Phylogenetic Beta-Diversity

Phylogenetic beta-diversity is effectively the turnover of branch lengths between samples in space and/or time. Like its species-level equivalent, phylogenetic betadiversity can be measured on a pair-wise basis (Lozupone and Knight 2005; Bryant et al. 2008; Nipperess et al. 2010) or as a single value for a set of samples (Anderson et al. 2010). Rarefaction of PD provides a means for deriving a single value of beta-diversity for a set of samples of any size via the ∆PD measure, which is a phylogenetic analogue of the additive partitioning approach of Crist and Veech (2006).

Morton et al. (1994) compiled data on small mammal assemblages for 245 sites in arid Australia. I calculated beta-diversity for two regions from this dataset – Tanami desert and Uluru-Kata Tjuta National Park, Northern Territory. These regions had a similar number of sites (Table 3) covering a roughly similarly sized area but differed in the number of vegetation types. The Tanami sites were all spinifex grassland while the Uluru sites comprised a mix of spinifex grassland, acacia shrubland and woodland (Morton et al. 1994). It might be expected therefore that the Uluru sites will show higher beta-diversity due to the diversity of habitats represented. In addition to ∆PD, I used the additive partitioning method to calculate species-level beta-diversity as the difference between total species richness of all sites in a region and the mean species richness of a single site (Lande 1996; Crist and Veech 2006).

Contrary to expectations, the Tanami desert sites showed greater species betadiversity and phylogenetic beta-diversity despite the lack of variation in vegetation type (Table 3). This pattern is driven by the much higher site-level (alpha) species richness in Uluru-Kata Tjuta National Park (Table 3, Fig. 5) without a concomitant increase in overall (gamma) species richness, resulting in a high degree of species overlap. Given the overlap in species among Uluru sites, it appears that most small mammals are not specialised for particular vegetation types.

Phylogenetic Dispersion

Phylogenetic dispersion is a measure of the average phylogenetic distance among species (or tips) (Webb et al. 2002) and is in effect a measure of tree shape (Davies and Buckley 2012). ∆PD provides a simple, intuitive measure of dispersion as the expected gain in PD of adding a second randomly selected species to the first. It can also be seen as a means of correcting for variation in species richness among samples, as it is well known that PD increases with species richness (Rodrigues and Gaston 2002).

Table 3 Comparison of diversity measures for small mammal assemblages of sites in the Tanami Desert and Uluru-Kata Tjuta National Park, Northern Territory, Australia


No. of sites

Species richness (alpha)

Species richness (gamma)

Species beta diversity (additive)

Phylogenetic beta diversity (∆PD)













Species beta diversity is calculated as the difference between the total species richness of a region (gamma) and the mean site-level species richness (alpha)

Fig. 5 Sample-based rarefaction curves for small mammal assemblages of sites in the Tanami Desert and Uluru-Kata Tjuta National Park, Northern Territory, Australia. See Morton et al. (1994) for a description of the data. Phylogenetic beta diversity (∆PD) is higher among the Tanami sites than the Uluru sites

I generated PD rarefaction curves and ∆PD values for the mammal faunas of 71 of the 79 terrestrial ecoregions recognised by Olson et al. (2001) as constituting the Australasian biogeographic realm. Data were sourced from the wildfinder database ( of the World Wildlife Fund. Eight ecoregions were excluded from the analysis because they had less than two species and thus a ∆PD value could not be calculated.

The ecoregions show huge variation in species richness and, as expected, Phylogenetic Diversity is highly dependent on species richness (Fig. 6). Tropical ecoregions (such as the central range Montane rainforests, New Guinea) have high species richness and high Phylogenetic Diversity (Fig. 6, Table 4). When considering phylogenetic dispersion, however, other ecoregions show unusually high or low values given their species richness (Table 4). The ecoregion with the lowest ∆PD is the New Caledonia dry forests. Because of its isolation, this fauna consists exclusively of bats and thus all the species are relatively closely related. The ecoregion with the highest ∆PD was the Mount Lofty woodlands of South Australia, reflecting relatively high numbers of marsupial species compared to the more tropically distributed bats and rodents.

Fig. 6 Species-based rarefaction curves for mammal assemblages of terrestrial ecoregions of the Australasian biogeographic realm Ecoregions are as defined by Olson et al. (2001). Data are sourced from the wildfinder database ( Three ecoregions are highlighted, as having minimum (New Caledonia dry forests), maximum (Mount Lofty woodlands) or median (Central Range montane rainforests) values of phylogenetic dispersion (∆PD)

Table 4 Comparison of diversity measures for mammal assemblages of selected ecoregions of the Australasian biogeographic realm


Species richness


diversity (Ma)

Phylogenetic dispersion (∆PD)

New Caledonia dry forests




Central range montane rainforests




Mount Lofty woodlands




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