Where does dosage compensation fit in?
Dosage compensation may indeed affect the short-term retention rate of duplicate genes after whole-genome duplication. Over longer time frames, however, proteins involved in complexes and pathways are not preferentially retained in the duplicate pairs originating from whole-genome duplications, neither in P. tetraurelia, as indicated by Aury et al. [1], nor in yeast [15] (except for ribosomal proteins [16]). In fact, whereas 17% of highly connected proteins (hubs) in the yeast protein-protein interaction network belong to a pair originating from the relatively ancient whole-genome duplication that has occurred in Saccharomyces cerevisiae, only 5% of the party hubs, which are coexpressed with their interaction partners, are part of such a pair [15]. Homologous complexes in yeast appear to have been created through stepwise partial duplications and not through whole-genome duplication [17]. The results of Aury et al. [1] do suggest that after more recent whole-genome duplication events,
