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. 2000 Nov;156(3):1393–1401. doi: 10.1093/genetics/156.3.1393

Maximum likelihood estimation of recombination rates from population data.

M K Kuhner 1, J Yamato 1, J Felsenstein 1
PMCID: PMC1461317  PMID: 11063710

Abstract

We describe a method for co-estimating r = C/mu (where C is the per-site recombination rate and mu is the per-site neutral mutation rate) and Theta = 4N(e)mu (where N(e) is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Theta are accurate and apparently unbiased for a wide range of parameter values. However, when both Theta and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.

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Selected References

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  1. Felsenstein J., Churchill G. A. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93–104. doi: 10.1093/oxfordjournals.molbev.a025575. [DOI] [PubMed] [Google Scholar]
  2. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. doi: 10.1007/BF01734359. [DOI] [PubMed] [Google Scholar]
  3. Fu Y. X. A phylogenetic estimator of effective population size or mutation rate. Genetics. 1994 Feb;136(2):685–692. doi: 10.1093/genetics/136.2.685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fukami-Kobayashi K., Tateno Y. Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J Mol Evol. 1991 Jan;32(1):79–91. doi: 10.1007/BF02099932. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. Kuhner M. K., Beerli P., Yamato J., Felsenstein J. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics. 2000 Sep;156(1):439–447. doi: 10.1093/genetics/156.1.439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Kuhner M. K., Yamato J., Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 1998 May;149(1):429–434. doi: 10.1093/genetics/149.1.429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nickerson D. A., Taylor S. L., Weiss K. M., Clark A. G., Hutchinson R. G., Stengård J., Salomaa V., Vartiainen E., Boerwinkle E., Sing C. F. DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet. 1998 Jul;19(3):233–240. doi: 10.1038/907. [DOI] [PubMed] [Google Scholar]
  13. 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]

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