An increasing number of studies report that functional divergence in duplicated 
genes is accompanied by gene expression changes, although the evolutionary 
mechanism behind this process remains unclear. Our genomic analysis on the yeast 
Saccharomyces cerevisiae shows that the number of shared regulatory motifs in 
the duplicates decreases with evolutionary time, whereas the total number of 
regulatory motifs remains unchanged. Moreover, genes with numerous paralogs in 
the yeast genome do not have especially low number of regulatory motifs. These 
findings indicate that degenerative complementation is not the sole mechanism 
behind expression divergence in yeast. Moreover, we found some evidence for the 
action of positive selection on cis-regulatory motifs after gene duplication. 
These results suggest that the evolution of functional novelty has a substantial 
role in yeast duplicate gene evolution.