Abstract
Knowing the amount of DNA polymorphism is essential to understand the mechanism of maintaining DNA polymorphism in a natural population. The amount of DNA polymorphism can be measured by the average number of nucleotide differences per site (π), the proportion of segregating (polymorphic) site (s) and the minimum number of mutations per site (s*). Since the latter two quantities depend on the sample size, θ is often used as a measure of the amount of DNA polymorphism, where θ = 4Nμ, N is the effective population size and μ is the neutral mutation rate per site per generation. It is known that θ estimated from π, s and s* under the infinite site model can be biased when the mutation rate varies among sites. We have therefore developed new methods for estimating θ under the finite site model. Using computer simulations, it has been shown that the new methods give almost unbiased estimates even when the mutation rate varies among sites substantially. Furthermore, we have also developed new statistics for testing neutrality by modifying Tajima's D statistic. Computer simulations suggest that the new test statistics can be used even when the mutation rate varies among sites.
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Selected References
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- Bertorelle G., Slatkin M. The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Mol Biol Evol. 1995 Sep;12(5):887–892. doi: 10.1093/oxfordjournals.molbev.a040265. [DOI] [PubMed] [Google Scholar]
- Horai S., Kondo R., Nakagawa-Hattori Y., Hayashi S., Sonoda S., Tajima K. Peopling of the Americas, founded by four major lineages of mitochondrial DNA. Mol Biol Evol. 1993 Jan;10(1):23–47. doi: 10.1093/oxfordjournals.molbev.a039987. [DOI] [PubMed] [Google Scholar]
- Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969 Apr;61(4):893–903. doi: 10.1093/genetics/61.4.893. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rogers A. Error introduced by the infinite-site model. Mol Biol Evol. 1992 Nov;9(6):1181–1184. doi: 10.1093/oxfordjournals.molbev.a040787. [DOI] [PubMed] [Google Scholar]
- Tajima F. Statistical analysis of DNA polymorphism. Jpn J Genet. 1993 Dec;68(6):567–595. doi: 10.1266/jjg.68.567. [DOI] [PubMed] [Google Scholar]
- Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tajima F. The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics. 1996 Jul;143(3):1457–1465. doi: 10.1093/genetics/143.3.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993 May;10(3):512–526. doi: 10.1093/oxfordjournals.molbev.a040023. [DOI] [PubMed] [Google Scholar]