Alison Feder

Really enjoying reading your updates/highlights from the meeting! Thanks for posting!

We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT

Happy to have started as an @hhmi.org Freeman Hrabowski Scholar! Incredibly grateful for this opportunity and am excited for some very cool new directions! We are *HIRING*, especially postdocs! Please reach out if you’re interested in uterine and pregnancy biology. Please repost!

There are a bunch of other really exciting projects that aren’t in preprint form yet that I’m looking forward to sharing with the world too, so stay tuned!

I'm grateful to get to come to lab each day and work with these brilliant people on interesting problems!

Hunter Colegrove extends a model of epithelial homoeostasis to investigate how mucosal gene therapy could be used to prevent the spread of pathogenic mutations in people with Fanconi anemia (with Ray Monnat)!

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

Yingnan Gao has a major overhaul on his paper investigating how to detect selection in lineage tracing data using tree balance statistics! #evoSky

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

Sam Hart describes and applies a method to distinguish differences in mutational processes between groups of cancers without signature decomposition (joint work with @kelleyharris.bsky.social and in collaboration with @nalcala.bsky.social )! #Genomics 🖥️ 🧬

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

Alex Robertson @alexrob.bsky.social has some very exciting new results describing when and how intracellular interactions among polioviruses can slow resistance evolution (with Ben Kerr)!: #VirEvol #evoSky
www.biorxiv.org/content/10.1...

Elena Romero led a new preprint detailing joint work with Lillian Cohn's lab at Fred Hutch describing really crazy parallelism in in vivo HIV escape from broadly neutralizing antibodies! #VirEvol #evoSky

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

The constant barrage of terrible news on bluesky has made me feel weird about promoting papers, but people in the lab have been doing so much amazing work over the past few months that I want to share a few brief teasers/links:

Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...

Flyer How to apply to the NSF-GRFP (in 7 weeks!). Check out our comprehensive guide and timeline for applying to the NSF-GRFP (or any fellowship!) on a deadline. Give it a shot — it’s not too late! Resource by Olivia Goldman, PhD and John Lê. Photos of authors. Cientifico Latino, Inc. logo. Link: cientificolatino.com/apply-in-7-weeks

Applying to the NSF-GRFP (or another fellowship) on a tight deadline?

We built a 7-week guide + timeline to get you from draft to submission. It’s not too late — you’ve got this! ✨

🔗 cientificolatino.com/apply-in-7-weeks

#NSFGRFP #GradSchool #Fellowship

Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...

In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n
www.biorxiv.org/cgi/content/...

Help us give a warm welcome to Dr. Chadi Saad-Roy, who is joining UBC Mathematics this fall as an Assistant Professor, jointly appointed in the Department of Microbiology and Immunology (‪@ubcmicroimmuno.bsky.social‬).

Full details tinyurl.com/4zwdmr8b

Amazing new work and video from Pleuni!

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...

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...

We are a computational lab focusing on developing machine learning algorithms for biological data. Currently we are working on inference tasks related to natural selection and demographic inference, as well as generative models for genomic data from humans, mosquitos, and other species.

The Mathieson Lab at the University of Pennsylvania is hiring a computational postdoc in machine learning and evolutionary biology. Apply with a CV and references: smathi@sas.upenn.edu. More info: https://saramathieson.github.io/lab #postdoc

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601

Extensive parallelism at the level of font choice suggests avenir is adaptive at the microbial population biology GRC

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

go.bsky.app/GGxRjzC

Simons Graduate Fellowships in Ecology and Evolution The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

There is one month left to apply for our Simons Graduate Fellowships in Ecology and Evolution! These awards provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in #ecology and #evolution. www.simonsfoundation.org/grant/simons... #science

📣 Applications now open
PATH award supports early-career researchers studying the pathogenesis of infectious diseases in humans

💰 $505K over 5 years
🔬 For mid-to-late assistant professors
📅 LOI due: 07/17/25

Apply now 👉 buff.ly/qcSSxbq

I’m grateful to SMBE for this recognition of the lab’s work, but also much more generally for the important role that they play in our scientific community.

Two scientists standing in front of a SMBE 2024 Puerto Vallarta sign

Five scientists on an ornate balcony at a conference venue

Since starting my lab, I’ve been back to meetings with several of my graduate students. Elena Romero got to go to SMBE 2023 enabled by one of SMBE's Young Investigator Travel Awards.

Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo Abstract. HIV’s exceptionally high recombination rate drives its intrahost diversification, enabling immune escape and multidrug resistance within people l

I’ve since been back to many SMBEs/regional meetings. SMBE has enabled me to organize symposia, including one with @ksxue.bsky.social when we were only graduate students! I’ve had the opportunity to publish in MBE, and to review for MBE and GBE. academic.oup.com/mbe/article/...

Four scientists wearing conference badges standing in front of a big tree at a conference venue.

SMBE was my first real conference. I went as an undergrad in 2011 (with many thanks to @jplotkin.bsky.social). It was a completely mind-blowing experience to get to go to Kyoto and talk about science for four days. It solidified my decision to go to graduate school in this field.

I'm really honored to have received the early career award from @official-smbe.bsky.social, a society that has been an important part of my scientific experience.

POSTDOC ALERT: Applications now open for SeaBridge postdoc fellowship; opportunity to work on leading-edge biotech w/researchers at the Seattle Hub for Synthetic Biology.
brotmanbaty.org/news/new-pos...
@marionpepper.bsky.social
@jshendure.bsky.social
@coletrapnell.bsky.social