Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

We separately measure the short-term ("raw") duplication and deletion rates , which include gene copies that will be removed soon after the duplication event and their dramatically reduced long-term counterparts r(*)dup, r(*)del. High deletion rate among recently duplicated proteins is consistent with a scenario in which they didn't have enough time to significantly change their functional roles and thus are to a large degree disposable. Systematic trends of each of the four duplication/deletion rates with the total number of genes in the genome were analyzed. All but the deletion rate of recent duplicates r(*)del were shown to systematically increase with Ngenes. Abnormally flat shapes of sequence identity histograms observed for yeast and human are consistent with lineages leading to these organisms undergoing one or more whole-genome duplications. This interpretation is corroborated by our analysis of the genome of Paramecium tetraurelia where the p-4 profile of the histogram is gradually restored by the successive removal of paralogs generated in its four known whole-genome duplication events.