Range of relatedness indices calculated
In order to obtain a diversity measure which steps outside the species abundance distribution, and which could therefore potentially strike out along a different axis to the linear richness-evenness combinations shown in the MDS of the mechanistic correlations among standard diversity indices, it would be helpful to introduce further attributes of the assemblage composition. One possibility is to combine biomass and abundance data, as in ABC curves (Section 16), but another – which we shall turn to now – is to introduce information on the relatedness of the species in each sample, as discussed at the start of this section. These indices are accessed through the final two tabs of the dialog box from Analyse>DIVERSE, namely Taxdisc and Phylogenetic. The nomenclature comes from the original papers on these topics (Warwick and Clarke’s taxonomic diversity and taxonomic distinctness indices, and Faith’s phylogenetic diversity), and does not imply that either set of indices is more appropriate to taxonomic or phylogenetic hierarchies. Other hierarchies (e.g. genetic, functional) could be equally appropriate and PRIMER does not now even need a hierarchy to compute the taxonomic distinctness measures – a distance among species matrix will suffice.
Taxonomic distinctness
Quantitative:
Taxonomic diversity: $\Delta$
Taxonomic distinctness: $\Delta^\ast$
Presence/absence:
Average taxonomic distinctness (AvTD): $\Delta^+$
Total taxonomic distinctness (TTD): $S\Delta^+$
Variation in taxonomic distinctness (VarTD): $\Lambda^+$
Phylogenetic diversity
Presence/absence:
Average phylogenetic diversity (AvPD): $\Phi^+$
(Total) phylogenetic diversity: $S \Phi^+$ (Faith’s ‘PD’)