Abstract
A simple method is proposed for estimating the average number of nucleotide substitutions per site within and between populations for the case where a large number of individuals are examined for many restriction enzymes. This method gives essentially the same results as those obtained by Nei and Li's method but saves a large amount of computer time. The variances of the quantities estimated can be obtained by the jackknife method, and these variances are very similar to those obtained by Nei and Jin's more sophisticated method. A similar simple method can also be applied to DNA sequence data.
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Selected References
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- Brown W. M. Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3605–3609. doi: 10.1073/pnas.77.6.3605. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Clark A. G. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol. 1990 Mar;7(2):111–122. doi: 10.1093/oxfordjournals.molbev.a040591. [DOI] [PubMed] [Google Scholar]
- Ferris S. D., Brown W. M., Davidson W. S., Wilson A. C. Extensive polymorphism in the mitochondrial DNA of apes. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6319–6323. doi: 10.1073/pnas.78.10.6319. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ferris S. D., Wilson A. C., Brown W. M. Evolutionary tree for apes and humans based on cleavage maps of mitochondrial DNA. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2432–2436. doi: 10.1073/pnas.78.4.2432. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kaplan N., Langley C. H. A new estimate of sequence divergence of mitochondrial DNA using restriction endonuclease mappings. J Mol Evol. 1979 Nov;13(4):295–304. doi: 10.1007/BF01731370. [DOI] [PubMed] [Google Scholar]
- Nei M., Jin L. Variances of the average numbers of nucleotide substitutions within and between populations. Mol Biol Evol. 1989 May;6(3):290–300. doi: 10.1093/oxfordjournals.molbev.a040547. [DOI] [PubMed] [Google Scholar]
- Nei M., Li W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269–5273. doi: 10.1073/pnas.76.10.5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nei M., Tajima F. DNA polymorphism detectable by restriction endonucleases. Genetics. 1981 Jan;97(1):145–163. doi: 10.1093/genetics/97.1.145. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nei M., Tajima F. Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics. 1983 Sep;105(1):207–217. doi: 10.1093/genetics/105.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]