We investigated patterns of rate asymmetry in sequence evolution among the gene 
pairs (ohnologs) formed by whole-genome duplication (WGD) in yeast species. By 
comparing three species (Saccharomyces cerevisiae, Candida glabrata, and S. 
castellii) that underwent WGD to a nonduplicated outgroup (Kluyveromyces 
lactis), and by using a synteny framework to establish orthology and paralogy 
relationships at each duplicated locus, we show that 56% of ohnolog pairs show 
significantly asymmetric protein sequence evolution. For ohnolog pairs that 
remain duplicated in two species there is a strong tendency for the 
faster-evolving copy in one species to be orthologous to the faster copy in the 
other species, which indicates that the evolutionary rate differences were 
established before speciation and hence soon after the WGD. We also present 
evidence that in cases where one ohnolog has been lost from the genome of a 
post-WGD species, the lost copy was likely to have been the faster-evolving 
member of the pair prior to its loss. These results suggest that a significant 
fraction of the retained ohnologs in yeast species underwent 
neofunctionalization soon after duplication.