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Concept
Nucleotide diversity
Summary
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 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. 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.
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, 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.
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Population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure. Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics.