Pseudogene revival drives repeated adaptation in fission yeast

Repeated (parallel or convergent) evolution is often taken as evidence of adaptation and is relevant to the predictability of evolution. However, much remains unknown about the genetic basis of repeated evolution. Here, we use genome editing to progressively knock out all the complete transposable elements, a rich source of mutations, in the fission yeast Schizosaccharomyces pombe. While progressive knockout has no apparent effect on the biology or fitness of S. pombe under normal conditions, certain transposable element knockout strains exhibit growth arrest under acid challenge. We next perform parallel replay experiments by evolving S. pombe strains with a single transposable element and without transposable element under acid stress. Adaptation occurs rapidly and repeatedly. We do not detect any new transposable element insertions at appreciable frequencies, indicating that the observed repeated adaptation is not driven by transposable element insertions. Instead, revival mutations in SPBC409.08, a pseudogene that encodes a putative transporter of the major facilitator superfamily, repeatedly undergo hard or soft selective sweeps and drive adaptation in all the replicates. Although the revival mutations exhibit a trend of diminishing returns, they also repeatedly become fixed in all evolved wild-type populations. This work unveils the significance of pseudogene revival on repeated evolution and thus evolutionary predictability.