The strength and form of natural selection on transcript abundance in the wild

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-seq 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 about how selection can be measured at the
transcriptome level to dissect the molecular mechanisms of contemporary
natural selection driven by climate change and emerging anthropogenic
threats. We anticipate that the approach described here will enable
critical information on the molecular mechanisms and targets of natural
selection to be obtained in real time.