New paper by Saskia Wilmsen and me just came out BioEssays: A new classification framework to understand evolutionary transitions in individuality Please find the OA paper here: onlinelibrary.wiley.com/doi/10.1002/...

You have heard of the gut microbiome but what do we know about plant microbiomes? Christopher Blake & colleagues examined the bacteria in the rhizosphere of Canola and suggest scope for better design interventions that support sustainable crop production. doi.org/10.1016/j.bc...

Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41... Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)

New preprint from our lab www.biorxiv.org/content/10.1...! Andrea Dos Santos and Clément Vulin combine experiments and models showing how adding glucose can strengthen negative interactions between microbial species. This can be used in tandem with antibiotic treatment to inhibit pathogens!

Very cool paper by Jyotsna Kalathera et al. from @iamsamayp.bsky.social 's-lab on Bottleneck size drives the evolution of cooperative traits in an aggregative multicellular myxobacterium just out @plosbiology.org Congratulations to all coauthors. journals.plos.org/plosbiology/...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

As we close the year, the ISME Early Career Scientist Committee is glad to spotlight @duhitasant.bsky.social , Postdoctoral Researcher at Rutgers University, and her paper “Eco-evolutionary robustness of wild bacterial communities to experimental perturbation”. doi.org/10.1093/isme... (1/2)

This is totally worth 5 minutes of your time and probably should be in every biology class. Nature is awesome. neal.fun/size-of-life/

Hey, fellow evolutionary biologists: If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community

"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community in a spatially structured environment #ISMEJournal by @mlaenoc.bsky.social et al academic.oup.com/ismej/advanc...

How do bacteria deal with double costs? And how costly are unusual levels of mistranslation anyway? In short - antibiotics are more of an issue than less/more mistranslation, but the latter changes how populations deal with antibiotics. For the long story, check out our new paper!

Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/

🗞️ New preprint from the lab, led by our postdoc Ana Garoña (not on here) in collab with @andreagiometto.bsky.social: “Experimental evolution of cellular miniaturization reveals a mechanism for cell size evolution”, aka: “honey, we shrank the yeasts!” 🎥 www.biorxiv.org/content/10.6...

Impact of fluctuating environments on the fitness and robustness of evolving laboratory and industrial Saccharomyces cerevisiae strains https://www.biorxiv.org/content/10.64898/2025.12.05.692621v1

Strong genotype-by-genotype and genotype-by-environment interactions induced by antibiotic resistance mutations https://www.biorxiv.org/content/10.64898/2025.12.03.692229v1

Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org www.nature.com/articles/s41...

Our new collaborative work led by @taliamycota.bsky.social Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social and collaborators: @plantricia.bsky.social et al. tinyurl.com/5yx2wmz5 (1/n)

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)

Happy to share our new review on oligonucleotide chemical evolution on early Earth. We discuss how iterative sequence selection and diversification could have shaped RNA pools, facilitating sequence exploration and the emergence of ribozymes. www.jstage.jst.go.jp/article/biop...

New online! Microbial genomics for antimicrobial resistance ecology and action

Out now at @plosbiology.org we evaluate the potential for antibiotic efflux and cell wall biogenesis as targets for reversing drug resistance and preventing its de novo evolution in Escherichia coli. Link below: journals.plos.org/plosbiology/...

New in JB: Black and Wakeman review the challenges of treating polymicrobial infections in various body sites, a topic near and dear to my heart. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology

Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community Microbial Ecology link.springer.com/article/10.1...

A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly... www.biorxiv.org/content/10.1...

Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.

Metabolic interplay drives population cycles in a cross-feeding microbial community @natcomms.nature.com from @oventurelli2.bsky.social www.nature.com/articles/s41...

Pseudomonas aeruginosa lasR is a keystone gene in polymicrobial cultures https://www.biorxiv.org/content/10.1101/2025.10.06.680631v1

#PaperCBGP 🆕📰‼️ Can we predict which bacteria will turn into #superbugs? 🦠 A study led by Dr. Alejandro Couce and published in PLoS Genetics (@plos.org#PaperCBGP  shows that a single DNA change can open “bridges” to modern resistances. 🔗 Read more here: https://shorturl.at/TRRwD

#PaperCBGP 🆕📰‼️ 🧬 Led by Alejandro Couce, researchers of the CBGP used experimental evolution to predict how the superbug enzyme KPC-2 could outsmart antibiotics ⚔️The study, published at @natecoevo.nature.com, lets us block it and protect our antibiotics 📎 shorturl.at/F7oOa

So this came online over the weekend: My dive into the "definition" of coevolution is online ahead of publication in @journal-evo.bsky.social! Don’t ask "when is it coevolution?" — ask "how?" doi.org/10.1093/evol...

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers! www.microbiologyresearch.org/content/jour...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

How can we build a general theory of mutualistic communities? After five years, we finally completed a new Neutral Theory of Cooperation that is fully solved analytically and displays remarkable properties @jordipinero.bsky.social @artemyte.bsky.social @manlius.bsky.social arxiv.org/abs/2506.09737

Mutation bias is a key predictor of adaptation rate https://www.biorxiv.org/content/10.1101/2025.09.22.677663v1

We have a new paper out in Molecular Ecology, led by @devinbendixsen.bsky.social ! Reproductive isolation due to divergent ecological selection is accompanied by vast genomic instability in experimentally evolved yeast populations onlinelibrary.wiley.com/doi/10.1111/...

New in Evolution: Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae, by Joleen Khey and Mike Travisano academic.oup.com/evolut/artic...

Ecological diversification in rapidly evolving populations https://www.biorxiv.org/content/10.1101/2025.09.15.676408v1

Our new paper @asn-amnat.bsky.social develops a Grand Unified Theory including both exploitative and interference competition doi.org/10.1086/737628. The R* rule of ecology (that 2 species cannot coexist on a single resource), is widely broken, including via a new trade-off we describe. 1/9

Cancer is an evolutionary disease, but does knowing a cancer’s evolutionary past help predict its future? Out today in @nature, we learnt the evolution of 2000 lymphoid cancers and found it was highly correlated with clinical outcomes! (1/7) rdcu.be/eFrrc

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution https://www.biorxiv.org/content/10.1101/2025.09.11.675703v1

Nature research paper: Commensal yeast promotes Salmonella Typhimurium virulence go.nature.com/4mTnRzG

NEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species. Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation! (1/3) www.biorxiv.org/content/10.1...

Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Experimental Populations of Caenorhabditis elegans https://www.biorxiv.org/content/10.1101/2025.09.03.674070v1

I’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵 doi.org/10.1101/2025... A thread 👇

Molecular adaptation reflects taxon-specific mutational biases https://www.biorxiv.org/content/10.1101/2025.09.03.674101v1

Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.

Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.

Natural protein structures have evolved exceptional robustness to mutations https://www.biorxiv.org/content/10.1101/2025.08.27.672565v1