Kabir Husain

Center for Living Systems -- seeking strong post docs at the interface of physics and biology. Consider applying by Oct. 13! docs.google.com/forms/d/e/1F...

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...

Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw

Top: Immunostaining reveals aggrecan (yellow) at the articular surfaces in the pelvic joint of an embryonic little skate (stage 33). The nucleus is stained using DAPI and is shown in red. Bottom: Phylogenetic tree adapted from Donoghue and Keating, annotated to show that synovial joints exist in extant jawed vertebrates (gnathostomes), but the study’s results do not support their existence in cyclostomes. The presence of reciprocally shaped and cavitated joints in the dermal skeleton of antiarchs suggests that joints that function by relative sliding (similar to synovial joints) first originated in stem gnathostomes.

When did synovial joints evolve? @neelimasharma.bsky.social @neilshubin.bsky.social &co reveal that stable, mobile & lubricated joints were present in the common ancestor of jawed fishes but lacking in jawless ones 🧪 @plosbiology.org plos.io/3CTC8La

Interested in a PhD in Physics of Life Theory? Applications for the EMBL PhD program are still open until March 10!

MRes Computational Cell Biophysics At the forefront of interdisciplinary research

Our interdisciplinary MRes is recruiting students for Sept 2025 entry : www.ucl.ac.uk/lifesciences...

Professor Jonathan Chubb

Slime mould

Listen to Professor Jonathan Chubb talking about slime moulds, the brainless organisms that can find their way around a maze, on BBC Radio 4's In Our Time at 9am this morning (02/01/25). www.bbc.co.uk/programmes/m...

Not one, but two PhD opportunities with a fantastic group in a brilliant scientific environment (and a great city!). Come be our colleague!

This is phenomenally elegant

Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Des…

This is a really important perspective on microbial ecology/evolution (Balakrishnan & Cremer). Quantitative physiology shows that microbes do not optimize growth, but instead express unutilized proteins that confer distinct dynamics when environments change.

www.sciencedirect.com/science/arti...

Evolution of evolvability in rapidly adapting populations - Nature Ecology & Evolution Evolvability modifier mutations alter the rates and benefits of future mutations, but it is difficult to predict when they will be favoured by natural selection. A mathematical framework shows that co...

From Ben Good: competition btwn linked mutations can..enhance selection for modifiers that increase benefits of future mutations, even when they impose a strong direct cost on fitness. However..modest direct benefits can..drive evolutionary dead ends to fixation. www.nature.com/articles/s41...

Pleased as punch to note, for my first post, that I just submitted a grant with the killer acronym of HiDenSeq (say it out loud...)

...and it's got an assay we called BALDy!

Surely the panel will weight names as much as scientific content in their decision, right?

Interested in studying Computational Cell Biophysics at UCL? Applications are open for our innovative MRes programme at the interface between physics and biology! ucl.ac.uk/lmcb/mres-ccb
Watch this video to find out more:
mediacentral.ucl.ac.uk/Player/9h335dB3