Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org Link: www.science.org/doi/10.1126/... Thread below: #mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol

Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load

Understanding the evolutionary mechanisms that maintain sex despite its direct costs is a long-standing challenge. Previous work has shown that sexual recombination can accelerate adaptation, in part ...

science.org

Shreyas Pai@theshreyaspai.bsky.social · last yr.

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)

We are destroying species' habitats, leading to a mass extinction event. This habitat destruction also reduces the genetic diversity _within_ species. Our latest work develops quantitative models to predict how much genetic diversity has been and _will be_ lost. 🧬🧪🧵 www.pnas.org/doi/10.1073/...

Large future genetic diversity losses are predicted from conservation indicators even with habitat protection | PNAS

Genetic diversity within species underpins evolutionary adaptation and has recently been included as a target for protection in the United Nations’...

pnas.org

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/...

Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments

Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...

journals.plos.org

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...

Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore

Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul

doi.org

James Hemker@jahemker.bsky.social · last yr.

Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...

An NIH-funded postdoctoral position is available in my lab. The project focuses on the structural and mechanistic basis of antibody recognition of M and M-like proteins of Strep A (Streptococcus pyogenes).

Excited to share this new preprint describing how Strep A proteins bind human factor H. Strep A is a major human pathogen that causes not only Strep throat but also severe invasive diseases, like 'flesh-eating disease'. www.biorxiv.org/content/10.1...

Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...

High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation

The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...

doi.org

Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!

Sophie Jean Walton@sophiejwalton.bsky.social · 10mo ago

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

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...

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...

biorxiv.org

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...

Having a great time at #smbe2025! So many great talks and conversations. Thank you again to @iamphioxus.bsky.social for the opportunity to present our work! Much of it is from the paper by @grantkinsler.bsky.social and @yuping-li.bsky.social journals.plos.org/plosbiology/... 1/n

A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation

Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...

journals.plos.org

Grateful to be talking at #Evol2025! Will be presenting on how long Nanopore reads need to be in order to accurately call structural variants in Drosophila at the population level. Talk is at 3pm on Saturday in the Genomics III section. If you can’t make it get in touch!

Looking forward to #evolution2025! I will be talking about how time-varying demography and selection shape the site frequency spectrum — Saturday at 4:15 pm, Population Genetics Theory IV. Come say hi if you are around!

Super excited for #Evol2025! I will be sharing some cool work on selection in the gut microbial communities at 9:30 am on Monday in the Evolutionary Ecology I session (Parthenon 2)!! Looking forward to chatting with folks as well!

I think this emphasizes the need for more concrete models of pleiotropy to help us know when these verbal models should even apply in principle (let alone in expts like @oliviamghosh.bsky.social's). In that vein, was very excited about the new work that @djhelam1.bsky.social‬ talked about at NITMB

Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin

The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the eff...

doi.org

Excited to share SpaceBar - our new method for labeling and detecting clones with imaging-based spatial transcriptomics platforms! w/ Yael Heyman and @arjunraj.bsky.social www.biorxiv.org/content/10.1... 🧵

How is functional variation at large-effect loci maintained in natural populations? Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n www.biorxiv.org/content/10.1...

Dominance reversal maintains large-effect resistance polymorphism in temporally varying environments

A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation1. Theory suggests that dominance reversal, whereby alleles subject to fluctuating selectio...

biorxiv.org