Abstract
A method for estimating the selfing rate using DNA sequence data was recently proposed by Milligan. Unfortunately, a number of errors make interpretation of his results problematic. In the present paper we first show how the usual coalescent process can be adapted to models that include selfing, and then use this result to find moment estimators as well as the likelihood surface for the selfing rate, s, and the scaled mutation rate, θ. We conclude that, regardless of the method used, large sample sizes are necessary to estimate s with any degree of certainty, and that the estimate is always highly sensitive to recent changes in the true value.
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Selected References
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- Brown A. H., Allard R. W. Estimation of the mating system in open-pollinated maize populations using isozyme polymorphisms. Genetics. 1970 Sep;66(1):133–145. doi: 10.1093/genetics/66.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Charlesworth B., Morgan M. T., Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993 Aug;134(4):1289–1303. doi: 10.1093/genetics/134.4.1289. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Griffiths R. C., Tavaré S. Sampling theory for neutral alleles in a varying environment. Philos Trans R Soc Lond B Biol Sci. 1994 Jun 29;344(1310):403–410. doi: 10.1098/rstb.1994.0079. [DOI] [PubMed] [Google Scholar]
- Hudson R. R., Kaplan N. L. The coalescent process in models with selection and recombination. Genetics. 1988 Nov;120(3):831–840. doi: 10.1093/genetics/120.3.831. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kaplan N. L., Darden T., Hudson R. R. The coalescent process in models with selection. Genetics. 1988 Nov;120(3):819–829. doi: 10.1093/genetics/120.3.819. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kaplan N. L., Hudson R. R., Langley C. H. The "hitchhiking effect" revisited. Genetics. 1989 Dec;123(4):887–899. doi: 10.1093/genetics/123.4.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kuhner M. K., Yamato J., Felsenstein J. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics. 1995 Aug;140(4):1421–1430. doi: 10.1093/genetics/140.4.1421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smith J. M., Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974 Feb;23(1):23–35. [PubMed] [Google Scholar]
- Stewart F. M. Variability in the amount of heterozygosity maintained by neutral mutations. Theor Popul Biol. 1976 Apr;9(2):188–201. doi: 10.1016/0040-5809(76)90044-7. [DOI] [PubMed] [Google Scholar]