Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution

The classical (two-round) hypothesis1 of vertebrate genome duplication proposes two successive whole-genome duplication(s) (polyploidizations) predating the origin of fishes, a view now being seriously challenged2,3,4,5,6,7. As the debate largely concerns the relative merits of the 'big-bang mode' theory8,9,10,11,12,13 (large-scale duplication) and the 'continuous mode' theory (constant creation by small-scale duplications)2,3,4,5,6,7,14, we tested whether a significant proportion of paralogous genes in the contemporary human genome was indeed generated in the early stage of vertebrate evolution. After an extensive search of major databases, we dated 1,739 gene duplication events from the phylogenetic analysis of 749 vertebrate gene families. We found a pattern characterized by two waves (I, II) and an ancient component. Wave I represents a recent gene family expansion by tandem or segmental duplications15, whereas wave II, a rapid paralogous gene increase in the early stage of vertebrate evolution, supports the idea of genome duplication(s) (the big-bang mode). Further analysis indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome.