The Estimation of the Number and the Length Distribution of Gene Conversion Tracts from Population DNA Sequence Data (original) (raw)

Abstract

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: ψ, which measures the probability of detecting a converted site, and φ, the parameter of the geometric distribution, from which the average true tract length, 1/(1 - φ), can be estimated. Expressions are provided for estimating φ by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of φ for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.

Full Text

The Full Text of this article is available as a PDF (3.9 MB).

Selected References

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

  1. Chovnick A. Gene conversion and transfer of genetic information within the inverted region of inversion heterozygotes. Genetics. 1973 Sep;75(1):123–131. doi: 10.1093/genetics/75.1.123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Hammer M. F., Bliss S., Silver L. M. Genetic exchange across a paracentric inversion of the mouse t complex. Genetics. 1991 Aug;128(4):799–812. doi: 10.1093/genetics/128.4.799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Hilliker A. J., Clark S. H., Chovnick A. The effect of DNA sequence polymorphisms on intragenic recombination in the rosy locus of Drosophila melanogaster. Genetics. 1991 Nov;129(3):779–781. doi: 10.1093/genetics/129.3.779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hudson R. R. Estimating the recombination parameter of a finite population model without selection. Genet Res. 1987 Dec;50(3):245–250. doi: 10.1017/s0016672300023776. [DOI] [PubMed] [Google Scholar]
  5. Popadić A., Anderson W. W. Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura. Mol Biol Evol. 1995 Jul;12(4):564–572. doi: 10.1093/oxfordjournals.molbev.a040236. [DOI] [PubMed] [Google Scholar]
  6. Riley M. A., Kaplan S. R., Veuille M. Nucleotide polymorphism at the xanthine dehydrogenase locus in Drosophila pseudoobscura. Mol Biol Evol. 1992 Jan;9(1):56–69. doi: 10.1093/oxfordjournals.molbev.a040708. [DOI] [PubMed] [Google Scholar]
  7. Rozas J., Aguadé M. Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11517–11521. doi: 10.1073/pnas.91.24.11517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Sawyer S. Statistical tests for detecting gene conversion. Mol Biol Evol. 1989 Sep;6(5):526–538. doi: 10.1093/oxfordjournals.molbev.a040567. [DOI] [PubMed] [Google Scholar]
  9. Slightom J. L., Blechl A. E., Smithies O. Human fetal G gamma- and A gamma-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell. 1980 Oct;21(3):627–638. doi: 10.1016/0092-8674(80)90426-2. [DOI] [PubMed] [Google Scholar]
  10. Stephens J. C. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol Biol Evol. 1985 Nov;2(6):539–556. doi: 10.1093/oxfordjournals.molbev.a040371. [DOI] [PubMed] [Google Scholar]