The mean and variance of phylogenetic diversity under rarefaction.
The mean and variance of phylogenetic diversity under rarefaction.
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DOI：
10.1111/2041-210x.12042
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发表时间：
2013-06-01
影响因子：
6.6
通讯作者：
Matsen FA 4th
中科院分区：
文献类型：
--
作者：
Nipperess DA;Matsen FA 4th
系统发育多样性（PD）取决于采样深度，这使得不同深度样本之间的PD比较复杂。处理给定多样性统计的不同样本深度的一种方法是稀疏化，这意味着采取给定大小的原始样本的随机子集。稀疏条件下物种丰富度的均值和方差的精确解析公式已经存在了一段时间，但PD没有这样的解决方案。我们推导了稀疏情况下PD的均值和方差的精确公式。我们确认，这些公式是正确的，通过比较精确的解决方案的平均值和方差计算的重复随机（蒙特卡洛）二次抽样的数据集Toohey森林，昆士兰州，澳大利亚的木本灌木的茎数。我们还使用两个例子来展示该方法的应用：确定澳大利亚生态区中哺乳动物多样性的热点，以及表征人类阴道微生物组。有一个非常高的解析和随机抽样方法之间的对应关系，用于计算稀疏下的PD的均值和方差，虽然蒙特卡罗方法需要大量的随机抽取收敛于方差的精确解。稀疏的哺乳动物PD的生态区在澳大拉西亚的一个共同的标准，25种揭示了非常不同的等级排序的生态区，表明完全不同的热点的多样性比unrarefied PD。这些方法在阴道微生物组中的应用表明，用于量化细菌性阴道病的经典评分与稀疏曲线的形状相关。稀疏下PD均值和方差的解析公式既精确又比重复子抽样有效。稀疏的PD允许许多应用程序，其中需要比较不同深度的样品。
Phylogenetic diversity (PD) depends on sampling depth, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD. We have derived exact formulae for the mean and variance of PD under rarefaction. We confirm that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome. There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance. Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve. The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.