Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan.
Philos Trans R Soc Lond B Biol Sci. 2010 Nov 27;365(1558):3599-609. doi: 10.1098/rstb.2010.0272.
We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.
我们提出了一个参数化的系统发育多样性（PD）度量类，该度量类对物种丰度和物种分类或系统发育距离都敏感。这项工作扩展了传统的参数化物种中性方法（基于“有效物种数”或 Hill 数），以考虑物种的亲缘关系，同时也将传统的系统发育方法（基于“总系统发育长度”）推广到包含物种丰度。所提出的度量方法量化了“任何感兴趣的时间间隔内的平均有效物种数”，或者“该时间间隔内的最大差异谱系的有效数量”。该度量方法与间隔长度的乘积量化了该间隔内系统发育树的“分支多样性”。新的度量方法概括和统一了许多现有的度量方法，并将分类多样性定义为一个特例。复制原则（或加倍属性）是物种中性多样性的一个重要要求，已被推广到 PD。广泛使用的 Rao 二次熵和系统发育熵不满足这个基本属性，但一个简单的转换将每个属性转换为我们的度量方法，这些方法满足该属性。该方法应用于森林数据，以解释疏伐的影响。
