Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark–recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host–pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time.

中文翻译：

---

自然选择对野生转录本丰度的强度和形式

已知基因转录变异有助于疾病易感性和适应，但我们目前对当代自然选择如何塑造转录本丰度知之甚少。在这里，我们提出了一个新的分析框架来量化野生脊椎动物转录组水平上正在进行的自然选择的强度和形式。我们估计了一群受细胞外黏液动物寄生虫（Tetracapsuloides bryosalmonae）影响的野生鲑鱼（Salmo trutta）中转录本丰度的选择。）通过标记-重新捕获现场采样以及将 RNA 测序与基于经典回归的选择分析相结合。我们显示，基于宿主的鳍转录组，寄生虫感染和随后的宿主存活与有丝分裂细胞周期过程的上调有关。我们还检测到与宿主免疫防御、宿主-病原体相互作用、细胞修复和维护相关的转录本的破坏性选择的广泛信号。我们的结果提供了关于如何在转录组水平上测量选择以剖析由气候变化和新出现的人为威胁驱动的当代进化的分子机制的见解。我们预计这里描述的方法将能够实时获得关于自然选择的分子过程和目标的关键信息。