Phylogenetic Diversity as a General Measure of Biodiversity
We have argued that the best general justification for the conservation of biodiversity comes from its instrumental value. We also note that there are many types of such value and that the consequences of conservation focused on instrumental value in general are inherently uncertain. The nature and location of aesthetic, recreational, and other cultural values will inevitably be subject to disagreement. Moreover, we are not in possession of the full facts about the ways in which existing species and ecosystems can benefit (or harm) us and we know even less about the effects that conserved species and ecosystems will have on us and our descendants in the future. Can we harness this uncertainty as a means of developing a general measure of biodiversity?
We have argued that, leaving aside species whose value is currently well understood e.g. charismatic megafauna, economically important crops etc., we are warranted in spending some amount of time and effort in the large-scale conservation of biodiversity via some general measure. So we should conserve at least some of Sober's unremarkable species on the grounds that they might be valuable in some respect, but we cannot predict which respect that will be. This implies that a general measure of biodiversity should not aim at conserving particular features, but rather at conserving a maximal variety of features.
While it is sensible under some circumstances to measure variety of features or of functions, characterisation of overall biological diversity (of the sort attempted by Numerical Taxonomy) fails on philosophical grounds. It is not possible to capture differences in morphology across the whole range of biological form because the idea of the occupation of morphospace makes sense only where we can anchor the dimensions of some particular morphospace to actual biological characteristics of closely related species (Maclaurin and Sterelny 2008, p. 15). The idea of a global morphospace is logically untenable because, as Goodman (1972, p. 437) argues, similarity and difference only make sense if we have some antecedent means of specifying the properties (or in the case of a morphospace, the dimensions) to be analysed. In taxonomy this almost always results in a focus on homologies. So in most cases the measurement of actual morphological diversity is best achieved by anchoring our analysis to actual differences in groups of related species, because only relatively closely related species differ in ways that make the analysis of morphospace tractable.
So while broad difference in form and function is what the moral argument tells us to conserve, it cannot be measured directly in a way that would benefit largescale conservation decision-making. Nonetheless, we can develop a general measure of biodiversity by exploiting the evolutionary processes that cause functional and morphological divergence within lineages. Both measures of species diversity and of phylogenetic diversity exploit evolution in just this way. If studies like those of Forest et al. (2007) are right, a general measure of biodiversity should be based on phylogenetic diversity, as that will best maximise feature diversity. We therefore conclude that phylogenetic diversity ought to play a fundamental role in conservation biology as the foundation of a general measure of biodiversity. That said, we noted in section “A maze of measures” that there are many measures of phylogenetic diversity. If conserving phylogeny is justified as a means of hedging our bets against uncertainty, this may help us to wrangle the current diversity in measures of phylogenetic diversity discussed earlier.
Variety in topological measures of phylogenetic diversity reflects the fact that phylogeny is complex. Species do not always bifurcate cleanly. Lineages reticulate and so on (Dagan and Martin 2006). Does this imply that, at large scales, phylogenetic diversity is undefined? We first note that such difficult cases are the exception rather than the rule at least across most of the phylogenetic tree. Secondly there are modifications of standard accounts of phylogenetic diversity designed to account for such phenomena as polytomies (see for example May 1990). Clearly overdispersion studies (see the above discussion of Webb et al. 2002) are at least based on the assumption that it is possible to make large scale phylogenetic comparisons between very different systems. We cannot, in principle, construct a theoretical morphospace that contains humans and fungi and tardigrades, but we can compare their phylogeny. However, there is an important caveat. Large-scale phylogenetic diversity is tractable using topological measures of phylogenetic diversity and timebased distance measures, but it less obviously so for trait-based distance measures of phylogenetic diversity.
The more we incorporate form and function into a measure of phylogenetic diversity, the less plausible it is to think that you can compare phylogenetic diversity in this very rich sense between distantly related clades. Use of distance-based trees incorporating information about character evolution for such purposes requires the further assumptions (1) that there is a fact of the matter as to what we should count as a character and (2) that all characters across all clades are of equal significance or contribute equally to biodiversity. To make this more concrete, we would have to assume that there is a fact of the matter as to how many characters contribute to the evolution of human cognition and that the biodiversity represented by the evolution of human cognition is of the same magnitude as the evolution of an equivalent number of characters in some other clade(s) for some other purpose(s).
-  Note that in treating this problem is essentially about morphology, we are running form and function together. This is because we think that, were we to measure all biological form and all biological function, the two groups of characteristics would intersect at the level of physiological traits. So any attempt to develop an overall measure of functional diversity will face the same problems that must be overcome in the development of an overall measure of morphological diversity
-  See for example the very wide variety of morphospaces discussed in McGee (1999, 2007). Indeed, it is notable that discussion of “convergent evolution in theoretical morphospace” (2007, pp. 90–2) actually focusses on a theoretical morphospace that models diversity in a single clade, namely the bryozoans (McKinney and Raup 1982)