Ben Good

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.

It's been a busy few months for our group so wanted to highlight a few other recent preprints we’ve posted that I haven’t had the chance to share yet... (1/n)

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.

We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology

www.cell.com/trends/micro...

Kudos to our superstar grad student @sophiejwalton.bsky.social! One of the most interesting and surprising (at least to me) studies I have been involved in. Very curious to know what people think of it! @benjaminhgood.bsky.social

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!

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...

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:

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...

Limited codiversification of the gut microbiota with humans A recent study by Suzuki & Fitzstevens et al ([1][1]) argued that dozens of species of gut bacteria have codiversified with modern human populations. Reanalysis of their data reveals that the correlat...

Drifting into speculation: I think these data support the picture that gut microbes can spread much faster than human genes. Strong geographic barriers can be still be very important (as in the Tsimane & Hadza case) but the magnitude of this effect
stands out compared to other contemporary pop'ns.

A figure panel depicting the amount of recent strain sharing of Ruminococcus bromii strains between different human populations.

Interestingly, of the subset of species shared w/ industrialized pop'ns, some show evidence of recent transmission, while others suggest a more ancient association. Among these, the genetic isolation between Tsimane & Hadza strains was generally larger than between comparable industrialized pop'ns