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. 1996 Feb;142(2):629–639. doi: 10.1093/genetics/142.2.629

Hierarchical Analysis of Nucleotide Diversity in Geographically Structured Populations

K E Holsinger 1, R J Mason-Gamer 1
PMCID: PMC1206994  PMID: 8852859

Abstract

Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of NEI's nucleotide diversity statistics and show that our modification has the same properties as WRIGHT's F(ST). We compare its statistical properties with several other F(ST) estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

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Selected References

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  1. Birky C. W., Jr, Fuerst P., Maruyama T. Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics. 1989 Mar;121(3):613–627. doi: 10.1093/genetics/121.3.613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Birky C. W., Jr, Maruyama T., Fuerst P. An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics. 1983 Mar;103(3):513–527. doi: 10.1093/genetics/103.3.513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cockerham C. C. Analyses of gene frequencies. Genetics. 1973 Aug;74(4):679–700. doi: 10.1093/genetics/74.4.679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Excoffier L., Smouse P. E., Quattro J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992 Jun;131(2):479–491. doi: 10.1093/genetics/131.2.479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Felsenstein J. How can we infer geography and history from gene frequencies? J Theor Biol. 1982 May 7;96(1):9–20. doi: 10.1016/0022-5193(82)90152-7. [DOI] [PubMed] [Google Scholar]
  6. Long J. C. The allelic correlation structure of Gainj- and Kalam-speaking people. I. The estimation and interpretation of Wright's F-statistics. Genetics. 1986 Mar;112(3):629–647. doi: 10.1093/genetics/112.3.629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lynch M., Crease T. J. The analysis of population survey data on DNA sequence variation. Mol Biol Evol. 1990 Jul;7(4):377–394. doi: 10.1093/oxfordjournals.molbev.a040607. [DOI] [PubMed] [Google Scholar]
  8. Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321–3323. doi: 10.1073/pnas.70.12.3321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Nei M., Chesser R. K. Estimation of fixation indices and gene diversities. Ann Hum Genet. 1983 Jul;47(Pt 3):253–259. doi: 10.1111/j.1469-1809.1983.tb00993.x. [DOI] [PubMed] [Google Scholar]
  10. Nei M. Evolution of human races at the gene level. Prog Clin Biol Res. 1982;103(Pt A):167–181. [PubMed] [Google Scholar]
  11. Nei M., Miller J. C. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 1990 Aug;125(4):873–879. doi: 10.1093/genetics/125.4.873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nei M., Tajima F. DNA polymorphism detectable by restriction endonucleases. Genetics. 1981 Jan;97(1):145–163. doi: 10.1093/genetics/97.1.145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Notohara M. The coalescent and the genealogical process in geographically structured population. J Math Biol. 1990;29(1):59–75. doi: 10.1007/BF00173909. [DOI] [PubMed] [Google Scholar]
  14. Saghai-Maroof M. A., Soliman K. M., Jorgensen R. A., Allard R. W. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014–8018. doi: 10.1073/pnas.81.24.8014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Slatkin M. Inbreeding coefficients and coalescence times. Genet Res. 1991 Oct;58(2):167–175. doi: 10.1017/s0016672300029827. [DOI] [PubMed] [Google Scholar]
  16. Takahata N., Palumbi S. R. Extranuclear differentiation and gene flow in the finite island model. Genetics. 1985 Feb;109(2):441–457. doi: 10.1093/genetics/109.2.441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Weir B. S., Basten C. J. Sampling strategies for distances between DNA sequences. Biometrics. 1990 Sep;46(3):551–582. [PubMed] [Google Scholar]
  18. Whittemore A. T., Schaal B. A. Interspecific gene flow in sympatric oaks. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2540–2544. doi: 10.1073/pnas.88.6.2540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Wolfe K. H., Li W. H., Sharp P. M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054–9058. doi: 10.1073/pnas.84.24.9054. [DOI] [PMC free article] [PubMed] [Google Scholar]

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