On the measurement of species diversity incorporating species differences

Abstract

When pairwise differences (relatedness) between species are numerically given, the average of the species differences weighted by relative frequencies can be used as a species diversity index. This paper first theoretically develops the indices of this type, then applies them to forestry data. As examples of diversity indices, this paper explores the taxonomic diversity and the newly introduced amino acid diversity, which is a modification of the nucleotide diversity in genetics. The first, mathematical part shows that both indices can be decomposed into three inner factors; evenness of relative frequencies (=the Simpson index), the simple average over species differences regardless of relative frequencies, and the taxonomic or genetic balance in relative frequencies. The taxonomic diversity has another decomposition: the sum over the Simpson indices at all the taxonomic levels. The second part examines the effects of different forest management techniques on diversity. It is shown that a thinning operation for promoting survival of specific desirable species also contributed to increasing the taxonomic diversity. If we calculated only conventional indices that do not incorporate species relatedness, we would simply conclude that the thinning did not significantly affect the diversity. The theoretical developments of the first part complement the result, leading us to a better interpretation about contrasting vegetation structures. The mathematical results also reveal that the amino acid diversity involves redundant species, which is undesirable when measuring diversity; hence, this index is used to demonstrates crucial points when we introduce species relatedness. The results suggest further possibilities of applying diversity indices incorporating species differences to a variety of ecological studies.

Parasite specialization from a phylogenetic perspective: a new index of host specificity

“…First, it is independent of study effort, just as the index used in biodiversity studies from which S TD is derived is independent of sample size (Rogers, Clarke & Reynolds, 1999 ;Clarke & Warwick, 1999, 2001, 2001. The strong link between study effort and the number of recorded host species has plagued past attempts to use this simple count as a measure of host specificity (Poulin, 1992).…”

“…It is inspired from measures of phylogenetic diversity recently proposed in the scientific literature, in particular in biodiversity and conservation studies (e.g. Faith, 1992 ;Humphries, Williams & VaneWright, 1995 ;Purvis & Hector, 2000 ;Shimatani, 2001 ;Barker, 2002). More specifically, it is derived from the measures of taxonomic distinctness developed in recent studies of marine biodiversity by , 1999, 2001, 2001.…”

Parasite biodiversity and its determinants in coastal marine teleost fishes of Brazil

“…Richness is a convenient measure, but it does not capture all facets of diversity (Purvis & Hector, 2000). It ignores the evolutionary relationships among species coexisting in an assemblage (see Shimatani, 2001). Applied to parasite assemblages, measures of diversity that incorporate information on the relationships among parasite species can shed light on how the assemblage has formed.…”

Studies on taxonomic diversity of plant communities and modeling its potential distribution in Yazılı Canyon Nature Park, Turkey

“…After signing this convention, the studies dealing with measuring biodiversity, examining biodiversity-environment relationships, and modeling and mapping of biodiversity using remote sensing data and GIS gained much more importance (Maddock and du Plessis, 1999;Özdemir and Donoghue, 2013;Özdemir, 2014). As mentioned before, diversity has been studied in different ways (Clarke and Warwick, 2001;Shimatani, 2001;Petchey et al, 2004;Ozkan, 2012;Negiz et al, 2015). Unlike the traditional diversity indices, taxonomic diversity is calculated considering the places in taxonomic hierarchy of the species.…”