Data from: Detecting cryptic indirect genetic effects

Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the phenotype of an interacting partner. IGEs can dramatically affect the expression and evolution of social traits. However, the interacting phenotype(s) through which they are transmitted are often unknown, or cryptic, and their detection would enhance our ability to accurately predict evolutionary change. To illustrate this challenge and possible solutions to it, we assayed male leg tapping behaviour using inbred lines of Drosophila melanogaster paired with a common focal male strain. The expression of tapping in focal males was dependent on the genotype of their interacting partner, but this strong IGE was cryptic. Using a multiple-regression approach, we identified male startle response as a candidate interacting phenotype: the longer it took interacting males to settle after being startled, the less focal males tapped them. A genome-wide association analysis identified approximately a dozen candidate protein-coding genes potentially underlying the IGE, of which the most significant was slowpoke. Our methodological framework provides information about candidate phenotypes and candidate SNPs that underpin a strong yet cryptic IGE. We discuss how this approach can facilitate the detection of cryptic IGEs contributing to unusual evolutionary dynamics in other study systems.

间接遗传效应（Indirect Genetic Effects, IGEs）指一个个体中表达的基因改变其互动伴侣表型的现象。IGEs可显著影响社会性状的表达与演化进程。然而，IGEs借以传递的互动表型往往尚未明确，或具有隐蔽性；对这类表型的检测，将有助于提升我们精准预测演化变化的能力。
为阐明这一研究难题及其可能的解决路径，我们以黑腹果蝇（Drosophila melanogaster）的近交系与通用焦点雄性品系配对，对雄性敲腿行为开展了检测。实验结果显示，焦点雄性的敲腿行为表达量取决于其互动伙伴的基因型，但这一强烈的IGEs却具有隐蔽性。
通过多元回归分析方法，我们将雄性惊跳反应鉴定为候选互动表型：互动雄性在受到惊跳后，恢复平静所需的时间越长，焦点雄性对其做出的敲腿行为便越少。全基因组关联分析则鉴定出约12个可能参与调控该IGEs的候选蛋白编码基因，其中显著性最高的为slowpoke基因。
本研究的方法学框架可为这类作用显著却隐蔽的IGEs提供候选表型与候选单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）相关信息。我们还进一步讨论了该方法如何助力在其他研究系统中，检测那些参与异常演化动态的隐蔽IGEs。