At the subspecies level, diversity can be measured by richness counts of the number of different varieties within a species (e.g., the number of landraces of one crop) or the number of alleles present in a metapopulation. These measures should be accompanied by evenness measures of the relative dominance of the varieties.
Genetic biodiversity can be estimated by measuring appropriate molecular markers. Most studies on genetic variation within species are based on random markers. Current work is investigating the use of markers targeted at genes exhibiting ecologically relevant activity (Tienderen et al. 2002). Indices of relatedness, whether based on cladistics (Clark and Warwick 1998) or genetic distance (Nei 1972; Takezaki and Nei 1996), have potential for measuring gene-level diversity both between and within species. They have the advantage of not requiring the actual genes to be exhaustively inventoried. Examples are the measures that have been used to estimate soil microbial biodiversity (Pankhurst et al. 1997) when the species are unknown (and the species concept may not even apply).
Despite very rapid developments in this field, it is our assessment that robust and widely applied gene-level diversity indicators are still a decade away. Until then, the species, imperfect as it is, is the most robust scientific basis for constructing most indicators.
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