Phylogenetics and Phylogenetic Diversity
Phylogenetic inference recreates the branching structure of evolutionary relationships between species via cladistic analysis from molecular and morphological data in the form of discrete character states or distance matrices of pairwise dissimilarities (Vandamme 2009). The computational models used differ both in methodology and epistemological grounding; prominent methods include Maximum Parsimony, Maximum Likelihood, and Bayesian Methodologies. Phylogenetic distance measures aim to quantify the relatedness of groups of species. As the phylogenetic tree represents the evolutionary relations between species it can also be used to calculate how distinct these species are relative to the tree in which they are nested. Methods differ in the way they characterize distance and uniqueness. Some do it in terms of speciation events and others in terms of change in genomes between species. Following Velland et al. (2011), we distinguish two types of fundamentally different measures of phylogenetic diversity (p. 196):
Node-based trees represent only topology. They are based only on information about speciation events and so we can infer from them only facts about relatedness. Such measures include: Taxonomic Distinctness (Vane-Wright et al. 1991) and Species Originality (Nixon and Wheeler 1992).
Distance-based trees include topological information as well as branch length. Branch length either represents the accumulation of evolutionary change or alternatively the passage of time. Such measures include: PD (Faith 1992, 1994); Originality of Species within a Set (Pavoine et al. 2005); Pendant Edge (Altschul and Lipman 1990) and Species Evolutionary History (Redding and Mooers 2006).
Both groups of methods represent speciation and its creation of distinct evolutionary trajectories and both provide, with varying degrees of success, a means to prioritize the conservation of phylogeny and therefore of species that are particularly distinct in their features and history.
The Roles of Phylogenetic Diversity
Although the role of phylogenetic diversity in conservation biology is open-ended, extant uses can be categorised into three distinct groups.
(i) Phylogenetic Diversity as a tool for prediction and explanation
Conservation is only possible when we have a good understanding of the dynamics of communities and ecosystems. Although we often think of this in ecological terms, evolution is an important contributing factor. In such contexts the measurement of phylogenetic diversity can help us distinguish these component forces at work. For example, all else being equal, we expect species that are closely related to be both morphologically similar and similar in the functional roles that they play in the ecosystems in which they are found. So we can use phylogenetic diversity to predict functional similarity. Such studies allow us to detect cases that stand in need of special explanation. These are cases where functional diversity is either higher (over-dispersion) or lower (functional diversity deficit) than expected (see for example Webb et al. 2002). The appropriateness of particular metrics will depend upon the explanatory or predictive target, although we note that common metrics show strong correlation with one another in many circumstances (Vellend et al. 2011, p. 207).
(ii) Phylogenetic diversity as a surrogate
Phylogenetic diversity has been employed as a surrogate for a wide variety of valuable features of ecological communities and ecosystems. For example, Srivastava et al. (2012) argue that phylogeny largely determines interactions among species, and so could help predict the cascade of extinctions through ecological networks and hence the way in which those extinctions impact ecosystem function. So, on this account, phylogenetic diversity is at least a surrogate for ecosystem function.
Forest et al. (2007) find a stronger correlation between phylogenetic diversity and feature diversity than between species diversity and feature diversity. So they recommend that we employ phylogenetic diversity, rather than species diversity, as a surrogate for feature diversity. Faith et al. (2010) argue that we should recognise phylogenetic diversity as a surrogate for features of value to human well-being:
We argue that an evolutionary perspective is essential for developing a better understanding of the links between biodiversity and human well-being. We outline the services provided by evolutionary processes, and propose a new term, 'evosystem services', to refer to these many connections to humans. (Faith D.P. et al. 2010, p. 66)
(iii) Phylogenetic diversity as a conservation goal
The third context in which one might employ phylogenetic diversity is as a goal of conservation. There are certainly examples of phylogenetically orientated conservation. The Edge of Existence Programme (edgeofexistence. org), run by the Zoological Society of London, focuses explicitly on the conservation of species that are endangered and phylogenetically distinct. There are many other conservation programmes that take phylogenetic diversity into account (e.g. WWF's Global 200). That said, phylogenetic diversity is not as widely used in conservation as it might be (Winter et al. 2012, p. 1). This is partly for methodological reasons:
Phylogenetic diversity has long been incorporated in planning tools, but it has not yet had much impact on conservation planning. Applications face limitations of available data on phylogenetic pattern. (Sarkar et al. 2006)
It is also partly due to scepticism about the correlations claimed above:
In our opinion, the justification for preserving phylogenetic diversity as a proxy for functional diversity or evolutionary potential has so far largely failed. Our current knowledge of the benefits to the (future) functioning of ecosystems and securing evolutionary potential remains equivocal. (Winter et al. 2012, p. 4)
Clearly there is limited employment of phylogenetic diversity as goal for large-scale conservation decision-making. There is also some skepticism about our empirical and philosophical justification for such uses. In the final section of this chapter it is this question about justification to which we turn.
-  Note “Pendant Edge” is a recent name (e.g. Redding, and Mooers 2006; Vellend et al. 2011) given to the idea introduced but not named in Altschul and Lipman's original very brief discussion note