Future Directions

As demonstrated here, rarefaction of PD has a straightforward application in standardising PD across samples so that they can be compared directly. Further, depending on the accumulation unit, the rarefaction formula can be extended to the calculation of metrics of phylogenetic evenness, phylogenetic beta-diversity and phylogenetic dispersion. However, the application of the PD rarefaction formula and its extension to other metrics is still very much in its infancy. Here I will outline some future directions for PD rarefaction.

Rarefaction by units of species allows for the comparison of locations while controlling for variation in species richness. This can easily be done by either rarefying all locations to a given number of species (Nipperess and Matsen 2013) or via ∆PD as demonstrated here. This kind of correction has previously been done by including species richness as an explanatory variable in a statistical model and taking the residuals (Davies et al. 2008) or by comparison to a null model derived by repeated subsampling (Davies et al. 2007). The latter method is often used as a statistical test of phylogenetic dispersion (also known as phylogenetic structure) where random draws are taken from a species pool, representing a null community assembly process (Webb 2000). Such methods are no longer necessary as the exact relationship between species richness and PD is described by the rarefaction curve (Nipperess and Matsen 2013). Further, the exact analytical solution is computationally efficient, allowing for practical application to very large datasets.

By removing the effect of species richness, we can identify “evolutionary hotspots” with higher than expected phylogenetic diversity (Davies et al. 2008; Nipperess and Matsen 2013) on a regional or global scale. We can then use the standardised PD values (called relative PD by Davies et al. 2007) to explore the environmental, ecological and historical processes that lead to the observed patterns of high or low phylogenetic dispersion (Kooyman et al. 2013). Ultimately, we may be able to develop the theory to predict these patterns (Davies et al. 2007), in a similar vein to what has been done for species richness (Arrhenius 1921; MacArthur and Wilson 1963; Rosindell et al. 2011). For example, the relationship of species richness with area is well known but the phylogeny-area relationship has only recently begun to be explored (Morlon et al. 2011). Rarefaction curves have an obvious connection to species-area curves (Olszewski 2004) and thus the development of PD rarefaction may well improve understanding of the phylogeny-area relationship. In particular, species-based rarefaction of PD allows for the separation of species diversity effects from those purely explained by phylogeny.

It is possible to predict how much Phylogenetic Diversity is yet to be sampled from the observed rarefaction curve. Rarefaction is the basis of several species diversity estimators, which attempt to calculate total diversity (including unseen species) for a set of individuals or samples by effectively extending the curve beyond the observed sampling depth (Colwell and Coddington 1994). It follows that a useful extension of PD rarefaction would be a PD estimator that predicts unseen branch length, given the observed rate of accumulation of PD. It is important to note that PD rarefaction calculates the expected branch length gained by adding additional accumulation units but does not predict where on the tree these branches will come from. Similarly, a biodiversity estimator based on PD rarefaction may be able to predict the amount of PD not yet sampled but would not be able to predict where these unseen branches would be added to an existing tree. This would be, nevertheless, an exciting development.

It has recently been proposed that the standardisation of samples for species diversity should not be done by rarefaction to the same size (i.e. no. of individuals), but rather by sample completeness (Alroy 2010; Jost 2010; Chao and Jost 2012). Completeness, when measured by a statistic known as coverage (Good 1953), is the proportion of individuals in a community that are represented by species in a sample from that community (Chao and Jost 2012). When samples differ in their coverage, they should be standardised to equal coverage before a “fair” comparison can be made. Much like expected species richness, the coverage of a sample can be estimated from the sample size and the distribution of individuals among the species in the sample (Chao and Jost 2012). Given that standardisation by sample completeness has been shown to yield a less biased comparison of species richness between communities (Chao and Jost 2012), it would be desirable to have a similar method of standardisation for PD. Since rarefaction of coverage is mathematically related to rarefaction of sample size, the recent work on estimating PD from sample size will no doubt form the basis from which estimated PD for sample coverage will be developed.

Finally, a general issue when considering any PD measure is uncertainty regarding the length of branches and the topology (branching pattern) of the tree. All PD measures (including those presented here) assume that the branch lengths and their arrangement in the tree are perfectly known. This is obviously an abstraction, although PD can be surprisingly robust to this source of variation (Swenson 2009). One solution to this dilemma is to calculate PD, including rarefied PD, for a large number of possible trees and report the mean and confidence limits. The output from a Bayesian phylogenetic analysis is a large number of trees, each with their own topology and corresponding branch lengths (see for example Jetz et al. 2012) and so lends itself well to this approach. However, when the possible trees number in the thousands and tens of thousands, this is obviously computationally intensive. An analytical solution, directly incorporating uncertainty into the calculation, would therefore be desirable. This is not an easy extension of the PD rarefaction solution because both variation in branch length and topology (affecting the probability of encountering internal branches) would need to be taken into account. It is worth remembering that phylogenetic relationships are not the only source of uncertainty when investigating real ecological communities – neither the abundance, nor even the presence (occupancy), of species are necessarily known with precision.

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