Amino-acid substitution rate per functional category. Branch lengths computed for each functional category between (a) MED4 and SS120, (b) SS120 and MIT9313 and (c) MED4 and MIT9313. In the three comparisons, branch-length values are aligned along a line with a slope much greater than 1, indicating that acceleration of the substitution rates occurs in every functional category. Axes represent the number of amino-acid substitutions per site. Red circle, amino-acid transport and metabolism; green circle, carbohydrate transport and metabolism; yellow circle, cell-cycle control; blue triangle, cell wall/membrane biogenesis; pink circle, coenzyme metabolism; red square, defense mechanisms; green square, energy production and conversion; yellow square, function unknown; blue square, general function prediction only; pink square, inorganic ion transport and metabolism; red triangle, intracellular trafficking; green triangle, lipid transport and metabolism; yellow triangle, nucleotide transport and metabolism; blue circle, posttranslational modification, protein turnover; pink triangle, replication, recombination and repair; red diamond, secondary metabolite biosynthesis, transport and catabolism; green diamond, signal transduction mechanisms; yellow diamond, transcription; blue diamond, translation; black circle, miscellaneous.