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. 1996 Jun;143(2):1033–1042. doi: 10.1093/genetics/143.2.1033

A Population Genetic Study of the Evolution of Sines. II. Sequence Evolution under the Master Copy Model

H Tachida 1
PMCID: PMC1207321  PMID: 8725248

Abstract

A transient population genetic model of SINE (short interspersed repetitive element) evolution assuming the master copy model is theoretically investigated. Means and variances of consensus frequency of nucleotides, nucleotide homozygosity, and the number of shared differences that are considered to have caused by mutations occurring in the master copy lineages are computed. All quantities investigated are shown to be monotone functions of the duration of the expansion period. Thus, they can be used to estimate the expansion period although their sampling variances are generally large. Using the theoretical results, the Sb subfamily of human Alu sequences is analyzed. First, the expansion period is estimated from the observed mean and variance of homozygosity. The expansion period is shown to be short compared to the time since the end of the expansion of the subfamily. However, the observed number of the shared differences is more than twice that expected under the master copy model with the estimated expansion period. Alternative models including that with multiple master copy loci to explain this observation are discussed.

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Selected References

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  1. Bailey W. J., Hayasaka K., Skinner C. G., Kehoe S., Sieu L. C., Slightom J. L., Goodman M. Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster. Mol Phylogenet Evol. 1992 Jun;1(2):97–135. doi: 10.1016/1055-7903(92)90024-b. [DOI] [PubMed] [Google Scholar]
  2. Batzer M. A., Kilroy G. E., Richard P. E., Shaikh T. H., Desselle T. D., Hoppens C. L., Deininger P. L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. doi: 10.1093/nar/18.23.6793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blake R. D., Hess S. T., Nicholson-Tuell J. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J Mol Evol. 1992 Mar;34(3):189–200. doi: 10.1007/BF00162968. [DOI] [PubMed] [Google Scholar]
  4. Britten R. J., Baron W. F., Stout D. B., Davidson E. H. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770–4774. doi: 10.1073/pnas.85.13.4770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Britten R. J. Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):6148–6150. doi: 10.1073/pnas.91.13.6148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Britten R. J. Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5992–5996. doi: 10.1073/pnas.91.13.5992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brookfield J. F. The generation of sequence similarity in SINEs and LINEs. Trends Genet. 1993 Feb;9(2):38–39. doi: 10.1016/0168-9525(93)90172-E. [DOI] [PubMed] [Google Scholar]
  8. Hammer M. F. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol. 1994 Sep;11(5):749–761. doi: 10.1093/oxfordjournals.molbev.a040155. [DOI] [PubMed] [Google Scholar]
  9. Horsthemke B., Beisiegel U., Dunning A., Havinga J. R., Williamson R., Humphries S. Unequal crossing-over between two alu-repetitive DNA sequences in the low-density-lipoprotein-receptor gene. A possible mechanism for the defect in a patient with familial hypercholesterolaemia. Eur J Biochem. 1987 Apr 1;164(1):77–81. doi: 10.1111/j.1432-1033.1987.tb10995.x. [DOI] [PubMed] [Google Scholar]
  10. Jurka J., Milosavljevic A. Reconstruction and analysis of human Alu genes. J Mol Evol. 1991 Feb;32(2):105–121. doi: 10.1007/BF02515383. [DOI] [PubMed] [Google Scholar]
  11. Jurka J., Smith T. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4775–4778. doi: 10.1073/pnas.85.13.4775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. KIMURA M., CROW J. F. THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION. Genetics. 1964 Apr;49:725–738. doi: 10.1093/genetics/49.4.725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kass D. H., Batzer M. A., Deininger P. L. Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution. Mol Cell Biol. 1995 Jan;15(1):19–25. doi: 10.1128/mcb.15.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kido Y., Himberg M., Takasaki N., Okada N. Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae. J Mol Biol. 1994 Sep 2;241(5):633–644. doi: 10.1006/jmbi.1994.1540. [DOI] [PubMed] [Google Scholar]
  15. Kimura M. Evolutionary rate at the molecular level. Nature. 1968 Feb 17;217(5129):624–626. doi: 10.1038/217624a0. [DOI] [PubMed] [Google Scholar]
  16. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989 Apr 11;17(7):2477–2491. doi: 10.1093/nar/17.7.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Leeflang E. P., Liu W. M., Hashimoto C., Choudary P. V., Schmid C. W. Phylogenetic evidence for multiple Alu source genes. J Mol Evol. 1992 Jul;35(1):7–16. doi: 10.1007/BF00160256. [DOI] [PubMed] [Google Scholar]
  18. Lehrman M. A., Goldstein J. L., Russell D. W., Brown M. S. Duplication of seven exons in LDL receptor gene caused by Alu-Alu recombination in a subject with familial hypercholesterolemia. Cell. 1987 Mar 13;48(5):827–835. doi: 10.1016/0092-8674(87)90079-1. [DOI] [PubMed] [Google Scholar]
  19. Maruyama T. The average number and the variance of generations at particular gene frequency in the course of fixation of a mutant gene in a finite population. Genet Res. 1972 Apr;19(2):109–113. doi: 10.1017/s0016672300014324. [DOI] [PubMed] [Google Scholar]
  20. Matera A. G., Hellmann U., Hintz M. F., Schmid C. W. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. doi: 10.1093/nar/18.20.6019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ohta T. Population genetics of an expanding family of mobile genetic elements. Genetics. 1986 May;113(1):145–159. doi: 10.1093/genetics/113.1.145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Okada N. SINEs. Curr Opin Genet Dev. 1991 Dec;1(4):498–504. doi: 10.1016/s0959-437x(05)80198-4. [DOI] [PubMed] [Google Scholar]
  23. Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 1988;27(3):194–202. doi: 10.1007/BF02100074. [DOI] [PubMed] [Google Scholar]
  24. Shen M. R., Batzer M. A., Deininger P. L. Evolution of the master Alu gene(s). J Mol Evol. 1991 Oct;33(4):311–320. doi: 10.1007/BF02102862. [DOI] [PubMed] [Google Scholar]
  25. Takahata N. Relaxed natural selection in human populations during the Pleistocene. Jpn J Genet. 1993 Dec;68(6):539–547. doi: 10.1266/jjg.68.539. [DOI] [PubMed] [Google Scholar]
  26. Takahata N. Repeated failures that led to the eventual success in human evolution. Mol Biol Evol. 1994 Sep;11(5):803–805. doi: 10.1093/oxfordjournals.molbev.a040160. [DOI] [PubMed] [Google Scholar]

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