Polyploidy can drive rapid adaptation in yeast

Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood(1–4). Polyploidy, usually whole genome duplication (WGD), is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations (2,5–7). For example, in diverse cell types and organisms, immediately after a WGD, newly formed polyploids missegregate chromosomes and undergo genetic instability(8–13). The instability following WGDs is thought to provide adaptive mutations in microorganisms(13,14) and can promote tumorigenesis in mammalian cells(11,15). Polyploidy may also affect adaptation independent of beneficial mutations through ploidy-specific changes in cell physiology(16). Here, we performed in vitro evolution experiments to directly test whether polyploidy can accelerate evolutionary adaptation. Compared to haploids and diploids, tetraploids underwent significantly faster adaptation. Mathematical modeling suggested that rapid adaptation of tetraploids was driven by higher rates of beneficial mutations with stronger fitness effects, which was supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provided large fitness gains. We identified several mutations whose beneficial effects were manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.