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. 2003 Jan;163(1):411–420. doi: 10.1093/genetics/163.1.411

Polymorphism and divergence for island-model species.

John Wakeley 1
PMCID: PMC1462400  PMID: 12586726

Abstract

Estimates of the scaled selection coefficient, gamma of Sawyer and Hartl, are shown to be remarkably robust to population subdivision. Estimates of mutation parameters and divergence times, in contrast, are very sensitive to subdivision. These results follow from an analysis of natural selection and genetic drift in the island model of subdivision in the limit of a very large number of subpopulations, or demes. In particular, a diffusion process is shown to hold for the average allele frequency among demes in which the level of subdivision sets the timescale of drift and selection and determines the dynamic equilibrium of allele frequencies among demes. This provides a framework for inference about mutation, selection, divergence, and migration when data are available from a number of unlinked nucleotide sites. The effects of subdivision on parameter estimates depend on the distribution of samples among demes. If samples are taken singly from different demes, the only effect of subdivision is in the rescaling of mutation and divergence-time parameters. If multiple samples are taken from one or more demes, high levels of within-deme relatedness lead to low levels of intraspecies polymorphism and increase the number of fixed differences between samples from two species. If subdivision is ignored, mutation parameters are underestimated and the species divergence time is overestimated, sometimes quite drastically. Estimates of the strength of selection are much less strongly affected and always in a conservative direction.

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Selected References

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  1. Akashi H. Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics. 1999 Jan;151(1):221–238. doi: 10.1093/genetics/151.1.221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bustamante C. D., Wakeley J., Sawyer S., Hartl D. L. Directional selection and the site-frequency spectrum. Genetics. 2001 Dec;159(4):1779–1788. doi: 10.1093/genetics/159.4.1779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bustamante Carlos D., Nielsen Rasmus, Sawyer Stanley A., Olsen Kenneth M., Purugganan Michael D., Hartl Daniel L. The cost of inbreeding in Arabidopsis. Nature. 2002 Apr 4;416(6880):531–534. doi: 10.1038/416531a. [DOI] [PubMed] [Google Scholar]
  4. Cherry Joshua L., Wakeley John. A diffusion approximation for selection and drift in a subdivided population. Genetics. 2003 Jan;163(1):421–428. doi: 10.1093/genetics/163.1.421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Donnelly P., Nordborg M., Joyce P. Likelihoods and simulation methods for a class of nonneutral population genetics models. Genetics. 2001 Oct;159(2):853–867. doi: 10.1093/genetics/159.2.853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fay Justin C., Wyckoff Gerald J., Wu Chung-I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature. 2002 Feb 28;415(6875):1024–1026. doi: 10.1038/4151024a. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Hartl D. L., Moriyama E. N., Sawyer S. A. Selection intensity for codon bias. Genetics. 1994 Sep;138(1):227–234. doi: 10.1093/genetics/138.1.227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Maruyama T. Effective number of alleles in a subdivided population. Theor Popul Biol. 1970 Nov;1(3):273–306. doi: 10.1016/0040-5809(70)90047-x. [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 strong-migration limit in geographically structured populations. J Math Biol. 1980 Apr;9(2):101–114. doi: 10.1007/BF00275916. [DOI] [PubMed] [Google Scholar]
  15. Neuhauser C., Krone S. M. The genealogy of samples in models with selection. Genetics. 1997 Feb;145(2):519–534. doi: 10.1093/genetics/145.2.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity (Edinb) 2001 Jun;86(Pt 6):641–647. doi: 10.1046/j.1365-2540.2001.00895.x. [DOI] [PubMed] [Google Scholar]
  17. Nordborg M. Structured coalescent processes on different time scales. Genetics. 1997 Aug;146(4):1501–1514. doi: 10.1093/genetics/146.4.1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rannala B. The Sampling Theory of Neutral Alleles in an Island Population of Fluctuating Size. Theor Popul Biol. 1996 Aug;50(1):91–104. doi: 10.1006/tpbi.1996.0024. [DOI] [PubMed] [Google Scholar]
  19. Rothman E. D., Sing C. F., Templeton A. R. A model for analysis of population structure. Genetics. 1974 Nov;78(3):943–960. doi: 10.1093/genetics/78.3.943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sawyer S. A., Hartl D. L. Population genetics of polymorphism and divergence. Genetics. 1992 Dec;132(4):1161–1176. doi: 10.1093/genetics/132.4.1161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Slatkin M., Bertorelle G. The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics. 2001 Jun;158(2):865–874. doi: 10.1093/genetics/158.2.865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Smith Nick G. C., Eyre-Walker Adam. Adaptive protein evolution in Drosophila. Nature. 2002 Feb 28;415(6875):1022–1024. doi: 10.1038/4151022a. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Wakeley J., Aliacar N. Gene genealogies in a metapopulation. Genetics. 2001 Oct;159(2):893–905. doi: 10.1093/genetics/159.2.893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Wakeley J. Nonequilibrium migration in human history. Genetics. 1999 Dec;153(4):1863–1871. doi: 10.1093/genetics/153.4.1863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wakeley J. The coalescent in an island model of population subdivision with variation among demes. Theor Popul Biol. 2001 Mar;59(2):133–144. doi: 10.1006/tpbi.2000.1495. [DOI] [PubMed] [Google Scholar]
  27. Wright S. Evolution in Mendelian Populations. Genetics. 1931 Mar;16(2):97–159. doi: 10.1093/genetics/16.2.97. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998 May;15(5):568–573. doi: 10.1093/oxfordjournals.molbev.a025957. [DOI] [PubMed] [Google Scholar]

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