Detecting positive selection in the budding yeast genome

Available abundant genomic data allows us to study the evolution of the yeast genome at a fine scale. In this study, we examined the adaptive evolution of coding and promoter regions in three Saccharomyces cerevisiae strains. First, using a maximum-likelihood approach, we identified 76 positively selected genes (PSG) whose coding regions likely have undergone positive selection in the recent past. These genes show significant bias in terms of biological function and they show over-representation of charged amino acids at positively selected sites. Next, using recent data on yeast transcription-start sites to define core-promoter regions, we identified 31 positively selected promoters, and their corresponding genes are significantly enriched in transmembrane transporter function. We found PSG show no correlation with promoter adaption or expression variation, suggesting that positive selection on coding regions and positive selection on promoter regions are not coupled. Together, our study provides insights into the evolution of S. cerevisiae strains from different environments.