Nucleotide diversity is a concept in molecular genetics which is used to measure the degree of polymorphism within a population.
One commonly used measure of nucleotide diversity was first introduced by Nei and Li in 1979. This measure is defined as the average number of nucleotide differences per site between any two DNA sequences chosen randomly from the sample population, and is denoted by π.
It is given by the formula:
where xi and xj are the respective frequencies of the ith and jth sequences, πij is the number of nucleotide differences per nucleotide site between the ith and jth sequences, and n is the number of sequences in the sample.
Nucleotide diversity is a measure of genetic variation. It is usually associated with other statistical measures of population diversity, and is similar to expected heterozygosity. This statistic may be used to monitor diversity within or between ecological populations, to examine the genetic variation in crops and related species, or to determine evolutionary relationships.
Nucleotide diversity can be calculated by examining the DNA sequences directly, or may be estimated from molecular marker data, such as Random Amplified Polymorphic DNA (RAPD) data and Amplified Fragment Length Polymorphism (AFLP) data.
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