Taxonomic or phylogenetic diversity is the genetic relationship between different groups of species.
The equation is often written in the equivalent form: The value of q determines which mean is used.
In many real datasets, the least abundant species is represented by a single individual, and then the effective number of species would equal the number of individuals in the dataset.
represents the proportional abundance of the ith genus or functional type, and qD equals genus diversity or functional type diversity, respectively.
[5][6][7] When interpreted in ecological terms, each one of these indices corresponds to a different thing, and their values are therefore not directly comparable.
The Shannon index equals log(1D), that is, q approaching 1, and in practice quantifies the uncertainty in the species identity of an individual that is taken at random from the dataset.
The Gini-Simpson index equals 1 - 1/2D and quantifies the probability that the two randomly taken individuals represent different species.
[1][2][3][7][8] Depending on the purposes of quantifying species diversity, the data set used for the calculations can be obtained in different ways.
Extrapolation from the sample to the underlying population of interest is not straightforward, because the species diversity of the available sample generally gives an underestimation of the species diversity in the entire population.
When species diversity values are compared among sets, sampling efforts need to be standardised in an appropriate way for the comparisons to yield ecologically meaningful results.
Resampling methods can be used to bring samples of different sizes to a common footing.
[12][13] The observed species diversity is affected not only by the number of individuals but also by the heterogeneity of the sample.