Corpus ID: 6658427

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

@article{Tajima1989StatisticalMF,
  title={Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.},
  author={Fumio Tajima},
  journal={Genetics},
  year={1989},
  volume={123 3},
  pages={
          585-95
        }
}
  • F. Tajima
  • Published 30 October 1989
  • Biology, Medicine
  • Genetics
The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method… Expand
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References

SHOWING 1-10 OF 50 REFERENCES
Evolutionary relationship of DNA sequences in finite populations.
TLDR
These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors. Expand
The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations.
TLDR
The number of heterozygous sites per individual and some related quantities that represent the statistical properties of the mutant frequency distribution are investigated, assuming that a very large number of independent sites are available for mutation. Expand
The coalescent process in models with selection and recombination.
TLDR
The statistical properties of the genealogical process for a random sample at a neutral locus linked to a locus with selection follow from the results obtained for the selected locus. Expand
A test of neutral molecular evolution based on nucleotide data.
TLDR
A conservative statistical test of the neutral theory of molecular evolution's prediction that regions of the genome that evolve at high rates, as revealed by interspecific DNA sequence comparisons, will also exhibit high levels of polymorphism within species is presented. Expand
On the number of segregating sites in genetical models without recombination.
TLDR
The distribution is obtained for the number of segregating sites observed in a sample from a population which is subject to recurring, new, mutations but not subject to recombination, and applies approximately to three population models. Expand
Molecular and phenotypic variation of the white locus region in Drosophila melanogaster.
TLDR
There is little evidence for strong associations between this phenotype and the polymorphisms at the DNA level, contrary to a simple prediction based on the theory of mutation selection-balance of partially recessive deleterious mutants which predicts less variation on X chromosomes. Expand
Excess polymorphism at the Adh locus in Drosophila melanogaster.
TLDR
Analysis of the patterns of variation suggest an excess of polymorphism within the D. melanogaster Adh locus, rather than lack of polymorphisms in the 5' flanking region, which indicates that the observed patterns ofVariation are incompatible with an infinite site neutral model. Expand
THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION.
TLDR
This article proposes to examine some of the population consequences of a system of different isoalleles whose frequency in the population is determined by the mutation rate and by random drift, and considers three possibilities: A system of selectively neutral isoallels, a systemof mutually heterotic alleles, and a mixture of heterotic and harmful mutants. Expand
TESTING THE CONSTANT‐RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
  • R. Hudson
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1983
TLDR
G Gillespie and Langley (1979) showed that under a constant-rate neutral allele model, X2LF is not Chi-squared distributed, and therefore the Langley and Fitch analysis does not constitute a test of the constant- rate neutral model. Expand
Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals.
TLDR
Analysis of nucleotide sequence variation in an approximately 900-base pair region of the human mitochondrial DNA molecule encompassing the heavy strand origin of replication and the D-loop revealed several significant biases, most notably a strand dependence of substitution type and a 32-fold bias favoring transitions over transversions. Expand
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