Hostname: page-component-745bb68f8f-lrblm Total loading time: 0 Render date: 2025-01-13T03:53:07.670Z Has data issue: false hasContentIssue false
  • English
  • Français

Effect of non-random sampling on the estimation of parameters in population genetics

Published online by Cambridge University Press:  14 April 2009

Fumio Tajima
Fumio Tajima
Affiliation:
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113, Japan
Rights & Permissions [Opens in a new window]

Summary

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

The amount and pattern of genetic variation in a population can be estimated from genes or DNA sequences sampled from the population. Although random sampling is assumed in almost all cases, we often do not know whether sampling is random or not. Using a simple non-random sampling model, the effects of non-random sampling on the estimation of parameters in population genetics were investigated. This non-random sampling model assumes that n genes are randomly sampled with replacement from m genes which were randomly sampled from a large random mating population, and various degrees of non-randomness can be generated by changing the value of m. The results obtained show that the effect of non-random sampling on the number of alleles and the number of segregating sites is substantially large whereas the effect of non-random sampling on heterozygosity and the average number of nucleotide differences is negligibly small unless non-randomness is extremely large. The effects of non-random sampling on the tests of neutrality were also investigated, and the results obtained indicate that the effect of non-random sampling is stronger on Fu and Li's tests than on Tajima's test.

Type
Research Article
Information
Genetics Research , Volume 66 , Issue 3 , December 1995 , pp. 267 - 276
Copyright
Copyright © Cambridge University Press 1995

References

Ewens, W. J., (1972). The sampling theory of selectively neutral alleles. Theoretical Population Biology 3, 87–112.CrossRefGoogle ScholarPubMed
Fu, Y.-X., & Li, W.-H., (1993). Statistical tests of neutrality of mutations. Genetics 133, 693–709.CrossRefGoogle ScholarPubMed
Hudson, R. R., & Kaplan, N. L., (1986). On the divergence of alleles in nested subsamples from finite populations. Genetics 113, 1057–1076.CrossRefGoogle ScholarPubMed
Kimura, M., (1968). Evolutionary rate at the molecular level. Nature 217, 624–626.CrossRefGoogle ScholarPubMed
Kimura, M., (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Kreitman, M., (1983). Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304, 412–417.CrossRefGoogle ScholarPubMed
Li, W.-H., (1976). Distribution of nucleotide differences between two randomly chosen cistrons in a subdivided population: the finite island model. Theoretical Population Biology 10, 303–308.CrossRefGoogle Scholar
Nei, M., (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590.CrossRefGoogle ScholarPubMed
Nei, M., & Roychoudhury, A. K., (1974). Sampling variances of heterozygosity and genetic distance. Genetics 76, 379–390.CrossRefGoogle ScholarPubMed
Roy, M.S., Geffen, E., Smith, D., Ostrander, E. A., & Wayne, R. K., (1994). Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci. Molecular Biology and Evolution 11, 553–570.Google ScholarPubMed
Slatkin, M., (1987). The average number of sites separating DNA sequences drawn from a subdivided population. Theoretical Population Biology 32, 42–49.CrossRefGoogle ScholarPubMed
Strobeck, C., (1987). Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117, 149–153.CrossRefGoogle Scholar
Tajima, F., (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460.Google ScholarPubMed
Tajima, F., (1989 a). DNA polymorphism in a subdivided population: the expected number of segregating sites in the two subpopulation model. Genetics 123, 229–240.CrossRefGoogle Scholar
Tajima, F. (1989 b). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.CrossRefGoogle ScholarPubMed
Tajima, F., (1990). Relationship between migration and DNA polymorphism in a local population. Genetics 126, 231–234.CrossRefGoogle Scholar
Tajima, F. (1993 a). Measurement of DNA polymorphism. In Mechanisms of Molecular Evolution (ed. Takahata, N., and Clark, A. G.), pp. 37–59. Sunderland, MA: Sinauer Associates.Google Scholar
Tajima, F. (1993 b). Statistical analysis of DNA polymorphism. Japanese Journal of Genetics 68, 567–595.Google Scholar
Watterson, G. A., (1975). On the number of segregating sites in genetic models without recombination. Theoretical Population Biology 7, 256–276.CrossRefGoogle ScholarPubMed