Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data

A way to estimate the index of nucleotide diversity (π) from band match frequencies in random amplified polymorphic DNA and amplified fragment length polymorphism data is described. π is shown to be a simple function of the proportion of mismatched bands between two individuals drawn at random from a population (φ) and the number of discriminating sites in the amplification system. The method is computationally and conceptually simple and avoids some of the assumptions inherent in other approaches: the relationship is independent of the base composition of the target DNA and avoids the bias inherent in estimations of allelic frequencies in dominant systems. Only two individuals from a population are needed to estimate π. This economy of material suggests utility of this approach in conservation genetics or other fields where obtaining large samples is impractical or undesirable.