Subtrees of selected pathways. The subtree of a pathway is reduced from the clocked phylogenetic tree of all genomes by collapsing the entire clades without this pathway into tips. The root is colored red for the pathway’s presence and blue for its absence. The colors of non-root nodes mark the pathway’s status changes from their immediate ancestral nodes: red for gains, blue for losses, and none for no change. The branches descending from nodes containing the pathway are colored green. The total number of blue and red nodes in a pathway’s subtree equals the parsimony score of the pathway. (A) Aerobic respiration (cytochrome C) with parsimony score 290 from 9383 genomes. (B) Methylotrophy with parsimony score 592 from 1353 genomes. (C) Phosphate acquisition with parsimony score 528 from 6005 genomes. (D) Nitrogen fixation with parsimony score 409 from 1121 genomes. (E) Arsenate detoxification with parsimony score 196 from 2182 genomes. (F) Mercury detoxification with parsimony score 944 from 2319 genomes. (G) Isopenicillin N biosynthesis with parsimony score 387 from 2236 genomes. (H) Lysine biosynthesis I with parsimony score 149 from 8372 genomes.