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 Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecu ...

differences per site between two DNA sequences in all possible pairs in the sample population, and is denoted by

\pi

. An estimator for

\pi

is given by: :

\hat = \frac \sum_ x_i x_j \pi_ = \frac \sum_^n \sum_^ 2 x_i x_j \pi_

where

x_i

and

x_j

are the respective frequencies of the

i

th and

j

th sequences,

\pi_

is the number of nucleotide differences per nucleotide site between the

i

th and

j

th sequences, and

n

is the number of sequences in the sample. The term in front of the sums guarantees an unbiased estimator, which does not depend on how many sequences you sample. Nucleotide diversity is a measure of

genetic variation Genetic variation is the difference in DNA among individuals or the differences between populations. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources of genetic variation, b ...

. 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 RAPD may refer to: *Relative afferent pupillary defect *Random amplification of polymorphic DNA {{dab ...

) data and Amplified Fragment Length Polymorphism ( AFLP) data.

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 Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genet ...

, as well as generating phylogenetic trees, and aligning DNA sequences. Available for Windows, Linux and Mac OS X (since ver. 5.x).
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.
Variscan
* R packag
PopGenome

* R packag
QSutils

References

Molecular genetics {{genetics-stub