It would be really interesting if we could calculate the average taxonomic distinctness (by Clarke and Warwick, 1998 in Journal of Applied Ecology) and the variation in taxonomic distinctness (Clarke and Warwick, 2001 in Marine Ecology Progress Series) with MOTHUR. The fisrt index measures the average path length between every pair of species traced through a taxonomic tree, and the second gives more information on the structure of the tree (the evenness of the community). I think these two indices could easily be applied to OTU-based and phylogenetic-based analyses, using the appropriate distance matrix. It would be very useful to compare communities, environments or treatments in terms of taxonomic diversity.
Thank you very much!