Phylogenetic pattern and the quantification of organismal biodiversity

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Abstract
Biodiversity can be explored at a number of different levels and in principle may be separately quantified at each. Phylogenetic pattern has the potential to quantify and estimate biodiversity at the finest scale, that is, variation among species in features or attributes. This scale is an important one for conservation, as it should form the basis for prioritizing conservation efforts at the species level. Further, recent published objections to differentially weighting species are answered by defining option value at this feature-level. Unfortunately, there has been no consensus on exactly how phylogeny can be used to value species, possibly because proper consideration of the link between pattern and underlying features generally has been unresolved. `Phylogenetic diversity' (PD) represents just one of several approaches that do consider diversity at the feature-level explicitly. These alternative approaches are discussed in the context of a general framework for using pattern to quantify diversity at a level below that of the original objects. The pattern framework highlights that estimation of biodiversity at a lower level using pattern will require decisions about the nature of the units of diversity, the kind of pattern to be used, the model relating unit items to pattern, and finally how this implies a pattern-based measure reflecting biodiversity. An alternative published model for relating features to a particular form of phylogenetic pattern is considered, and shown to make unwarranted assumptions. A possible alternative definition of the underlying units of diversity is examined, which may represent a different form of option value, also quantifiable using phylogeny. A possible alternative pattern to a phylogenetic tree for the prediction of feature diversity is also discussed. The appeal of these alternative approaches depends on the goals of conservation; in addition, justification for prioritizing or weighting requires that any practical approach avoid arbitrary, unwarranted, assumptions.