Congrats!

New from our group, led by Nick Collier:

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

We posted a new theory preprint. I am very interested to hear what the community thinks about it.

We looked at the dynamics of evolution on several (simple) models of modular genotype-phenotype-fitness maps and found that populations approach a quasi-steady state we call "module-selection balance".

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...

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/...

Happy to share the final version of @oliviamghosh.bsky.social's paper on inferring low dimensional phenotype-fitness maps from high-throughput fitness measurements across environments. Fun collaboration with @oliviamghosh.bsky.social, @grantkinsler.bsky.social, & @petrovadmitri.bsky.social

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

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 to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!

ecoevorxiv.org/repository/v...

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population Analysis of hundreds of single-cell genomes from Yellowstone National Park shows bacterial species are less cohesive than previously thought.

Happy that our work on the evolution of Yellowstone cyanobacteria is now published in @elife.bsky.social: doi.org/10.7554/eLif...! Did a lot of work in revision—many thanks to the anonymous reviewers for great suggestions! Also see the eLife digest for a summary: elifesciences.org/digests/9084...

Before 2025 closes out, I wanted to make a thread on my proudest recent paper! (Ok, it's from 2024, but I haven't done a bluesky thread on it before).

Allen et al. (2024) "Nonlinear social evolution and the emergence of collective action", PNAS Nexus

academic.oup.com/pnasnexus/ar...

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

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/...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

Schematic diagram showing microbial strains migrating between mouse gut microbiomes.

(while the underlying biology is very different, there are some striking parallels to the migration of bacterial strains across different local gut microbiomes)

We think these intermediate levels of migration could be very interesting, by preserving the large-scale spatial structure of GCs, while still allowing positively selected lineages to expand across a wider range of GCs than would otherwise be possible - potentially balancing diversity & selection.

Schematic diagram illustrating spatial migration of B cells during affinity maturation.

We show that these local migrations follow a clock-like process @ a rate of ∼1/50 cell divisions - roughly uniform across lineages & time. Plus, migrant B cells continue to evolve w/in their new germinal centers at similar rates, such that the largest lineages in each GC often originate from another

& last but not least, a new preprint led by PhD student John McEnany (w/ Ivana Cjivovic) looking @ the evolutionary dynamics within our immune system. Using spatial transcriptomics data from the tonsil, we identify a surprisingly large role for local migration of B cells during affinity maturation.

📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social

Understanding this effect really changed how I think about the fates of new mutations in the presence of clonal interference – and leads to a mathematical formalism that I hope will be useful in other contexts as well.

In this regime, invading ecotypes effectively "mortgage" their ecological advantage to increase their initial growth rate. But they eventually pay a price at higher freqs, when their ecological advantage suddenly dissipates. This echoes recent findings by P. Barrat-Charlaix & @neher.io in SI models.

Schematic showing how a rapidly evolving population clusters into a smaller number of distinct ecotypes, comprising individuals with similar resource uptake strategies but different genotypes & overall fitness.

We show that despite this large mutational influx, rapidly evolving pop'ns naturally cluster into a smaller # of distinct “ecotypes”, even when their genetic diversity is much larger. This non-eq analogue of competitive exclusion is driven by a dynamical priority effect that favors resident strains.

Schematic diagram showing an evolving ecosystem at high and low mutation rates.

Most existing models of evolving ecosystems assume that evolution occurs very slowly, so that the ecosystem can always equilibrate before the next mutation appears. Here we focus on the more empirically relevant case where ecology & evolution act on similar timescales, as often occurs for microbes.

Another new preprint from former PhD student Daniel Wong (now @ ENS) has been a long time in the making, and builds on our recent efforts to model eco-evolutionary feedbacks in rapidly evolving microbial populations that compete for different resources (1/n)

📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...

Their adaptive reversion model may provide part of the answer, but strong assumptions still needed to account for long-term optimization of ~90% of all protein coding sites. For me, this remains one of the more interesting puzzles of microbial pop gen, since it's such a common trend across species.

Reversions mask the contribution of adaptive evolution in microbiomes The timescale dependence of dN/dS in bacteria is better explained by adaptive than purifying dynamics, suggesting comparative genomics can underestimate past adaptation.

How natural selection manages to optimize such weak fitness costs in the face of all the adaptation & genetic hitchhiking we think is happening on shorter evolutionary timescales is still a major puzzle. Previous work by Paul Torrillo & @contaminatedsci.bsky.social suggests that it's not so easy!

Clonal dN/dS dynamics in human gut bacteria after correcting for recombination.

We use this finding to re-examine models of purifying selection & adaptive reversion in human gut bacteria. After correcting for HGT, we show that most protein-coding variants are eliminated ~10x more slowly than previously assumed. Yet they are still reliably purged on 10-100k yr timescales.

Schematic showing how homologous recombination can influence dN/dS between conspecific strains of bacteria.

Many studies have found that w/in-species dN/dS decays w/ the genetic distance between strains, which is often attributed to natural selection. Here Zhiru shows that a large portion of this trend can be quantitatively explained by the accumulation of horizontally transferred DNA segments over time.

Dynamics of dN/dS within recombining bacterial populations The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...

The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.