Rarefaction and extrapolation of phylogenetic diversity

Abstract

Summary1. Traditional species diversity measures do not make distinctions among species. Faith's phylogenetic diversity (PD), which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species, takes into account phylogenetic differences among species and has found many applications in various research fields. In this paper, we extend Faith's PD to represent the total length of a phylogenetic tree from any fixed point on its main trunk. 2. Like species richness, Faith's PD tends to be an increasing function of sampling effort and thus tends to increase with sample completeness. We develop in this paper the 'PD accumulation curve' (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness. 3. To make fair comparisons of Faith's PD among several assemblages based on sampling data from each assemblage, we derive both theoretical formulae and analytic estimators for seamless rarefaction (interpolation) and extrapolation (prediction). We develop a lower bound of the undetected PD for an incomplete sample to guide the extrapolation; the PD estimator for an extrapolated sample is generally reliable up to twice the size of the empirical sample. 4. We propose an integrated curve that smoothly links rarefaction and extrapolation to standardize samples on the basis of sample size or sample completeness. A bootstrap method is used to obtain the unconditional variances of PD estimators and to construct the confidence interval of the expected PD for a fixed sample size or fixed degree of sample completeness. This facilitates comparison of multiple assemblages of both rarefied and extrapolated samples. 5. We illustrate our formulae and estimators using empirical data sets from Australian birds in two sites. We discuss the extension of our approach to the case of multiple incidence data and to incorporate species abundances.

Biodiversity hotspots: A shortcut for a more complicated concept

“…However, because diversity, or evolutionary history, is distributed unequally between taxa as well as between areas, taking into consideration only traditional species diversity may not be sufficient to fully capture differences among species (Chao et al, 2014). Therefore, to quantify biodiversity the focus shifted from pure species counting to a more integrative approach that quantifies the evolutionary information represented within groups of taxa (i.e.…”

Monitoring Changes in Genetic Diversity

“…Consistent sampling is required to eliminate error or correction for the lowest sample size will often be necessary, resulting in a loss of information and sensitivity (but see Dornelas et al 2013). Recent advances have provided robust methods that correct for sampling biases in estimates of phylogenetic diversity (e.g., Chao et al 2015). van Zonneveld et al (2014) concluded that the number of 'locally common' alleles (defined as alleles restricted to a limited area of a species' distribution, but having high frequencies in these areas) may also be good indicators of overall genetic diversity.…”

Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers

“…The rarefaction formula for Faith's PD was developed by Nipperess and Matsen (2013) and Nipperess (chapter "The Rarefaction of Phylogenetic Diversity: Formulation, Extension and Application"). Recently, Chao et al (2015) derived an integrated sampling, rarefaction, and extrapolation methodology to compare Faith's PD of a set of assemblages. Like species richness, Faith's PD does not consider species abundances.…”