Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2002 May;161(1):435–445. doi: 10.1093/genetics/161.1.435

Analysis of multilocus zygotic associations.

Rong-Cai Yang 1
PMCID: PMC1462116  PMID: 12019256

Abstract

While nonrandom associations between zygotes at different loci (zygotic associations) frequently occur in Hardy-Weinberg disequilibrium populations, statistical analysis of such associations has received little attention. In this article, we describe the joint distributions of zygotes at multiple loci, which are completely characterized by heterozygosities at individual loci and various multilocus zygotic associations. These zygotic associations are defined in the same fashion as the usual multilocus linkage (gametic) disequilibria on the basis of gametic and allelic frequencies. The estimation and test procedures are described with details being given for three loci. The sampling properties of the estimates are examined through Monte Carlo simulation. The estimates of three-locus associations are not free of bias due to the presence of two-locus associations and vice versa. The power of detecting the zygotic associations is small unless different loci are strongly associated and/or sample sizes are large (>100). The analysis of zygotic associations not only offers an effective means of packaging numerous genic disequilibria required for a complete characterization of multilocus structure, but also provides opportunities for making inference about evolutionary and demographic processes through a comparative assessment of zygotic association vs. gametic disequilibrium for the same set of loci in nonequilibrium populations.

Full Text

The Full Text of this article is available as a PDF (129.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. BENNETT J. H. On the theory of random mating. Ann Eugen. 1954 Mar;18(4):311–317. doi: 10.1111/j.1469-1809.1952.tb02522.x. [DOI] [PubMed] [Google Scholar]
  2. Barton N. H. Estimating multilocus linkage disequilibria. Heredity (Edinb) 2000 Mar;84(Pt 3):373–389. doi: 10.1046/j.1365-2540.2000.00683.x. [DOI] [PubMed] [Google Scholar]
  3. Brown A. H., Feldman M. W., Nevo E. Multilocus Structure of Natural Populations of HORDEUM SPONTANEUM. Genetics. 1980 Oct;96(2):523–536. doi: 10.1093/genetics/96.2.523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown A. H. Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Popul Biol. 1975 Oct;8(2):184–201. doi: 10.1016/0040-5809(75)90031-3. [DOI] [PubMed] [Google Scholar]
  5. Cockerham C. C., Tachida H. Linkage disequilibria in finite populations. Theor Popul Biol. 1986 Jun;29(3):293–311. doi: 10.1016/0040-5809(86)90012-2. [DOI] [PubMed] [Google Scholar]
  6. Hedrick P. W. Gametic disequilibrium measures: proceed with caution. Genetics. 1987 Oct;117(2):331–341. doi: 10.1093/genetics/117.2.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hill W. G. Tests for association of gene frequencies at several loci in random mating diploid populations. Biometrics. 1975 Dec;31(4):881–888. [PubMed] [Google Scholar]
  8. Lewontin R C. The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. Genetics. 1964 Jan;49(1):49–67. doi: 10.1093/genetics/49.1.49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ota T., Cockerham C. C. Detrimental genes with partial selfing and effects on a neutral locus. Genet Res. 1974 Apr;23(2):191–200. doi: 10.1017/s0016672300014816. [DOI] [PubMed] [Google Scholar]
  10. Pritchard J. K., Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet. 2001 Jun 14;69(1):1–14. doi: 10.1086/321275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Reich D. E., Cargill M., Bolk S., Ireland J., Sabeti P. C., Richter D. J., Lavery T., Kouyoumjian R., Farhadian S. F., Ward R. Linkage disequilibrium in the human genome. Nature. 2001 May 10;411(6834):199–204. doi: 10.1038/35075590. [DOI] [PubMed] [Google Scholar]
  12. Thompson E. A., Deeb S., Walker D., Motulsky A. G. The detection of linkage disequilibrium between closely linked markers: RFLPs at the AI-CIII apolipoprotein genes. Am J Hum Genet. 1988 Jan;42(1):113–124. [PMC free article] [PubMed] [Google Scholar]
  13. Thompson T. Two Brothers with Haemophilia. Proc R Soc Med. 1912;5(SECT):123–123. [PMC free article] [PubMed] [Google Scholar]
  14. Thomson G., Baur M. P. Third order linkage disequilibrium. Tissue Antigens. 1984 Oct;24(4):250–255. doi: 10.1111/j.1399-0039.1984.tb02134.x. [DOI] [PubMed] [Google Scholar]
  15. Weir B. S., Cockerham C. C. Mixed self and random mating at two loci. Genet Res. 1973 Jun;21(3):247–262. doi: 10.1017/s0016672300013446. [DOI] [PubMed] [Google Scholar]
  16. Yang R. C. Zygotic associations and multilocus statistics in a nonequilibrium diploid population. Genetics. 2000 Jul;155(3):1449–1458. doi: 10.1093/genetics/155.3.1449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Zapata C. The D' measure of overall gametic disequilibrium between pairs of multiallelic loci. Evolution. 2000 Oct;54(5):1809–1812. [PubMed] [Google Scholar]
  18. Zaykin D., Zhivotovsky L., Weir B. S. Exact tests for association between alleles at arbitrary numbers of loci. Genetica. 1995;96(1-2):169–178. doi: 10.1007/BF01441162. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES