Figure 1.

Phyletic patterns are corrupted by gene gains and losses. The consensus phylogenetic tree on top is the species' tree based on genomic content [26]. Small black and white squares indicate, respectively, presences and absences of genes in each species. (a) TCA cycle. Blue box indicates the 'canonical' cycle, as known from saprophytic Enterobacteriaceae with large genomes. (b) Glycolysis. The green box indicates omnipresent COGs in the evolutionarily ancient bottom part of glycolysis, and the red box indicates three COGs coding for phosphoglycerate mutase activity. None of the patterns in the red box is close to the patterns in the green box, even though all these COGs are functionally linked. (c) Most genomes have just one of the two types of thymidylate synthase, but the blue boxes indicate several exceptions to this rule. (d) The full names of the species listed along the top of (a) and the TCA enzymes corresponding to the COGs shown in (a-c).