Pierotti Saul, Brettell Ian, Fitzgerald Tomas, Herder Cathrin, Aadepu Narendar, Pylatiuk Christian, Wittbrodt Joachim, Birney Ewan, Loosli Felix
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.
Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
Bioinformatics. 2025 Jun 2;41(6). doi: 10.1093/bioinformatics/btaf342.
Boldness-shyness is considered a fundamental axis of behavioural variation in humans and other species, with obvious adaptive causes and evolutionary implications. Besides an individual's own genetics, this phenotype is also affected by the genetic make-up of peers in the individual's social environment. To identify genetic determinants of variation along the bold-shy behavioural axis, a reliable experimental and analytical set-up able to highlight direct and indirect genetic effects is needed.
We describe a custom assay designed to detect bold-shy behaviours in medaka fish, combining an open-field and novel-object component. We use this assay to explore direct and social genetic effects on the behaviours of 307 pairs of fish from five inbred medaka strains. Applying a hidden Markov model (HMM) to classify behavioural modes, we find that direct genetic effects influence the proportions of time the five strains spent in slow-moving states, explaining up to 29.7% of the variance in time spent in those states. We also found that an individual's behaviour is influenced by the genetics of its tank partner, explaining up to 8.64% of the variance in the time spent in slow-moving states. Our behavioural assay in combination with the HMM analysis is applicable to follow-up genetic linkage studies of genetic variants involved in direct behavioural effects and indirect social genetic effects. A suitable genetic resource for such studies, the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel has recently been established.
The code associated with this work is available on GitHub (https://github.com/birneylab/medaka_behaviour_pilot) and Software Heritage (swh: 1: dir: c9abec1c5d62d22e43c9e97d995c56261784d9ab). Experimental data have been uploaded to the EBI Bioimage Archive (https://doi.org/10.6019/S-BIAD1421).
大胆-害羞被认为是人类和其他物种行为变异的一个基本轴，具有明显的适应性原因和进化意义。除了个体自身的基因外，这种表型还受到个体社会环境中同伴基因组成的影响。为了确定沿大胆-害羞行为轴变异的遗传决定因素，需要一个可靠的实验和分析设置，能够突出直接和间接的遗传效应。
我们描述了一种定制的检测方法，用于检测青鳉鱼的大胆-害羞行为，该方法结合了旷场和新物体成分。我们使用这种检测方法来探索对来自五个近交青鳉品系的307对鱼的行为的直接和社会遗传效应。应用隐马尔可夫模型（HMM）对行为模式进行分类，我们发现直接遗传效应影响五个品系在缓慢移动状态下所花费时间的比例，解释了这些状态下所花费时间方差的高达29.7%。我们还发现个体的行为受到其水箱伙伴基因的影响，解释了在缓慢移动状态下所花费时间方差的高达8.64%。我们的行为检测方法与HMM分析相结合，适用于对涉及直接行为效应和间接社会遗传效应的遗传变异进行后续的遗传连锁研究。最近已经建立了用于此类研究的合适遗传资源——青鳉近交清须-卡尔斯鲁厄（MIKK）面板。
与这项工作相关的代码可在GitHub（https://github.com/birneylab/medaka_behaviour_pilot）和软件遗产（swh: 1: dir: c9abec1c5d62d22e43c9e97d995c56261784d9ab）上获取。实验数据已上传至欧洲生物信息研究所生物图像存档库（https://doi.org/10.6019/S-BIAD1421）。
