Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1999 Jun;152(2):763–773. doi: 10.1093/genetics/152.2.763

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.

P Beerli 1, J Felsenstein 1
PMCID: PMC1460627  PMID: 10353916

Abstract

A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/.

Full Text

The Full Text of this article is available as a PDF (205.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  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. Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method. Genet Res. 1992 Dec;60(3):209–220. doi: 10.1017/s0016672300030962. [DOI] [PubMed] [Google Scholar]
  3. Felsenstein J. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet. 1973 Sep;25(5):471–492. [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Hudson R. R., Slatkin M., Maddison W. P. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992 Oct;132(2):583–589. doi: 10.1093/genetics/132.2.583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol. 1989 Aug;29(2):170–179. doi: 10.1007/BF02100115. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. Nath H. B., Griffiths R. C. Estimation in an island model using simulation. Theor Popul Biol. 1996 Dec;50(3):227–253. doi: 10.1006/tpbi.1996.0030. [DOI] [PubMed] [Google Scholar]
  11. Nath H. B., Griffiths R. C. The coalescent in two colonies with symmetric migration. J Math Biol. 1993;31(8):841–851. doi: 10.1007/BF00168049. [DOI] [PubMed] [Google Scholar]
  12. Nei M., Feldman M. W. Identity of genes by descent within and between populations under mutation and migration pressures. Theor Popul Biol. 1972 Dec;3(4):460–465. doi: 10.1016/0040-5809(72)90017-2. [DOI] [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. Rannala B., Hartigan J. A. Estimating gene flow in island populations. Genet Res. 1996 Apr;67(2):147–158. doi: 10.1017/s0016672300033607. [DOI] [PubMed] [Google Scholar]
  15. Slatkin M., Hudson R. R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991 Oct;129(2):555–562. doi: 10.1093/genetics/129.2.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Slatkin M., Maddison W. P. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics. 1989 Nov;123(3):603–613. doi: 10.1093/genetics/123.3.603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Takahata N., Slatkin M. Genealogy of neutral genes in two partially isolated populations. Theor Popul Biol. 1990 Dec;38(3):331–350. doi: 10.1016/0040-5809(90)90018-q. [DOI] [PubMed] [Google Scholar]
  18. Tufto J., Engen S., Hindar K. Inferring patterns of migration from gene frequencies under equilibrium conditions. Genetics. 1996 Dec;144(4):1911–1921. doi: 10.1093/genetics/144.4.1911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Wakeley J. Segregating sites in Wright's island model. Theor Popul Biol. 1998 Apr;53(2):166–174. doi: 10.1006/tpbi.1997.1355. [DOI] [PubMed] [Google Scholar]
  20. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 1994 Sep;39(3):306–314. doi: 10.1007/BF00160154. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES