Measuring phylogenetic biodiversity

Biodiversity has been described as the ‘biology of numbers and difference’ (Gaston 1996). Because species are different from one another, traditional metrics of biodiversity such as species richness or evenness increase when there are more species or when abundance is more equally apportioned among these species (see Chapters 4 and 5). Not only are species different from one another, the magnitude of these differences varies tremendously depending on the set of species in question. Consider two hypothetical islands, each with only two species of vertebrate animals in equal abundance: two birds in one case and a bird plus a mammal in the other. Both islands have species richness = 2 (for vertebrates) and the same maximal value of species evenness. However, our intuition tells us that a bird plus a mammal represents more biodiversity than does two birds (Purvis & Hector 2000). Metrics of phylogenetic diversity quantify the difference. Differences among species can be characterized by measuring any number of traits, such as body size and shape, dietary requirements, physiological tolerance of various stressors, etc. (see Chapter 17). Particular traits may be of special interest to a researcher for various reasons, such as their hypothesized role in mediating species interactions (e.g. beak size in birds) or their importance in tolerating different environmental conditions (e.g. leaf thickness in plants). However, the degree of similarity or difference among species will depend strongly on the choice of traits measured, and many traits are only applicable to particular groups of organisms (e.g. photosynthetic rate in plants). A far more general method for quantifying diversity among species is an assessment of the species’ evolutionary relationships, in the form of either taxonomy or a phylogeny. Modern phylogenies are derived from DNA-sequence data, which can be acquired for all organisms on the tree of life. The phylogenetic distance between two species is an estimate of the amount of time since the most recent common ancestor of both species, in other words the time that each has evolved independently of the other. While individual traits may show ‘convergence’, that is, similar values evolving in distantly related lineages, the phylogenetic distance represents a proxy for the magnitude of phenotypic differences (across a large number of traits) expected between any two species (Cavender-Bares et al. 2009). Biologists have been interested in the phylogenetic component of biodiversity for two main reasons: (i) to explicitly incorporate species differences (via a common currency applicable to all taxa from bacteria to primates), rather than just species numbers, into conservation prioritization and (ii) to yield insights into the structure of ecological communities. In the first case, recognizing that difficult prioritization decisions need to be made concerning the investment of limited resources for conservation, it has been argued that the aim should not be just to protect the greatest number of species possible, but to protect sets of species that are most taxonomically distinct or that represent the greatest possible variety of biological features (VaneWright et al. 1991; Faith 1992; Mooers et al. 2005; Isaac et al. 2007). To this end, considerable effort has been aimed at quantifying the evolutionary distinctness (and therefore conservation value) of