Nucleotide diversity is a concept in molecular genetics which is used to measure the degree of polymorphism within a population. It was first introduced by Nei and Li in 1979. ^[1]

It 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:

\pi = \sum_{ij} x_i x_j \pi_{ij} = \sum_{i=1}^n \sum_{j=1}^i x_i x_j \pi_{ij}

where x_i and x_j are the respective frequencies of the ith and jth sequences, π_ij 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. The summation is taken over all distinct pairs i,j, without repetition.

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 ^[2], or to determine evolutionary relationships^[3].

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 ^[4] and Amplified Fragment Length Polymorphism (AFLP) data ^[5].

Software

• DnaSP — DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data.
• MEGA, Molecular Evolutionary Genetics Analysis, is a software package used for estimating rates of molecular evolution, as well as generating phylogenetic trees, and aligning DNA sequences. Available for Windows and Linux.
• Arlequin3 software can be used for calculations of nucleotide diversity and a variety of other statistical tests for intra-population and inter-population analyses. Available for Windows, Linux, and Mac.

References