Classic Measures and Their Phylogenetic Generalizations

Generalized Entropies

The species richness of an assemblage is a simple count of the number of species present. It is the most intuitive and frequently used measure of biodiversity, and is a key metric in conservation biology (MacArthur and Wilson 1967; Hubbell 2001; Magurran 2004). However, it does not incorporate any information about the abundances of species, and it is a very hard number to estimate accurately from small samples (Colwell and Coddington 1994; Chao 2005; Gotelli and Colwell 2011).

Shannon entropy is a popular classical abundance-based diversity index and has been used in many disciplines. Shannon entropy is

where S is the number of species in the assemblage, and the ith species has relative abundance pi. Shannon entropy gives the uncertainty in the species identity of a randomly chosen individual in the assemblage. Another popular measure is the Gini-Simpson index,

which gives the probability that two randomly chosen individuals belong to different species. These two abundance-sensitive measures, along with species richness, can be united into a single family of generalized entropy:

The parameter q determines the sensitivity of the measure to the relative frequencies of the species. When q = 0, qH becomes S − 1; When q tends to 1, qH tends to Shannon entropy. When q = 2, qH reduces to the Gini-Simpson index. This family was found many times in different disciplines (Havrdra and Charvat 1967; Daróczy 1970; Patil and Taillie 1979; Tsallis 1988; Keylock 2005). There are many other families of generalized entropies, notably the Rényi entropies (Rényi 1961).

Although the traditional abundance-sensitive generalized entropies and their special cases have been useful in many disciplines (e.g., see Magurran 2004), they do not behave in the same intuitive linear way as species richness. In ecosystems with high diversity, mass extinctions hardly affect their values (Jost 2010). They also lead to logical contradictions in conservation biology, because they do not measure a conserved quantity (e.g., under a given conservation plan, the proportion of “diversity” lost and the proportion preserved can both be 90 % or more); see Jost (2006, 2007) and Jost et al. (2010). Thus, changes in their magnitude cannot be properly compared or interpreted. Also, the main measure of similarity in the additive approach for traditional measures, the within-group or “alpha” diversity divided by the total or “gamma” diversity, does not actually quantify the compositional similarity of the assemblages under study. This ratio can be arbitrarily close to unity (supposedly indicating high similarity) even when the assemblages being compared have no species in common. Finally, these measures each use different units (e.g., the Gini-Simpson index is a probability whereas Shannon entropy is in units of information), so they cannot be compared with each other. All these problems are consequences of their failure to satisfy the replication principle. Hill numbers obey the replication principle and resolve all these problems; see section “Hill numbers and the replication principle”.