A single determinant for the rate of yeast protein evolution

Abstract: A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. To overcome these difficulties, we employ an alternative method, principal component regression, which is a multivariate regression of evolutionary rate against the principal components of the predictor variables. We carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network). Strikingly, our analysis reveals a single dominant component which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single determinant among the seven predictors. The dominant component explains nearly half the variation in the rate of synonymous and protein evolution. Our results support the hypothesis that selection against the cost of translation-error-induced protein misfolding governs the rate of synonymous and protein sequence evolution in yeast.