The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations

Abstract

AbstractThrough its fermentative capacities,Saccharomyces cerevisiaewas central in the development of civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology giving rise tobona fidedomesticated populations. Here, we conduct a population genomic study of domesticated and wild populations ofS. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence withS. paradoxus. We fitted models of distribution of fitness effects to infer the rate of adaptive (ωa) and non-adaptive (ωna) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection toS. cerevisiaeprotein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withωnaand positively correlated withωa. However, the effect of recombination onωawas found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withωna, suggesting it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population’s demography. Together, our results provide a detailed characterization of adaptive mutations in protein-coding genes acrossS. cerevisiaepopulations.