Thanks, thermokarst. I was looking at the q2-ghost-tree plugin tutorial at Q2-ghost-tree Plugin: Community Tutorial for Creating Hybrid-Gene Phylogenetic Trees which notes that "The most popular application of this method is for fungal microbiome analysis using ITS sequences which provide great species identification, but make poor quality multiple sequence aligments (MSAs) and subsequently poor phylogenetic trees." which I take to mean that the trees should only be used for SH but not for, say, UniFrac distances?