Unrooted Maximum Likelihood (ML) trees based on concatenation of ribosomal proteins (A) and RNA polymerase subunits and transcription factors (B). For clarity, the two datasets from Brochier et al. (2004) were scaled down to the same number of species by removing Methanosarcina mazei and Methanosarcina acetivorans from the transcription dataset. Numbers at nodes are bootstrap values (BV). The scale bars represent the number of changes per position for a unit branch length. Trees were produced by exhaustive searches performed by PROTML. Branch lengths and likelihood values were calculated by TREE-PUZZLE (JJT model including a Γ-correction (8 categories of sites)). Numbers at nodes are bootstrap values computed with PUZZLEBOOT from 1000 replications. Asterisks indicate constrained nodes (supported by BV = 100% in preliminary NJ and heuristic ML analyses). The names of groups showing incongruent positions between the two trees are underlined.