Figure 1. The correlation between the fast-evolving sites and compositional heterogeneity for a series of subsets, each subset having 1,000 sites.

The 5,000 fastest-evolving sites are marked with five solid circles. The large z-score value means strong among-site compositional heterogeneity. The “character similarity” is negatively correlated with evolutionary rate i.e. sites that are incompatible with few other sites are considered rapidly evolving. The x-axis shows the sorted positions from the most highly variable to the most conserved.