Shreyas Pai

@kaylinchong.bsky.social's r-eel-y fantas-tick work!

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

Absolutely phenomenal stuff from Kepler!

An eclectic encounter: ticks feeding on an electric eel and the untapped potential of natural history collections Abstract. Parasites are quite likely the most diverse guild of species on earth. Nevertheless, they remain under-documented despite their impact on the hea

🎃🕷️Tick or treat?

Just in time for spooky season... I found a tick on an electric eel in the MCZ collections.

Not even the fish are safe!

Check it out here: doi.org/10.1093/jme/...

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

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

YouTube video by TEDx Talks The social lives of viruses | Asher Leeks | TEDxNewEngland

I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.

#socialviruses #evosky #virosky 🧪

Happy to see this paper finally out in @pnas.org!

#phage #microbiology #MicroSky #VirEvol 🦠 🧫 🔬

Gift link: www.pnas.org/eprint/YYDZ9...

Frequency-dependent fitness effects are ubiquitous In simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

How common are frequency dependent fitness effects?

New preprint out today 👇
doi.org/10.1101/2025...

Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025

Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

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)