ethical scientists. Our...

Hi y'all! Know any recent or upcoming college graduates who are interested in microbiology and looking for (full-time! paid!) research experience? Please point them towards RaMP! Darian Doakes and I will be co-mentors for an MGE project that I think is going to be really cool. Apps+recs due 5/25

Happy 37th birthday to the LTEE!
the-ltee.org/history/