Abstract
In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.
Highlights
It is well accepted that incorporating phylogenetic information into alpha and beta diversity measures can be useful in a variety of ecological contexts
Phylogenetic alpha diversity measures were more closely related to community state than were discrete measures based on Operational Taxonomic Unit (OTU) clustering for the datasets investigated here
This result is especially interesting given that the Simpson index, the Shannon index, or counting applied to OTU tables are very common ways of characterizing microbial diversity (Fierer et al, 2007; Grice et al, 2009; Hill et al, 2003; Dethlefsen & Relman, 2011)
Summary
It is well accepted that incorporating phylogenetic information into alpha (singlesample) and beta (between-sample) diversity measures can be useful in a variety of ecological contexts. Phylogenetic diversity (Faith, 1992) phylogenetic generalization of species count phylogenetic quadratic entropy (Rao, 1982; Warwick & Clarke, 1995) phylogenetic generalization of the Simpson index phylogenetic entropy (Allen, Kon & Bar-Yam, 2009) phylogenetic generalization of the Shannon index qD(T) (Chao, Chiu & Jost, 2010) phylogenetic generalization of Hill numbers. Starting with Faith’s original definition of phylogenetic diversity (Faith, 1992), which generalizes species count, there are phylogenetic generalizations of the Simpson index to Rao’s quadratic entropy (Rao, 1982; Warwick & Clarke, 1995), the Shannon index to phylogenetic entropy (Allen, Kon & Bar-Yam, 2009), and the Hill numbers to qD(T) (Chao, Chiu & Jost, 2010). Many diversity measures can be tidily expressed in the framework of Leinster & Cobbold (2012), the expression of phylogenetic diversity measures for non-ultrametric trees is complex
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