BACKGROUND: Genes in populations are in constant flux, being gained through 
duplication and occasionally retained or, more frequently, lost from the genome. 
In this study we compare pairs of identifiable gene duplicates generated by 
small-scale (predominantly single-gene) duplications with those created by a 
large-scale gene duplication event (whole-genome duplication) in the yeast 
Saccharomyces cerevisiae.
RESULTS: We find a number of quantifiable differences between these data sets. 
Whole-genome duplicates tend to exhibit less profound phenotypic effects when 
deleted, are functionally less divergent, and are associated with a different 
set of functions than their small-scale duplicate counterparts. At first sight, 
either of these latter two features could provide a plausible mechanism by which 
the difference in dispensability might arise. However, we uncover no evidence 
suggesting that this is the case. We find that the difference in dispensability 
observed between the two duplicate types is limited to gene products found 
within protein complexes, and probably results from differences in the relative 
strength of the evolutionary pressures present following each type of 
duplication event.
CONCLUSION: Genes, and the proteins they specify, originating from small-scale 
and whole-genome duplication events differ in quantifiable ways. We infer that 
this is not due to their association with different functional categories; 
rather, it is a direct result of biases in gene retention.