Time for the meta-post of the year! During 2021, the blog racked up 28 posts (counting this one), about the same pace as 2020. That’s okay.
As usual, let’s pick one post a month to represent the blogging year of 2021:
January: A model of polygenic adaptation in an infinite population. We look at some equations and make two animations following Jain & Stephan (2017).
February: The Fulsom Principle: Smart people will gladly ridicule others for breaking supposed rules that are in fact poorly justified.
March: Theory in genetics. As I’m using more modelling in my work, here is some inspiration from an essay by Brian Charlesworth. As I hadn’t read Guest & Martin (2021) at the time, the post only cites Robinaugh at al. (2020) and music theory youtuber Adam Neely, and that’s also quite good.
April: Researchers in ecology and evolution don’t use Platt’s strong inference, and that’s okay. This post is reacting to a paper that advocates explicit hypotheses in evolution and ecology, a paper I think qualifies as ”wrong, but wrong in an interesting and productive way” (can’t remember who said that).
Also, this post also got one of the coveted Friday Links mentions on Dynamic Ecology, before it shut down. End of an era, death of blogs etc.
May: Convincing myself about the Monty Hall problem Probably my favourite post of the year. It also shows the value of a physical model: I had what felt like the crucial moment that made the problem click as I was physically acting out Monty Hall choices with myself. Also, first shout-out to Guest & Martin (2021), a paper that will be cited again on the blog, I’m sure. I think the Monty Hall problem is a great example of their claim that a precise mathematical theory can’t defeat intuition unless you run the numbers and do the calculations.
June: no posts, distracted by work and pandemic, I guess.
July: Journal club of one: ”A unifying concept of animal breeding programmes”. Rather long post about a paper about a graphical method for displaying simulated breeding structures, and whether this qualifies as a formal specification or not.
August: ”Dangerous gene myths abound” , reacting to an article by Philip Ball. The breathless hype around genomics is often embarrassing, but criticisms of reductionism in genetics love attacking caricatures.
September: Belief in science, some meditations on how little it knows and how science ”works whether you believe in it or not”
October–November: extended blog vacation
December: Well, there are only two to choose from, but the other day I posted some notes about two methods that try to infer recent population history from linkage disequilibrium.
Outwith the blog, there were also some papers published. I’m really behind on giving them their own blog posts, but that might be rectified in time. The blog runs on its own schedule where papers remain ”recent” for several years.
- Johnsson M, Wall H, Lopes Pinto FA, Fleming RH, McCormack HA, Benavides-Reyes C, Dominguez-Gasca N, Sanchez-Rodriguez E, Dunn IC, Rodriguez-Navarro AB, Kindmark A, de Koning D-J. Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems. Preprint. (Blog post)
- Johnsson M, Wahlen A, Ros-Freixedes R, Gorjanc G, Chen C-Y, Herring WO, de Koning D-J, Hickey JM. Genetic variation in recombination rate in the pig. Genetics Selection Evolution. (Blog post.)
- Johnsson M, Henriksen R, Wright D. The neural crest cell hypothesis: no unified explanation for domestication. Genetics. We examine the genomic evidence for the popular neural crest cell hypothesis of domestication, and find it lacking.
- Johnsson M, Jungnickel, MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genetics Selection Evolution. Reviewing causative variants in farm animals, and thinking of what to do to find more of them.
- Powell O, Mrode R, Gaynor RC, Johnsson M, Gorjanc G, Hickey JM. Genomic evaluations using data recorded on smallholder dairy farms in low- to middle-income countries. JDS Communcations.
- Gozalo-Marcilla M, Buntjer J, Johnsson M, Batista L, Diez F, Werner CR, Chen C-Y, Gorjanc G, Mellanby RJ, Hickey JM, Ros-Freixedes R. (2021). Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds. Genetics Selection Evolution.
- Dadousis C, Somavilla A, Ilska JJ, Johnsson M, Batista L, Mellanby RJ, Headon D, Gottardo P, Whalen A, Wilson D, Dunn IC, Gorjanc G, Kranis A, Hickey JM. A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens. Genetics Selection Evolution.
- Fallahshahroudi A, Johnsson M, Sorato E, Ubhayasekera SJ, Bergquist J, Altimiras J, Jensen P. Effects of the Domestic Thyroid Stimulating Hormone Receptor (TSHR) Variant on the Hypothalamic—Pituitary—Thyroid Axis and Behavior in Chicken. Genetics.
What else is new? Astute readers may have noticed that my job description has changed from ”postdoc” to ”researcher”. Now, ”researcher” is a little bit of an ambiguous title because some institutions also use it for time limited positions — but no, dear reader, I am now permanently employed at the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences where, among other things, I lead the ”Genome dynamics of livestock breeding” project financed by the research council Formas. This will be great fun, and also show on the blog in time, I’m sure.