Methodological Considerations

Even using metrics based on the Ws, there are several ways of evaluating evolutionary distinctiveness. Ws gives information on the total distribution of evolutionary divergence in the entire data set. An advantage of this index is that each phylogeny has its scores scaled between 0 and 1 and thus phylogenetic diversity can be represented by many species with small values (from phylogenies with many species), or few species with large values (from phylogenies with few species). However, this feature also introduces a limitation. If there is high beta-diversity (differentiation among sites) in each phylogeny (e.g. if each species only occurs at a single site), then small phylogenies have the potential to dominate the ranking of individual sites (as the most divergent species in small phylogenies have higher Ws values than the most divergent species in large phylogenies). In contrast, if there is low betadiversity, then phylogenies with many species will have many species at individual sites, and thus will be able to 'compete' with the smaller phylogenies by having Ws totals that reflect the sum of several co-occurring species. In this latter case (low beta-diversity), Ws will be strongly correlated with overall species richness of a phylogeny.

Using the sum of 1st and 2nd ranks circumvents these problems. The power of this metric is that it gets at a simple question – where are the most divergent two species from each phylogeny, summed across sites and phylogenies. The downside is that, of course, it does not include information from species below the 1st and 2nd ranks. Thus it is purely targeted at examining the distribution of phylogenetically basal species, rather than the total sum of phylogenetic diversity. This needs to be borne in mind in its interpretation.

Another promising application of Ws ranks is in the detection of places of recent diversification. This can be achieved by focusing on the inverse of the most phylogenetic divergent species as used here, i.e., through awarding first and second prizes for the most and second most recent species of the phylogeny. Likewise, the methods of standardization and rarefaction can be very helpful for dealing with diverse sampling protocols and identifying the influence of different phylogenies to the ranking. Although evolutionary potential is a factor that requires genetic studies to be formally tackled (see Mace and Purvis 2008; the analysis of Grandcolas and Trewick in chapter “What Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict Species”), the identification of sites that accumulate species with recent diversification is a first step to set out future study projects and monitoring strategies for testing this hypothesis. So, the possibility of identifying these sites should not be neglected.

Both of these metrics can then be adjusted to focus on micro-endemics, by using the measure Wes from Posadas et al. (2001) and the approach of 1st and 2nd ranks of Wes as developed here for the Ws. Wes is simply the Ws divided by the number of sites (or any measure of spatial distribution) the species occurs. The use of Wes, rather than Ws has the same issues with 'sum' versus 1st and 2nd ranks concepts as above. With Wes the Ws values are 'diluted' by being divided across each site that a species is recorded from and the main benefit is that sites will score more highly in proportion to the uniqueness of their species composition.

The resampling methods used here assure that ranking is not driven by a single or very small set of phylogenies, and the resampling with multiple drops indicates the tendency of sites remaining in similar ranking positions with the addition of phylogenies. To the best of our knowledge, this is the first time a set of phylogenetic studies are analysed this way (but see the proposition of Miranda-Esquivel, chapter “Support in Area Prioritization Using Phylogenetic Information”), and this seems to be a very promising way of integrating the problems of diversity of sampling effort.

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