Figure 4.

Distribution of Robinson–Foulds distances between the phylogeny proposed by Hug et al. and UFBoot samples obtained using three subsets of fast-evolving sites, SRC10 to SRC12: (1) fast-evolving sites flanked by any number of gaps in green, (2) fast-evolving sites flanked by gap-rich regions in blue, and (3) fast-evolving sites flanked by gap-poor regions in orange. Gap-rich regions were defined as containing 2000 gaps or more, while gap-poor regions were defined as containing 500 or less gaps. A total of 105 sites from distributions 1 and 2 were randomly selected and used to generate UFBoot samples in order to match the number of fast-evolving sites flanked by gap-rich regions.