Substitution rates of individual aligned amino acid positions can differ between clades of orthologs.

<p>Substitution rates of individual aligned amino acid positions can differ between clades of orthologs from actinomycetes (left, Pearson correlation 0.47) or eukaryotes (right, 0.19). Each axis reflects amino acid variation rate in one of the replicate organism trees described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone-0025246-g004" target="_blank">Figure 4</a>. Each point is an aligned amino acid sequence position. Sites that have experienced a rate-shift (Type I) are green while those that exhibit an amino acid frequency-shift (Type II) are red.