The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data
(A) A Venn diagram illustrates the distribution patterns of level 1 molecular functions in the three superkingdoms, Archaea (A), Bacteria (B), and Eukarya (E). (B) The phylogenomic tree (tree length = 6820 steps) portraying the evolution of level 1 GO terms, with Venn distribution group-labeled leaves. Nonparametric bootstrap support (BS) values are shown above branches, which are supported by more than 50% of 1,000 replications. The tree was rooted by the Lundberg method. RI = retention index = 0.95, CI = consistency index = 0.85, Hi = homoplasy index = 0.15, and g1 = gamma distribution parameter = –0.72. (C) Boxplots shows the distribution of level 1 GO terms along the timeline in the three taxonomic groups. (D) Boxplots shows the number of level 1 GO terms per genome. Comparisons are significant at 0.001. A: Archaea, B: Bacteria, E: Eukarya.