Overdominant and partially dominant mutations drive short-term adaptation in diploid yeast

Abstract

Identification of adaptive targets in experimental evolution typically relies on extensive replication and allele reconstructions. An alternative approach is to directly assay all mutations in an evolved clone by generating pools of segregants that contain random combinations of the evolved mutations. Here, we apply this method to 6 clones isolated from 4 diploid populations that were clonally evolved for 2,000 generations in rich glucose medium. Each clone contains [~]20-25 mutations relative to the ancestor. We derived intermediate genotypes between the founder and the evolved clones by bulk mating sporulated cultures of each evolved clone to a barcoded haploid version of the founder. We competed the barcoded segregants en masse and quantified the fitness of each barcode. We estimated average fitness effects of evolved mutations using barcode fitness and whole genome sequencing for a subset of segregants or time-course whole population whole genome sequencing. In contrast to our previous work in haploid populations, we find that diploids carry fewer evolved mutations with a detectable fitness effect (6%), contributing a modest fitness advantage (up to 5.4%). In agreement with theoretical expectations, reconstruction experiments show that all adaptive mutations manifest some degree of dominance over the ancestral allele, and most are overdominant. Competition assays under conditions that deviated from the evolutionary environment show that adaptive mutations are often pleiotropic.