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Application

The following is a demonstration of the application of PD rarefaction, and the derived ∆PD statistics, to real ecological datasets. These applications are not intended to provide definitive answers to ecologically important questions but are, rather, simple demonstrations of how PD rarefaction can allow new analyses to be undertaken and, hopefully, new insights gained.

In all these applications, I have used published data on mammals. This is principally for convenience as mammals (Bininda-Emonds et al. 2007) and birds (Jetz et al. 2012) are the only major taxonomic groups for which comprehensive specieslevel supertrees are available. I have used an updated version of the mammal supertree of Bininda-Emonds et al. (2007) published as supplementary material by Fritz et al. (2009). In this supertree, all branch lengths are measured in units of time (millions of years between branching events), allowing for a straight-forward interpretation of PD as cumulative evolutionary history (Proches et al. 2006).

All analyses were conducted using the statistical software, R version 2.15.2 (R Core Team 2012). Phylogenetic information was processed using the ape package in R (Paradis et al. 2004). PD rarefaction analyses used the phylodiv, phylocurve and phylorare functions, written by the author and available from: davidnip- peress.blogspot.com.au.

Standardisation of Sampling

The most commonly used application for rarefaction is standardisation to allow comparisons to be made between datasets with differing amounts of sampling effort. Standardisation can be achieved by rarefying all datasets back to a common (typically the minimum) number of accumulation units (Sanders 1968; Gotelli and Colwell 2001).

Law et al. (1998) surveyed bats in ten State Forests of the south-west slopes region of New South Wales, Australia. Survey methods were a combination of ultrasonic detectors, harp-traps, mist-nets and trip-lines. For the purposes of this demonstration, only data from the harp-traps will be used. A harp-trap is a rectangular frame, stringed vertically with nylon line, placed so as to intercept the flight path of low-flying bats (Tidemann and Woodside 1978). A bat striking the nylon lines of the trap will tumble down into a collecting bag at the bottom.

Sampling effort among State Forests was variable with between 8 and 30 trapnights. Comparison of bat diversity between State Forests is therefore confounded by variation in sampling effort, as can be seen when plotting separate PD rarefaction curves for each State Forest (Fig. 3). To correct for variation in trapping effort, expected PD for each State Forest was calculated for the common value of 15 individuals, which was the minimum number recovered from a State Forest (Fig. 3). While rarefying to eight trap-nights (samples) would also be an appropriate method of standardisation, data on the bat species caught per trap-night were not available in Law et al. (1998). Standardising for sample effort changed the rank order of the sites for Phylogenetic Diversity (Table 1). A test of the rank correlation between the standardised and non-standardised PD values was relatively high but non-significant (Spearman's correlation coefficient, rho = 0.57, p = 0.084). Therefore, what one concludes about the relative bat diversity (and perhaps conservation importance) among these sites is dependent upon whether or not sampling effort is taken into account.

Fig. 3 An example of standardisation of Phylogenetic Diversity (PD) by rarefaction. Data are abundances of bats caught in harp-traps in State Forests of the south-west slopes region of New South Wales, Australia. See Law et al. (1998) for a description of the data. Plotting separate individuals-based curves (grey lines) for each site shows considerable variation in sampling effort, with the raw value of PD being dependent on the number of trapped individuals. To allow for comparison between sites, PD is rarefied to an expected value for 15 individuals for all sites (indicated by black vertical line)

Table 1 Comparison of diversity measures for bat assemblages for ten state forests of the south-west slopes region of New South Wales, Australia

State forest

Individuals (N)

Species richness (S)

Phylogenetic diversity (PDN)

Standardised phylogenetic diversity (PD15)

Bago

99

6

159

132

Maragle

208

8

170

136

Buccleuch

100

7

211

150

Bungongo

70

6

221

140

Woomargama

121

7

198

133

Carabost

153

8

198

155

Murraguldrie

95

6

214

133

Ellerslie

46

4

134

105

Tumblong

77

7

188

151

Minjary

15

3

113

113

Original data was taken from Law et al. (1998). Phylogenetic Diversity is measured in units of millions of years

 
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