Fig 3. Location of synonymous and nonsynonymous polymorphisms.

Nucleotide alignments of opa (Gc = 69 and Mc = 17) and pil (Gc = 148 and Mc = 71) were analyzed for the presence of synonymous (opa, panel a and pil, panel c) and nonsynonymous polymorphisms (opa, panel b and pil, panel d). The graph demonstrates the diversity values (Pi or Theta) present amongst sequences based on the location in the nucleotide alignment. The nucleotide diversity occurring between Gc and Mc (thick black line), within Gc (red line), within Mc (blue line), and within each species of Gc (dashed red lines) and Mc (dashed blue lines) are shown. The lines along the top indicate the conserved regions (black line), the variable regions (dark gray boxes), and the opa membrane-spanning regions (light gray boxes). A larger number of both synonymous and nonsynonymous polymorphisms can be seen within the variable regions of opa within Gc and Mc. Compared to opa, relatively few polymorphisms are present within pil, however, the polymorphisms present occur within the variable mini-cassettes.