Abstract
A statistical approach to the analysis of DNA sequences has been developed, which provides a confidence interval estimate for the proportion of naturally occurring amino acid polymorphisms that are selectively neutral. When applied to the gnd gene coding for 6-phosphogluconate dehydrogenase in a sample of seven natural isolates of Escherichia coli, the method indicates that the proportion of observed amino acid polymorphisms that are selectively neutral is unlikely to be greater than 49% (upper 95% confidence limit). On the other hand, the observations are also consistent with a model in which all of the observed amino acid substitutions are mildly deleterious with an average selection coefficient approximating 1.6 X 10(-7). Various models for the distribution of configurations at silent sites are also investigated.
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Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Dykhuizen D., Hartl D. L. Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics. 1980 Dec;96(4):801–817. doi: 10.1093/genetics/96.4.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ewens W. J. The sampling theory of selectively neutral alleles. Theor Popul Biol. 1972 Mar;3(1):87–112. doi: 10.1016/0040-5809(72)90035-4. [DOI] [PubMed] [Google Scholar]
- Hartl D. L., Dykhuizen D. E. Potential for selection among nearly neutral allozymes of 6-phosphogluconate dehydrogenase in Escherichia coli. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6344–6348. doi: 10.1073/pnas.78.10.6344. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hedrick P. W., Thomson G. A two-locus neutrality test: applications to humans, E. coli and lodgepole pine. Genetics. 1986 Jan;112(1):135–156. doi: 10.1093/genetics/112.1.135. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kimura M. Rare variant alleles in the light of the neutral theory. Mol Biol Evol. 1983 Dec;1(1):84–93. doi: 10.1093/oxfordjournals.molbev.a040305. [DOI] [PubMed] [Google Scholar]
- Kreitman M. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature. 1983 Aug 4;304(5925):412–417. doi: 10.1038/304412a0. [DOI] [PubMed] [Google Scholar]
- Li W. H., Wu C. I., Luo C. C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 1985 Mar;2(2):150–174. doi: 10.1093/oxfordjournals.molbev.a040343. [DOI] [PubMed] [Google Scholar]
- Maruyama T., Kimura M. Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6710–6714. doi: 10.1073/pnas.77.11.6710. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Milkman R., Crawford I. P. Clustered third-base substitutions among wild strains of Escherichia coli. Science. 1983 Jul 22;221(4608):378–380. doi: 10.1126/science.6346486. [DOI] [PubMed] [Google Scholar]
- Nasoff M. S., Baker H. V., 2nd, Wolf R. E., Jr DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase. Gene. 1984 Mar;27(3):253–264. doi: 10.1016/0378-1119(84)90070-2. [DOI] [PubMed] [Google Scholar]
- Ohta T. Slightly deleterious mutant substitutions in evolution. Nature. 1973 Nov 9;246(5428):96–98. doi: 10.1038/246096a0. [DOI] [PubMed] [Google Scholar]
- Ota T. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature. 1974 Nov 29;252(5482):351–354. doi: 10.1038/252351a0. [DOI] [PubMed] [Google Scholar]
- Watterson G. A. An analysis of multi-allelic data. Genetics. 1978 Jan;88(1):171–179. doi: 10.1093/genetics/88.1.171. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Watterson G. A. Heterosis or neutrality? Genetics. 1977 Apr;85(4):789–814. doi: 10.1093/genetics/85.4.789. [DOI] [PMC free article] [PubMed] [Google Scholar]