Fig 4. Concordant evolution of pairs of sites.

Each panel shows the same phylogeny twice, with the dots in each side of the panel indicating substitutions at the corresponding site. a. Concordant evolution of sites 188 and 192 in CYTB is likely explained by epistatic interaction, as revealed by strong clustering of consecutive substitutions in the two sites (all four of which occurred very rapidly one after the other) and lack of clustering of non-consecutive substitutions. b. Concordant evolution of sites 42 and 67 in ATP6 is likely explained by concurrent additive episodic selection, as revealed by strong clustering of both consecutive and non-consecutive substitutions in the same parts of the tree.