Abstract
A method for estimating the nucleotide diversity from AFLP data is developed by using the relationship between the number of nucleotide changes and the proportion of shared bands. The estimation equation is based on the assumption that GC-content is 0.5. Computer simulations, however, show that this method gives a reasonably accurate estimate even when GC-content deviates from 0.5, as long as the number of nucleotide changes per site (nucleotide diversity) is small. As an example, the nucleotide diversity of the wild yam, Dioscorea tokoro, was estimated. The estimated nucleotide diversity is 0.0055, which is larger than estimations from nucleotide sequence data for Adh and Pgi.
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Selected References
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- Clark A. G., Lanigan C. M. Prospects for estimating nucleotide divergence with RAPDs. Mol Biol Evol. 1993 Sep;10(5):1096–1111. doi: 10.1093/oxfordjournals.molbev.a040057. [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., Miller J. C. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 1990 Aug;125(4):873–879. doi: 10.1093/genetics/125.4.873. [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]
- Stephens J. C., Gilbert D. A., Yuhki N., O'Brien S. J. Estimation of heterozygosity for single-probe multilocus DNA fingerprints. Mol Biol Evol. 1992 Jul;9(4):729–743. doi: 10.1093/oxfordjournals.molbev.a040755. [DOI] [PubMed] [Google Scholar]
- Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tajima F., Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol. 1984 Apr;1(3):269–285. doi: 10.1093/oxfordjournals.molbev.a040317. [DOI] [PubMed] [Google Scholar]
- Terauchi R., Terachi T., Miyashita N. T. DNA polymorphism at the Pgi locus of a wild yam, Dioscorea tokoro. Genetics. 1997 Dec;147(4):1899–1914. doi: 10.1093/genetics/147.4.1899. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomas C. M., Vos P., Zabeau M., Jones D. A., Norcott K. A., Chadwick B. P., Jones J. D. Identification of amplified restriction fragment polymorphism (AFLP) markers tightly linked to the tomato Cf-9 gene for resistance to Cladosporium fulvum. Plant J. 1995 Nov;8(5):785–794. doi: 10.1046/j.1365-313x.1995.08050785.x. [DOI] [PubMed] [Google Scholar]
- Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995 Nov 11;23(21):4407–4414. doi: 10.1093/nar/23.21.4407. [DOI] [PMC free article] [PubMed] [Google Scholar]