PMC

Numbers of gene duplications in three family size classes (two- to three-member families, four-member families, five- to eight-member families). A duplication was dated prior to one of two major cladogenetic events, (a) the coelomate–nematode divergence, and (b) the deuterostome–protostome divergence, if its occurrence prior to the event was supported by a significant internal branch. Chi-square tests of the uniformity across family size classes of the proportion of duplications prior to the cladogenetic event : (**) P < 0.01; (***) P< 0.001.

Numbers of gene duplications in two- to eight-member families. A duplication was dated prior to one of the three a major cladogenetic events (the animal–fungus divergence, the coelomate–nematode divergence, and the deuterostome–protostome divergence) if its occurrence prior to the event was supported by a significant internal branch. Chi square tests of the hypothesis that the proportion of duplications prior to a cladogenetic event differed from that in Drosophila: (***) P < 0.001. Numbers of duplication events were as follows: Caenorhabditis elegans, 463; Drosophila 567; human, 1760.

(a) Phylogenetic tree showing the major cladogenetic events used in timing gene duplications: (A–F) the animal–fungus divergence; (C–N), the coelomate–nematode divergence; (D–P), the deuterostome–protostome divergence. The topology of the tree and the divergence time estimates (±SE) are from . However, gene duplications were timed relative to cladogenetic events independent of a molecular clock assumption. (b) Hypothetical gene family containing two human members (A and B). If the internal branch (indicated by arrow) is significantly supported, we can conclude (independent of the rooting of the tree) that A and B diverged prior to the deuterostome–protostome divergence. (c) Hypothetical four-member human gene family having a topology of the form (AB) (CD) consistent with the hypothesis of two rounds of genome duplication (the 2R hypothesis). (d) Hypothetical four-member human gene family having a topology of the form (A) (BD) inconsistent with the 2R hypothesis.