Skip to main content
Genetics logoLink to Genetics
. 2003 Feb;163(2):803–810. doi: 10.1093/genetics/163.2.803

The coalescent and infinite-site model of a small multigene family.

Hideki Innan 1
PMCID: PMC1462437  PMID: 12618415

Abstract

The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage disequilibrium are obtained, and a coalescent-based method for simulating patterns of polymorphism in a small multigene family is developed. The pattern of DNA variation is much more complicated than that in a single-copy gene, which can be simulated by the standard coalescent. Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered.

Full Text

The Full Text of this article is available as a PDF (177.5 KB).

Selected References

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

  1. Araki H., Inomata N., Yamazaki T. Molecular evolution of duplicated amylase gene regions in Drosophila melanogaster: evidence of positive selection in the coding regions and selective constraints in the cis-regulatory regions. Genetics. 2001 Feb;157(2):667–677. doi: 10.1093/genetics/157.2.667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bahlo M. Segregating sites in a gene conversion model with mutation. Theor Popul Biol. 1998 Dec;54(3):243–256. doi: 10.1006/tpbi.1998.1379. [DOI] [PubMed] [Google Scholar]
  3. Bailey Jeffrey A., Gu Zhiping, Clark Royden A., Reinert Knut, Samonte Rhea V., Schwartz Stuart, Adams Mark D., Myers Eugene W., Li Peter W., Eichler Evan E. Recent segmental duplications in the human genome. Science. 2002 Aug 9;297(5583):1003–1007. doi: 10.1126/science.1072047. [DOI] [PubMed] [Google Scholar]
  4. Bettencourt Brian R., Feder Martin E. Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes. J Mol Evol. 2002 May;54(5):569–586. doi: 10.1007/s00239-001-0044-7. [DOI] [PubMed] [Google Scholar]
  5. Fu Y. X., Li W. H. Statistical tests of neutrality of mutations. Genetics. 1993 Mar;133(3):693–709. doi: 10.1093/genetics/133.3.693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Griffiths R. C., Watterson G. A. The number of alleles in multigene families. Theor Popul Biol. 1990 Feb;37(1):110–123. doi: 10.1016/0040-5809(90)90029-u. [DOI] [PubMed] [Google Scholar]
  7. Hey J. A multi-dimensional coalescent process applied to multi-allelic selection models and migration models. Theor Popul Biol. 1991 Feb;39(1):30–48. doi: 10.1016/0040-5809(91)90039-i. [DOI] [PubMed] [Google Scholar]
  8. Hudson R. R., Kreitman M., Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May;116(1):153–159. doi: 10.1093/genetics/116.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hudson R. R. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983 Apr;23(2):183–201. doi: 10.1016/0040-5809(83)90013-8. [DOI] [PubMed] [Google Scholar]
  10. Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969 Apr;61(4):893–903. doi: 10.1093/genetics/61.4.893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. King L. M. The role of gene conversion in determining sequence variation and divergence in the Est-5 gene family in Drosophila pseudoobscura. Genetics. 1998 Jan;148(1):305–315. doi: 10.1093/genetics/148.1.305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lynch M., Conery J. S. The evolutionary fate and consequences of duplicate genes. Science. 2000 Nov 10;290(5494):1151–1155. doi: 10.1126/science.290.5494.1151. [DOI] [PubMed] [Google Scholar]
  13. McDonald J. H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991 Jun 20;351(6328):652–654. doi: 10.1038/351652a0. [DOI] [PubMed] [Google Scholar]
  14. Nagylaki T. The evolution of multigene families under intrachromosomal gene conversion. Genetics. 1984 Mar;106(3):529–548. doi: 10.1093/genetics/106.3.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ohta T. Allelic and nonallelic homology of a supergene family. Proc Natl Acad Sci U S A. 1982 May;79(10):3251–3254. doi: 10.1073/pnas.79.10.3251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ohta T. On the evolution of multigene families. Theor Popul Biol. 1983 Apr;23(2):216–240. doi: 10.1016/0040-5809(83)90015-1. [DOI] [PubMed] [Google Scholar]
  17. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wiuf C., Hein J. The coalescent with gene conversion. Genetics. 2000 May;155(1):451–462. doi: 10.1093/genetics/155.1.451. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES