DOI: 10.5061/dryad.vn85pg1
title: Data from: Comparing two classes of alpha diversities and their corresponding beta and (dis)similarity measures, with an application to the Formosan sika deer (Cervus nippon taiouanus) reintroduction program

description: 1. Diversity partitioning, which decomposes gamma diversity into alpha and
 beta components, is commonly used to obtain measures that quantify
 spatial/temporal diversity and compositional similarity or dissimilarity
 among assemblages. We focus on the decomposition of diversity as measured
 by Hill numbers (parameterized by a diversity order q≧0). 2. At least
 three diversity-partitioning schemes based on Hill numbers have been
 proposed. These schemes differ in the way they formulate alpha diversity.
 We focus on comparing two classes of alpha diversities, developed
 respectively by Routledge (1979) and Chiu et al. (2014). Both are defined
 for all diversity orders q≧0. Because these two approaches to quantifying
 alpha have not been compared in the literature; it has been unclear how to
 choose a proper alpha formulation for practical applications. 3. We review
 the two classes of alpha diversities and discuss the properties of their
 corresponding beta and (dis)similarity measures. Our research offers clear
 guidelines regarding the choice of an alpha formula: (i) If the goal is to
 assess compositional (dis)similarity among (unweighted) species relative
 abundance datasets, then the two alpha formulas are identical, leading to
 the same beta and (dis)similarity measures. (ii) If the goal is to assess
 compositional (dis)similarity among (unweighted) species raw abundance
 datasets, then Chiu et al.’s approach should be used. Their beta can be
 monotonically transformed to various (dis)similarity measures in the range
 [0, 1]. (iii) If each assemblage is weighted by its absolute, total
 abundance (i.e., assemblage size), but the goal is to assess compositional
 (dis)similarity among species relative abundance datasets, then
 Routledge’s approach should be used. In this case, construction of
 legitimate (dis)similarity measures among species relative abundance
 datasets for unequal assemblage sizes/weights, for any order q≧0, has not
 been addressed in the literature. Here we propose non-monotonic
 transformations of Routledge’s beta to fill this gap. 4. The extension of
 our analysis to phylogenetic diversity partitioning is generally parallel.
 We apply various species and phylogenetic dissimilarity measures to
 Taiwan’s plant data; the results provide insights into the assessment of a
 reintroduction program of Formosan sika deer into a forest area. Pertinent
 sampling and related issues are also discussed.
description: Kenting_Abundance_DataThe absolute abundances (i.e., individuals) of 67 woody plant species (DBH 1-2 cm) for the 2008 census and 2013 census of the Kenting Karst Forest Dynamics Plot, Taiwan. See the main text and Appendix S5 of Chao et al. (2019) for analysis details.Kenting_Phylo_TreeThe phylogenetic tree (in Newick format) of 67 plant species (DBH 1-2 cm) for two censuses (2008 and 2013) of the Kenting Karst Forest Dynamics Plot, Taiwan. See the main text and Appendix S5 of Chao et al. (2019) for analysis details.