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| '''Nucleotide diversity''' is a concept in [[molecular genetics]] which is used to measure the degree of [[polymorphism (biology)|polymorphism]] within a population.
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| <ref>
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| {{cite journal
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| |title=Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases
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| |journal=PNAS
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| |date=October 1, 1979
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| |first=
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| |last=
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| |coauthors=Masatoshi Nei and Wen-Hsiung Li
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| |volume=76
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| |issue=10
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| |pages=5269–73
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| |pmid=291943 |pmc=413122
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| |url=
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| |doi=10.1073/pnas.76.10.5269
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| |author=Nei, M.}}
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| </ref>
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| 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''.
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| It is given by the formula:
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| : <math>\pi = \sum_{ij} x_i x_j \pi_{ij} = 2 * \sum_{i=1}^n \sum_{j=1}^{i-1} x_i x_j \pi_{ij}</math>
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| where ''x<sub>i</sub>'' and ''x<sub>j</sub>'' are the respective frequencies of the ''i''th and ''j''th sequences, ''π<sub>ij</sub>'' 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.
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| 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,<ref>{{cite journal
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| |title=Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implications for the origin of agriculture
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| |journal=Molecular Biology and Evolution
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| |date=December 2007
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| |first=
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| |last=
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| |coauthors=Ozkan H, Walther A, Kohl J, Dagan T, Salamini F, Martin W
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| |volume=24
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| |issue=12
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| |pages=2657–68
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| |pmid=17898361
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| |url= |doi=10.1093/molbev/msm192
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| |author=Kilian, B}}</ref> or to determine evolutionary relationships.<ref>{{cite journal
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| |title=Nucleotide diversity in gorillas
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| |journal=Genetics
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| |date=March 2004
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| |first=
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| |last=
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| |coauthors=Jensen-Seaman MI, Chemnick L, Ryder O, Li WH
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| |volume=166
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| |issue=3
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| |pages=1375–83
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| |pmid=15082556 |pmc=1470796 |doi= 10.1534/genetics.166.3.1375|url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=15082556
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| |author=Yu, N.}}</ref>
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| 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 <ref>{{cite journal
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| |title=Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data
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| |journal=Molecular Phylogenetics and Evolution
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| |date=January 2001
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| |first=
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| |last=
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| |coauthors=
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| |volume=18
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| |issue=1
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| |pages=143–8
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| |pmid= 11161751 |doi=10.1006/mpev.2000.0865
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| |url=
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| |author=Borowsky, Richard L.}}</ref> and Amplified Fragment Length Polymorphism ([[Amplified fragment length polymorphism|AFLP]]) data.<ref>{{cite journal
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| |title=A method for estimating nucleotide diversity from AFLP data
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| |journal=Genetics
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| |first=
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| |last=
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| |coauthors=Ryohei Terauchib Günter Kahlb and Fumio Tajima
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| |volume=151
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| |issue=3
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| |pages=1157–64
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| |pmid= 10049931 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=10049931
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| |author=Innan, Hideki
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| |date= March 1, 1999
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| |pmc=1460529 }}</ref>
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| ==Software==
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| * [http://www.ub.es/dnasp/ DnaSP] — DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data.
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| * [http://www.megasoftware.net/ 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 OSX (since ver. 5.x).
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| * [http://cmpg.unibe.ch/software/arlequin3/ 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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| * [http://www.ub.edu/softevol/variscan/ Variscan]
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| ==References==
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| {{Reflist}}
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| {{DEFAULTSORT:Nucleotide Diversity}}
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| [[Category:Molecular genetics]]
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| {{genetics-stub}}
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Hello. Allow me introduce the author. Her title is Refugia Shryock. To gather coins is a factor that I'm totally addicted to. Hiring is her working day occupation now and she will not alter it anytime soon. North Dakota is our beginning location.
my web blog; abcwealthbuilder.com