Fig 2.

Zonal phylogenetic tree of nascent MrkD protein. The five nodes inside the dashed circle denote primary zone structural (protein) variants, i.e., evolutionarily long-term alleles, with each represented by multiple alleles synonymously differentiated from one another (the number of synonymous [syn] changes within each such variant is shown in square brackets, next to the corresponding node). For each primary zone node, the number of alleles (pie slices) and number of representatives/strains (number inside each pie slide) for each allele are shown as a pie diagram inside the node. The red nodes outside the dashed circle denote external zone structural (protein) variants, i.e., evolutionarily recent alleles, each represented by a single allele without any accumulation of synonymous variation within the variant. The node size indicates the number of strains representing the variant (in the external zone; the lowest and highest being 1 and 4, respectively). Amino acid mutation information is shown along each branch, with the number of synonymous (syn) changes in parentheses, if any. The branch length depicts the number of amino acid changes. The name of the protein variant (node) is denoted in gray next to the node. The mutational hot spot positions are underlined. Stars indicate that an E. coli sequence is present.