Most mutations were nonsynonymous, especially at the nodes of new clades, with affected genes encoding regulatory functions, lipid metabolism, and envelope biogenesis. Most mutations were nonsynonymous, especially at the nodes of new clades, with affected genes encoding regulatory functions, lipid metabolism, and envelope biogenesis. (A) Numbers of synonymous and nonsynonymous mutations shared by each of the isolates and associated with nodes in the phylogeny (Fig. 1B); (B) distribution of the synonymous and nonsynonymous mutations at each node by clusters of the following orthologous groups: lipid transport and metabolism (COG I), transcription and signal transduction (COGs K and T), cell wall/membrane/envelope biogenesis (COG M), and amino acid transport and metabolism (COG E). Inês N. Silva et al. mSystems 2016; doi:10.1128/mSystems.00029-16