Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. 2003 Jan; 163(1): 367–374.
PMCID: PMC1462429

Bayesian analysis of genetic differentiation between populations.


We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.

Full Text

The Full Text of this article is available as a PDF (106K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Sillanpä Mikko J, Corander Jukka. Model choice in gene mapping: what and why. Trends Genet. 2002 Jun;18(6):301–307. [PubMed]
  • Tomiuk J, Guldbrandtsen B, Loeschcke V. Population differentiation through mutation and drift--a comparison of genetic identity measures. Genetica. 1998;102-103(1-6):545–558. [PubMed]
  • Uimari P, Sillanpä MJ. Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genet Epidemiol. 2001 Nov;21(3):224–242. [PubMed]
  • Anderson EC, Thompson EA. A model-based method for identifying species hybrids using multilocus genetic data. Genetics. 2002 Mar;160(3):1217–1229. [PMC free article] [PubMed]
  • Ayres KL, Balding DJ. Measuring departures from Hardy-Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity (Edinb) 1998 Jun;80(Pt 6):769–777. [PubMed]
  • Ayres KL, Balding DJ. Measuring gametic disequilibrium from multilocus data. Genetics. 2001 Jan;157(1):413–423. [PMC free article] [PubMed]
  • Dawson KJ, Belkhir K. A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res. 2001 Aug;78(1):59–77. [PubMed]
  • Edwards SV, Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution. 2000 Dec;54(6):1839–1854. [PubMed]
  • Holsinger Kent E, Lewis Paul O, Dey Dipak K. A Bayesian approach to inferring population structure from dominant markers. Mol Ecol. 2002 Jul;11(7):1157–1164. [PubMed]
  • Kitada S, Hayashi T, Kishino H. Empirical Bayes procedure for estimating genetic distance between populations and effective population size. Genetics. 2000 Dec;156(4):2063–2079. [PMC free article] [PubMed]
  • Nagylaki T. Fixation indices in subdivided populations. Genetics. 1998 Mar;148(3):1325–1332. [PMC free article] [PubMed]
  • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000 Jun;155(2):945–959. [PMC free article] [PubMed]
  • Rannala B, Mountain JL. Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9197–9201. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Cited in Books
    Cited in Books
    NCBI Bookshelf books that cite the current articles.
  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles
  • Taxonomy
    Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
  • Taxonomy Tree
    Taxonomy Tree

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...