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Biology · 术语表

什么是 Diversity?

Definition 14.4 University Biology — Year 3 · 第 14 章 — Microbiomes and Symbioses

For a community of SS species with relative abundances p1,…,pSp_{1},\dots, p_{S} (∑pi=1\sum p_{i} = 1): the richness is SS; the Shannon index H=−∑ipiln⁡piH = -\sum_{i} p_{i}\ln p_{i} measures the uncertainty about the species of a randomly drawn individual, and eHe^{H} is the number of equally abundant species that would give the same uncertainty (the effective number of species); the Simpson index D=∑ipi2D = \sum_{i} p_{i}^{2} is the probability that two individuals drawn at random are of the same species, and 1/D1/D is another effective number, weighted toward the common species. Richness depends on how many individuals one has looked at: a rarefaction curve plots the species found against the number of individuals sampled, and flattens when most species have been seen.

示例

Example 14.6 (Two guts)

A sample of 10001000 reads from one person yields 150150 species, with H=3.5H = 3.5 and 4040 singletons; a sample of 50005000 reads from another yields 260260 species. The second is not necessarily more diverse: it was sampled five times more deeply, and rarefying it to 10001000 reads may give 150150 too. The first sample’s coverage is 1−40/1000=96 %1 - 40/1000 = 96\,\%: four per cent of the bacteria in that gut belong to species the sample never saw, and a deeper sample will find them. Effective numbers, e3.5≈33e^{3.5} \approx 33 species’ worth of evenness against a richness of 150150, say that a few species dominate — which is how every gut looks.

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