BACKGROUND: The direct examination of large, unbiased samples of young gene 
duplicates in their early stages of evolution is crucial to understanding the 
origin, divergence and preservation of new genes. Furthermore, comparative 
analysis of multiple genomes is necessary to determine whether patterns of gene 
duplication can be generalized across diverse lineages or are species-specific. 
Here we present results from an analysis comprising 68 duplication events in the 
Saccharomyces cerevisiae genome. We partition the yeast duplicates into ohnologs 
(generated by a whole-genome duplication) and non-ohnologs (from small-scale 
duplication events) to determine whether their disparate origins commit them to 
divergent evolutionary trajectories and genomic attributes.
RESULTS: We conclude that, for the most part, ohnologs tend to appear remarkably 
similar to non-ohnologs in their structural attributes (specifically the 
relative composition frequencies of complete, partial and chimeric duplicates), 
the discernible length of the duplicated region (duplication span) as well as 
genomic location. Furthermore, we find notable differences in the features of S. 
cerevisiae gene duplicates relative to those of another eukaryote, 
Caenorhabditis elegans, with respect to chromosomal location, extent of 
duplication and the relative frequencies of complete, partial and chimeric 
duplications.
CONCLUSIONS: We conclude that the variation between yeast and worm duplicates 
can be attributed to differing mechanisms of duplication in conjunction with the 
varying efficacy of natural selection in these two genomes as dictated by their 
disparate effective population sizes.