Fig 1. Phylogenetic approach for detection of concordantly and discordantly evolving site pairs.

The approach is based on counting the rapid consecutive substitutions at site pairs. Two substitutions at sites 1 (gray dots) and 2 (black dots) are consecutive if they occur in the same line of descent (i.e., one is ancestral to the other) and no other substitutions at these sites occurred over the time period between them. A deficit of rapid consecutive substitutions implies discordant evolution of these two sites (here, 0 pairs of consecutive substitutions; left), while an excess of such substitutions implies their concordant evolution (here, 3 pairs of consecutive substitutions; right).