Distribution of substitutions in proteins A and H are not uniform.

<p>A) Substitutions in the 512 codons of gene <i>A</i>. The dashed vertical line indicates the origin of replication, the other vertical lines indicate the starts of A* and B, and the end of B (residues: A = 1–512; A* = 173–512; B = 364–484). Red indicates missense substitutions and black indicates silent substitutions in genes <i>A</i> or <i>A*</i>, not <i>B</i>. Fainter colors indicate the substitution was not detected at day 50. Triangles mark substitutions found in all four chemostats, squares mark substitutions found in more than one chemostat and circles are unique to each chemostat. Sa = S43a, Sb = S43b, Ea = E37a, Eb = E37b. The symbols above the line for Ea indicate parallel substitutions that arose in Ea by 180 days <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060401#pone.0060401-Wichman3" target="_blank">[27]</a>. The black circle above the Sa line indicates a silent substitution that affected the same amino acid as the red circle on the line. B) Substitutions in protein H. Graphic of predicted domains from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060401#pone.0060401-Ruboyianes1" target="_blank">[64]</a>. Red triangles indicate missense substitutions, pink indicates the substitution was not detected at day 50, and purple indicates a second missense substitution at that residue. The vertical numbers indicate position in the protein sequence. PTD = predicted transmembrane domain. Not to scale.