Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2001 Jun;158(2):885–896. doi: 10.1093/genetics/158.2.885

Distinguishing migration from isolation: a Markov chain Monte Carlo approach.

R Nielsen 1, J Wakeley 1
PMCID: PMC1461674  PMID: 11404349

Abstract

A Markov chain Monte Carlo method for estimating the relative effects of migration and isolation on genetic diversity in a pair of populations from DNA sequence data is developed and tested using simulations. The two populations are assumed to be descended from a panmictic ancestral population at some time in the past and may (or may not) after that be connected by migration. The use of a Markov chain Monte Carlo method allows the joint estimation of multiple demographic parameters in either a Bayesian or a likelihood framework. The parameters estimated include the migration rate for each population, the time since the two populations diverged from a common ancestral population, and the relative size of each of the two current populations and of the common ancestral population. The results show that even a single nonrecombining genetic locus can provide substantial power to test the hypothesis of no ongoing migration and/or to test models of symmetric migration between the two populations. The use of the method is illustrated in an application to mitochondrial DNA sequence data from a fish species: the threespine stickleback (Gasterosteus aculeatus).

Full Text

The Full Text of this article is available as a PDF (315.3 KB).

Selected References

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

  1. Bahlo M., Griffiths R. C. Inference from gene trees in a subdivided population. Theor Popul Biol. 2000 Mar;57(2):79–95. doi: 10.1006/tpbi.1999.1447. [DOI] [PubMed] [Google Scholar]
  2. Beerli P., Felsenstein J. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics. 1999 Jun;152(2):763–773. doi: 10.1093/genetics/152.2.763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brooks A. S., Wood B. Palaeoanthropology. The Chinese side of the story. Nature. 1990 Mar 22;344(6264):288–289. doi: 10.1038/344288a0. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. Nielsen R. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics. 2000 Feb;154(2):931–942. doi: 10.1093/genetics/154.2.931. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Nielsen R. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theor Popul Biol. 1998 Apr;53(2):143–151. doi: 10.1006/tpbi.1997.1348. [DOI] [PubMed] [Google Scholar]
  8. Nielsen R., Palsbøll P. J. Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size. Mol Phylogenet Evol. 1999 Apr;11(3):477–484. doi: 10.1006/mpev.1998.0597. [DOI] [PubMed] [Google Scholar]
  9. Nielsen R., Slatkin M. Likelihood analysis of ongoing gene flow and historical association. Evolution. 2000 Feb;54(1):44–50. doi: 10.1111/j.0014-3820.2000.tb00006.x. [DOI] [PubMed] [Google Scholar]
  10. Stringer C. B., Andrews P. Genetic and fossil evidence for the origin of modern humans. Science. 1988 Mar 11;239(4845):1263–1268. doi: 10.1126/science.3125610. [DOI] [PubMed] [Google Scholar]
  11. Tavaré S. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor Popul Biol. 1984 Oct;26(2):119–164. doi: 10.1016/0040-5809(84)90027-3. [DOI] [PubMed] [Google Scholar]
  12. Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
  13. Wakeley J. Distinguishing migration from isolation using the variance of pairwise differences. Theor Popul Biol. 1996 Jun;49(3):369–386. doi: 10.1006/tpbi.1996.0018. [DOI] [PubMed] [Google Scholar]
  14. Wakeley J., Hey J. Estimating ancestral population parameters. Genetics. 1997 Mar;145(3):847–855. doi: 10.1093/genetics/145.3.847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wakeley J. The variance of pairwise nucleotide differences in two populations with migration. Theor Popul Biol. 1996 Feb;49(1):39–57. doi: 10.1006/tpbi.1996.0002. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Wilson I. J., Balding D. J. Genealogical inference from microsatellite data. Genetics. 1998 Sep;150(1):499–510. doi: 10.1093/genetics/150.1.499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wolpoff M. H. Interpretations of multiregional evolution. Science. 1996 Nov 1;274(5288):704–707. doi: 10.1126/science.274.5288.704d. [DOI] [PubMed] [Google Scholar]
  19. 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]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES