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New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

Because I have gotten so many questions about this paper, I have started an FAQ on the blog post: mol-evol.github.io/pangenome-be... Thanks to @benjaminhgood.bsky.social and @uncultured.carinilab.com for questions (acknowledged on the post). More questions welcome - i'll do my best to answer.

Because I have gotten so many questions about this paper, I have started an FAQ on the blog post: mol-evol.github.io/pangenome-be... Thanks to @benjaminhgood.bsky.social and @uncultured.carinilab.com for questions (acknowledged on the post). More questions welcome - i'll do my best to answer.

Love this quote: "We used to make fun of Edgar Anderson by saying that he was finding hybrids under every bush. Then we realized that even the bushes were hybrids." academic.oup.com/jeb/article/...

to clarify - core genes are those whose p is substantially above p* (loose wording on my behalf to say "always") apols.

I have written a document that explains my preprint. It has generated a lot of interest, and a lot of emails to me. So, this is the explanation, minus most of the maths and formal science-speak: mol-evol.github.io/pangenome-be...

Published at @pnas.org www.pnas.org/doi/epdf/10....

This is already covered in the paper in four places: the Introduction, in Box 1, in the "Selection at two levels" section, and in the supplementary information where I explicitly address selfish elements. No need to add anything - it was never forgotten in the first place.

New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

Prokaryotic Pangenomes Are Bet-Hedging Devices www.biorxiv.org/content/10.6...

Sir David Attenborough is older than horizontal gene transfer. Well, he was born before the first experiments that demonstrated HGT. #clickbait #NotTheSameThing

"If the accessory genome was truly dispensable, then the interesting part of pangenomics would, of course, be the core."

A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...

This robot installs 80 panels/hour. One every 45 sec. 1,920/day ≈ 0.0008 GW/day per line. Sounds small. It’s not. Scale this across thousands of lines and #solar becomes manufacturing, not construction. 👉 10,000 lines = 8 GW/day. That’s HOW China is winning the energy game.

New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...

I'm blogging over on substack - no subscription needed. open.substack.com/pub/profmcin...

I’ll be there. Hup!!

Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1

Interesting. www.rte.ie/brainstorm/2...

What's even wilder is that models like scGPT and Geneformer are now doing this at the single-cell level — learning gene regulatory patterns from raw expression data with zero biological annotation. They're rediscovering cell types and disease states purely from the structure of the data.

A transformer model trained on raw DNA, with no biological instruction whatsoever, learned to distinguish between genetic codes. Nobody taught it what a codon is. That is just “wow”.

We have a new Masters programme in Liverpool. Please pass on to anybody you think might be interested: news.liverpool.ac.uk/2026/02/13/n...

This looks really great. I’ve been following this for a while.

On this last point: the implication is (and I wrote this in the paper) that evolution is not optimising biochemical (or other) activity as a primary focus, but the context-dependent function. And this is liable to change often.

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

True story.

@jomcinerney.bsky.social proposes that genomes do not encode fixed functions but rather “probability distributions” over functional and phenotypic outcomes, and introduces “genomic perplexity” as a measure of gene-context incompatibility. 🔗 doi.org/10.1093/molbev/msag041 #evobio #molbio

@guigau.bsky.social Saw PanGBank earlier. Very nice 👍

This looks absolutely great. For those of us interested in pangenomes, I am sure this will be a super place to get data and the interface is very clean (plotly). Congrats to the authors (I don't know if they are on bsky): pangbank.genoscope.cns.fr

I'm in a coffee shop wrestling with Endnote, while 1980s power ballads blast out from a giant speaker. The sun is shining for the first time this year, but I got paper submission deadlines. I hope nobody sees me cry.

New paper out in MBE! 🧵 "Genomic Perplexity and the Evolution of Context-Dependent Function" The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI

Very interesting paper. www.science.org/doi/10.1126/...

Ever wondered if writing a grant proposal was actually worth your time? Presenting....The Grant Portfolio Evaluator - (for entertainment only) mol-evol.github.io/grant-evalua...

PanForest: predicting genes in genomes using random forests academic.oup.com/bioinformati... #jcampubs

Ever wondered if writing a grant proposal was actually worth your time? Presenting....The Grant Portfolio Evaluator - (for entertainment only) mol-evol.github.io/grant-evalua...

Interested in pangenomics ? This paper just out from Alan Beavan (not on socials), @blackpassiflora.bsky.social and @jomcinerney.bsky.social is a must: doi.org/10.1093/bioi...

Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.

New paper out in Bioinformatics! PanForest uses random forests to predict gene presence/absence in bacterial genomes based on other genes present. Joint work with Alan Beavan & Maria Rosa Domingo-Sananes. 🔗 doi.org/10.1093/bioinformatics/btag005

Well done Roberto.

Anybody involved in leadership at any level in universities should read this article. Twice. www.rte.ie/brainstorm/2...

the program will output multiple support measures for internal branches

My word. The Taoiseach, in China, says "platforms can be misused and abused or they can be used for positive reasons as well..." and says that should be considered carefully "before jumping to conclusions" on whether it's appropriate for the Government to be on X.

Not once, in all my time on Twitter, did I come across a 'gender critical' activist who made me think, 'maybe I have this wrong?' In fact, watching people like Graham Linehan slide further and further into Right Wing and Far Right ideology confirmed that they are the ideologues.

Sponges are notoriously difficult to understand in evolutionary biology terms. I think this paper is a big step forward : www.science.org/doi/10.1126/...

Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...