Martin Johnsson

New paper claxon, together with @mrtnj.bsky.social. Final paper of the PhD project of Mohamma Sallam! 🧬🐔
rdcu.be/eR4Tl

PhD Student in Animal Science | slu.se SLU - Science and Education for Sustainable Life

We're hiring a PhD student to work on genomic prediction and genetic variation in farm animals.

There will be cattle, genomics, simulation, and there might be poultry.

And if you already have a PhD, consider sharing with someone who hasn't, and might be a good fit. :)

www.slu.se/en/about-slu...

Q&A: inbreeding and its implications for conservation - BMC Biology Inbreeding depression plays a role in the decline, endangerment, and extinction of small populations, and thus inbreeding has received much attention in conservation biology. The term inbreeding is us...

All those questions about inbreeding in conservation that you were afraid to ask.

A bunch of early career scientists is here to explain something that even Wright and Fisher couldn't agree on, the (not so) simple question of what is inbreeding.

link.springer.com/article/10.1...

There's something oddly fitting about a Werner Herzog trading card sitting on top of a medal awarded for pain research.

A reoccurring frustration for philosophers of science: Many scientists know how to do science like people know how to ride a bike. When they reflect on the practice of science, they repeat platitudes about how science works. Those platitudes are often wrong, sometimes even about their own field

I also particularly liked Gwendal Restoux's (INRAE) talk on genetic resources and potential strategies to make use thereof, and Anna Wolc's (Hyline, Iowa State) thorough update on the state of machine learning for poultry breeding and management.

And Tanmay Debnath (University of Edinburgh) talked about ML for phenotyping of the tibia.

Outwith of our project, there were more contributions about the keel, with genetic parameters from Pascal Duenk (Wageningen), and a poster on keel ossification from Lisa Hildebrand (FLI).

We had a pretty strong lineup from our department and the international FFAR keel bone project:

I talked about our genomic selection efforts, Khrystyna Kurta about genome-wide association and bone composition, and Moh Sallam about ML and new phenotypes for the keel.

European Society for Poultry Genetics meeting 2025, some impressions.

#espg2025 #WPSA

When large-effect damaging alleles enter small populations https://www.biorxiv.org/content/10.1101/2025.09.11.675554v1

Elin Hernlund presenting in front of a slide that shows 3D models of a human, a horse, a dog and a cow.

Researcher day with the Beijer laboratories. Here: Elin Hernlund, my fellow Beijer researcher in the laboratory for animal science, talking about her models of shape and posture of domestic animals.

(It doesn't help that Prisma's import publications function has been broken since what, 2019? Please, pretty please with sugar on top, let us enter the publication list as a pdf like VR does.)

This year, the profile was cut down to a small text box, and we're back to list of 10 publications to be entered in Prisma. Gone are the ambitions to include more stuff than publications; it's now not even clear whether preprints count.

Last year's call introduced the academic profile for describing the merits of applicants in a broader way than before, including a wider understanding of an academic contribution than just a publication list. It came with a prescribed template, which was unfortunately quite awkward and bad.

The new format for the Formas Explore 2025 call--I say it's an improvement overall. Fewer boxes to fill in, and in the end a bit more space for implementation and references, so one doesn't have to hunt characters as much.

The new format of the academic profile is a step backwards, though.

On that note, it's time to seriously learn Bibtex, so I can let go of the Zotero plugin and rid myself of Microsoft Word.

Here's one powerful opening sentence:

"Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media."

Sad but probably justified! :(

My next lecture in the course is QTL, so it's still there, but it has morphed, and a lot of it is about molecular trait mapping, eQTL and that stuff now.

Researchers should feel this often in contact with the literature. "There are tons of research about this ... but to different ends, and from other perspectives."

She illustrated this with an anecdote about getting to know roaches (the fishes), wanting to know about their behaviour and learning, and going to the library to find only books about catching and cooking fish.

Then philospher Jonna Bornemark talked about a model of knowledge (by her and Nicolaus Cusanus), going from sensations and drives through imagination, instrumental knowledge, intellectual critique, the absence of knowledge (the highest form of knowledge) and then back around again.

This course (Genome Analysis for MSc students) is always fun. When I came in to talk GWAS, my colleague had this on the board and a linkage map of the chicken Z chromosome on the projector. :)

Maria Knutson Wedel talking in front of a audience of SLU colleagues and students.

Vice Chancellor Maria Knutson Wedel, SLU, opening the first "studium generale", a series of meetings on knowledge--I suppose--and reflection.

A whiteboard with DNA sequence of microsatellites and a circuit diagram, half erased, on top of each other.

Circuits and microsats on the whiteboard.

The price of perfection: Opting out of variety - a danger to animal immunity and survival | slu.se For thousands of years, humans have been controlling the breeding of dogs, horses and farm animals. Despite the benefits, this has led to unexpectedly high risks for the animals. With knowledge from r...

Genetic variation is the key to species resilience, enabling populations to adapt to changing environmental conditions. Our research group will take a deep dive into the variation present in the genes encoding for central roles of the immune system. www.slu.se/en/news/2025...

Me right now reading “It is also the 18th anniversary of ggplot2…”

Continuous Evolution in the NK Treadmill Model Abstract. The NK fitness landscape is a well-known model with which to study evolutionary dynamics in landscapes of different ruggedness. However, the model is static, and genomes are typically small,...

My favourite paper from the dissertation was this one, on the NK Treadmill model: direct.mit.edu/artl/article...

The E(NK) model: Extending the NK model to incorporate gene‐by‐environment interactions and epistasis for diploid genomes The haploid NK model developed by Kauffman can be extended to diploid genomes and to incorporate gene-by-environment interaction effects in combination with epistasis. To provide the flexibility to i...

And there are examples of using NK-style models for plant breeding, for instance: onlinelibrary.wiley.com/doi/10.1002/...

It's funny how you're sometimes the most computer-minded among biologists and sometimes the most biology-brained among computer people. I feel I might have been on the latter pole yesterday, trying to drag the discussion down into the mud of application.

Blue skies over Borlänge, and a hydroelectric dam.

Going home from Borlänge and Högskolan Dalarna after Priyanka Mehra's PhD defence--an exciting full day of theoretical genetics and computational modelling.

du.diva-portal.org/smash/record...