Nucleotide diversity is a concept in
molecular genetics
Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the ...
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 biomolecules wi ...
differences per site between two
DNA sequences in all possible pairs in the sample population, and is denoted by
.
An estimator for
is given by:
:
where
and
are the respective frequencies of the
th and
th sequences,
is the number of nucleotide differences per nucleotide site between the
th and
th sequences, and
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, ...
. It is usually associated with other statistical measures of population diversity, and is similar to
expected heterozygosity
Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism.
Mo ...
. 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.
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 genetics ...
, as well as generating phylogenetic trees, and aligning DNA sequences. Available for Windows, Linux and Mac OS X (since ver. 5.x).
Arlequin3software 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
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