📣 The Whelan lab is hiring a bioinformatics postdoc 📣

Together with @fabricejpierre.bsky.social, we are offering a 1-year bioinformatic PDRA position in comparative genomics of Pseudomonas aeruginosa. To find out more please visit whelanlab.co.uk/contact/. Applications close 3 April 2026!

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium):
taxonium.org/atb
That's a big tree!

(unless you're used to SC2 trees)

We benchmarked ~30 existing measures in codon substitution models, and built a consensus-based measure that performs best. We hope this work sparks renewed interest in exploring amino acid similarity in this context.

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area.
doi.org/10.64898/202...

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Join us for the first PCI Genomics Recommenders' Meeting happening on Feb 9th and 11th!

Seeking expressions of interest from researchers abroad for a Canada Impact+ Research Chair ($1M/year × 8 + up to $6M CFI) in AI-enabled antibiotic discovery and/or AMR, phage & phage-based derivatives. Email me a short vision, CV, and 3–5 key papers. Deadline: March 10, 2026 (Intake 2: June 15).

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

My department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have.
apply.interfolio.com/177547

New diamond open access journal Replication Research welcomes reports of replication of previous works. #AcademicChatter
www.uni-muenster.de/Ejournals/index.php/repl...

Proud of the latest edition of my free intro biostats book.

gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/

Not complete but at a good point to take a break, and I think its quite usable

dm me with comments , ideas etc

What your Discussion section isn’t Today, the next instalment in a short series inspired by bad papers I’ve read (some of them, I have to admit, my own). I’ve let myself rant about what a Methods sections shouldn’t be, and what a Re…

Too many authors use a scientific paper's Discussion to thoroughly shred their own work. That, and two more common mistakes in writing Discussions:

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
1/n

On life, entropy, and the heat death of the universe a poem

In case you missed it, check out my latest #substack on life, entropy, and the arrow of time.

Trying to get a bit more poetic with this one. If this isn't your thing, stay tuned next week, for another prose post.

gibbological.substack.com/p/on-life-en...

Haha, thanks!

This could be your view!

Obligatory new job swag and selfie. Excited to start as an Assistant Professor at the University of New Brunswick in Fredericton, Canada!

Come work with me! douglaslab.ca

A high-quality genome assembly for carpenter bees We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span. 48% of the assembly is scaffolded into…

Lopezguerra & Douglas recommend the high-quality Xylocopa violacea reference genome by Nash et al., 2024, Heredity, the first annotated pseudo-chromosomal assembly for any Xylocopa bee! 🐝 A crucial step for pollinator research, conservation, and even cancer therapy studies #ERGA tinyurl.com/vwknzu2b

At PCI Genomics, we are pleased to have recommended all ERGA manuscripts and publications to date, helping to bring together this vital body of work at the heart of European biodiversity genomics.

🔗 genomics.peercommunityin.org
#ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience

An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky

Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...

Howard's: evolution of microbial genes, genomes and communities. Can be experimental or computational. If interested, contact Howard Ochman, howard.ochman@austin.utexas.edu
Homepage: web.biosci.utexas.edu/ochman/index...

We just published our first paper in the Peer Community Journal - diamond open access, no APCs!
Awesome experience, with less than a week from submission after receommendation by #pcigenomics.
Highly recommended!
#molpalmuc
@lmumuenchen.bsky.social
@peercommunityin.bsky.social

Assistant Professor (Research), Department of Microbiology & Immunology, (C2-240724) Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at ...

Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely.

mcgill.wd3.myworkdayjobs.com/en-US/McGill...

Please let us know if you have any questions or comments! This was a collaboration with several co-authors, including @cyanophage.bsky.social, @lbobay.bsky.social, @bjesseshapiro.bsky.social, Samuel Chaffron, and others!

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer - Nature Ecology & Evolution The authors analyse 8,790 prokaryotic pangenomes to identify the ecological variables associated with recent versus old horizontal gene transfer events, finding that gene transfers are more common amo...

Our work complements a recent analysis focused on 16S data: doi.org/10.1038/s415...

By analyzing marine metagenome-assembled genomes, we identified widespread evidence for HGT across marine prokaryotes and found the association with co-occurrence remains robust after accounting for other factors!

Co-occurring microbes have previously been found to undergo more HGT, but other factors could explain this observation (esp. phylo distance and similar env pressures).

New preprint (and brief🧵)! “Co-occurrence drives horizontal gene transfer (HGT) among marine prokaryotes”. doi.org/10.1101/2025...