Figure 1. A graphical example of potential ways in which polytomies in the phylogenetic tree may influence different metrics of community phylogenetic diversity.

The boxes indicate whether or not that species is found in the community. If the box is shaded grey, then the species is present in the community. If the box is not shaded, then the species is absent from the community. The left panel is a fully resolved phylogenetic tree and the three different measures of phylogenetic diversity (MPD, MNND, and FI) using four example assemblages. The MPD is the mean pair-wise phylogenetic distance between all taxa in the assemblage. The MNND is the mean nearest phylogenetic neighbor distance for all taxa in the assemblage. The FI (Faith's Index) quantifies the shared branch lengths between species in an assemblage as a proportion of the total branch lengths in the species pool phylogeny. The right panel shows the same phylogeny with one node now a polytomy and the same measures of phylogenetic diversity using this less resolved phylogeny with an increased total branch length. In all cases the FI measured is influenced as it represents a proportion of the total branch length. The MPD and MNND metrics are not influenced if the polytomy does not include species in the assemblage, but if it does include species in the assemblage these metrics may artificially increase or decrease.