Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. https://profmcinerney.substack.com/ 🇮🇪 https://mol-evol.github.io/https://bsky.app/profile/jomcinerney.bsky.socialhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mlkwxns7b22mNew 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 🧵👇11 May 2026 09:18 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlkwxns7b22mhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mlpw53aqgk23Because I have gotten so many questions about this paper, I have started an FAQ on the blog post: https://mol-evol.github.io/pangenome-bet-hedging/#faq 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. [contains quote post or other embedded content]13 May 2026 08:47 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlpw53aqgk23https://bsky.app/profile/jomcinerney.bsky.social/post/3mlpw53aqgk23Because I have gotten so many questions about this paper, I have started an FAQ on the blog post: https://mol-evol.github.io/pangenome-bet-hedging/#faq 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. [contains quote post or other embedded content]13 May 2026 08:47 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlpw53aqgk23https://bsky.app/profile/jomcinerney.bsky.social/post/3mlpv3c75cy2vto clarify - core genes are those whose p is substantially above p* (loose wording on my behalf to say "always") apols. [contains quote post or other embedded content]13 May 2026 08:28 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlpv3c75cy2vhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mlorpu44cd2vI 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: https://mol-evol.github.io/pangenome-bet-hedging/ [contains quote post or other embedded content]12 May 2026 21:55 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlorpu44cd2vhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mllkyvpdwk27This 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. [contains quote post or other embedded content]11 May 2026 15:17 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mllkyvpdwk27https://bsky.app/profile/jomcinerney.bsky.social/post/3mlkwxns7b22mNew 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 🧵👇11 May 2026 09:18 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlkwxns7b22mhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mlkq3z4quc2iProkaryotic Pangenomes Are Bet-Hedging Devices https://www.biorxiv.org/content/10.64898/2026.05.08.723712v111 May 2026 07:15 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mlkq3z4quc2ihttps://bsky.app/profile/jomcinerney.bsky.social/post/3mleozdksn22wSir David Attenborough is older than horizontal gene transfer. Well, he was born before the first experiments that demonstrated HGT. #clickbait #NotTheSameThing08 May 2026 21:40 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mleozdksn22whttps://bsky.app/profile/jomcinerney.bsky.social/post/3mldjmfefj223A short piece about what "the pangenome" is and is not. https://open.substack.com/pub/profmcinerney/p/the-pangenome-is-not-a-parts-list?r=xx9b9&utm_campaign=post&utm_medium=web&showWelcomeOnShare=true08 May 2026 10:31 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mldjmfefj223https://bsky.app/profile/jomcinerney.bsky.social/post/3ml4vhzl7m225New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks https://www.biorxiv.org/content/10.64898/2026.04.28.721069v205 May 2026 19:14 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3ml4vhzl7m225https://bsky.app/profile/jomcinerney.bsky.social/post/3ml4vhzl7m225New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks https://www.biorxiv.org/content/10.64898/2026.04.28.721069v205 May 2026 19:14 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3ml4vhzl7m225https://bsky.app/profile/jomcinerney.bsky.social/post/3mk5zfwocwc2bI'm blogging over on substack - no subscription needed. https://open.substack.com/pub/profmcinerney/p/the-fourth-wave?utm_campaign=post-expanded-share&utm_medium=web23 Apr 2026 12:32 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mk5zfwocwc2bhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mk3xsshvw22oI’ll be there. Hup!! [contains quote post or other embedded content]22 Apr 2026 16:58 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mk3xsshvw22ohttps://bsky.app/profile/jomcinerney.bsky.social/post/3mjyw7wrr6k2bhttps://open.substack.com/pub/profmcinerney/p/why-evolution-plays-the-lottery?r=xx9b9&utm_campaign=post&utm_medium=web&showWelcomeOnShare=true21 Apr 2026 11:52 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mjyw7wrr6k2bhttps://bsky.app/profile/jomcinerney.bsky.social/post/3midec5ihr22dInteresting. https://www.rte.ie/brainstorm/2026/0330/1565137-return-to-office-policies-remote-working-management-benefits-drawbacks/31 Mar 2026 04:40 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3midec5ihr22dhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mhym4dnhjc2zA 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”.26 Mar 2026 22:00 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mhym4dnhjc2zhttps://bsky.app/profile/jomcinerney.bsky.social/post/3mhfkeok4wc25We have a new Masters programme in Liverpool. Please pass on to anybody you think might be interested: https://news.liverpool.ac.uk/2026/02/13/new-msc-in-wildlife-health-and-conservation-launched-in-partnership-with-chester-zoo/19 Mar 2026 08:09 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mhfkeok4wc25https://bsky.app/profile/jomcinerney.bsky.social/post/3mgrxx47c2k2eThis looks really great. I’ve been following this for a while. [contains quote post or other embedded content]11 Mar 2026 13:18 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mgrxx47c2k2ehttps://bsky.app/profile/jomcinerney.bsky.social/post/3mgrxast25k2eOn 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. [contains quote post or other embedded content]11 Mar 2026 13:06 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mgrxast25k2ehttps://bsky.app/profile/jomcinerney.bsky.social/post/3mgroz55am22sI'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 https://academic.oup.com/mbe/article/43/3/msag041/849749811 Mar 2026 10:38 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mgroz55am22shttps://bsky.app/profile/jomcinerney.bsky.social/post/3mgchsw6y6k2fTrue story. [contains quote post or other embedded content]05 Mar 2026 09:20 +0000at://did:plc:rhkp2onvwl3rc7t2bcsqmspx/app.bsky.feed.post/3mgchsw6y6k2f