- THIS ARTICLE
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Misawa, K.
- Articles by Tajima, F.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Misawa, K.
- Articles by Tajima, F.
Genetics, Vol 147, 1959-1964, Copyright © 1997
INVESTIGATIONS |
Estimation of the Amount of DNA Polymorphism When the Neutral Mutation Rate Varies Among Sites
K. Misawa and F. Tajima
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113, Japan
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 ({pi}), 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, {theta} is often used as a measure of the amount of DNA polymorphism, where {theta} = 4N{mu}, N is the effective population size and {mu} is the neutral mutation rate per site per generation. It is known that {theta} estimated from {pi}, 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 {theta} 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.
This article has been cited by other articles:
 |
|
 |
|
  S. L. Kosakovsky Pond and S. D. W. Frost Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection Mol. Biol. Evol., May 1, 2005; 22(5): 1208 - 1222. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. D. W. Frost, M.-J. Dumaurier, S. Wain-Hobson, and A. J. L. Brown Genetic drift and within-host metapopulation dynamics of HIV-1 infection PNAS, May 24, 2001; (2001) 131056998. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Markovtsova, P. Marjoram, and S. Tavaré The Effects of Rate Variation on Ancestral Inference in the Coalescent Genetics, November 1, 2000; 156(3): 1427 - 1436. [Abstract] [Full Text]
|
|
|
|
|
|
S. Meyer, G. Weiss, and A. von Haeseler Pattern of Nucleotide Substitution and Rate Heterogeneity in the Hypervariable Regions I and II of Human mtDNA Genetics, July 1, 1999; 152(3): 1103 - 1110. [Abstract] [Full Text]
|
|
|
|
|
|
S. D. W. Frost, M.-J. Dumaurier, S. Wain-Hobson, and A. J. L. Brown Genetic drift and within-host metapopulation dynamics of HIV-1 infection PNAS, June 5, 2001; 98(12): 6975 - 6980. [Abstract] [Full Text] [PDF]
|
|