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. 2000 Feb;154(2):923–929. doi: 10.1093/genetics/154.2.923

Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.

M Nordborg 1
PMCID: PMC1460950  PMID: 10655241

Abstract

It is shown that partial self-fertilization can be introduced into neutral population genetic models with recombination as a simple change in the scaling of the parameters. This means that statistical and computational methods that have been developed under the assumption of random mating can be used without modification, provided the appropriate parameter changes are made. An important prediction is that all forms of linkage disequilibrium will be more extensive in selfing species. The implications of this are discussed.

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Selected References

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  1. Andolfatto P., Nordborg M. The effect of gene conversion on intralocus associations. Genetics. 1998 Mar;148(3):1397–1399. doi: 10.1093/genetics/148.3.1397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Clark A. G., Weiss K. M., Nickerson D. A., Taylor S. L., Buchanan A., Stengård J., Salomaa V., Vartiainen E., Perola M., Boerwinkle E. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet. 1998 Aug;63(2):595–612. doi: 10.1086/301977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Conway D. J., Roper C., Oduola A. M., Arnot D. E., Kremsner P. G., Grobusch M. P., Curtis C. F., Greenwood B. M. High recombination rate in natural populations of Plasmodium falciparum. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4506–4511. doi: 10.1073/pnas.96.8.4506. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Donnelly P., Tavaré S. Coalescents and genealogical structure under neutrality. Annu Rev Genet. 1995;29:401–421. doi: 10.1146/annurev.ge.29.120195.002153. [DOI] [PubMed] [Google Scholar]
  5. Dye C., Williams B. G. Multigenic drug resistance among inbred malaria parasites. Proc Biol Sci. 1997 Jan 22;264(1378):61–67. doi: 10.1098/rspb.1997.0009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Golding G. B., Strobeck C. Linkage disequilibrium in a finite population that is partially selfing. Genetics. 1980 Mar;94(3):777–789. doi: 10.1093/genetics/94.3.777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Griffiths R. C., Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol. 1996 Winter;3(4):479–502. doi: 10.1089/cmb.1996.3.479. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Hudson R. R., Kaplan N. L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985 Sep;111(1):147–164. doi: 10.1093/genetics/111.1.147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet. 1999 Jun;22(2):139–144. doi: 10.1038/9642. [DOI] [PubMed] [Google Scholar]
  12. Liu F., Charlesworth D., Kreitman M. The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics. 1999 Jan;151(1):343–357. doi: 10.1093/genetics/151.1.343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Milligan B. G. Estimating long-term mating systems using DNA sequences. Genetics. 1996 Feb;142(2):619–627. doi: 10.1093/genetics/142.2.619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nordborg M., Donnelly P. The coalescent process with selfing. Genetics. 1997 Jul;146(3):1185–1195. doi: 10.1093/genetics/146.3.1185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pluzhnikov A., Donnelly P. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics. 1996 Nov;144(3):1247–1262. doi: 10.1093/genetics/144.3.1247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Pollak E. On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics. 1987 Oct;117(2):353–360. doi: 10.1093/genetics/117.2.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Watterson G. A. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975 Apr;7(2):256–276. doi: 10.1016/0040-5809(75)90020-9. [DOI] [PubMed] [Google Scholar]
  19. Wiuf C., Donnelly P. Conditional genealogies and the age of a neutral mutant. Theor Popul Biol. 1999 Oct;56(2):183–201. doi: 10.1006/tpbi.1998.1411. [DOI] [PubMed] [Google Scholar]
  20. Wiuf C., Hein J. Recombination as a point process along sequences. Theor Popul Biol. 1999 Jun;55(3):248–259. doi: 10.1006/tpbi.1998.1403. [DOI] [PubMed] [Google Scholar]

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