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Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.

Pubmed ID: 12930761


  • Falush D
  • Stephens M
  • Pritchard JK



Publication Data

August 21, 2003

Associated Grants

  • Agency: NIGMS NIH HHS, Id: F32 GM019634
  • Agency: NHLBI NIH HHS, Id: HL 54485
  • Agency: NHLBI NIH HHS, Id: HL 54512

Mesh Terms

  • African Continental Ancestry Group
  • Algorithms
  • Alleles
  • Animals
  • Bayes Theorem
  • Chromosomes
  • Computer Simulation
  • Drosophila melanogaster
  • Evolution, Molecular
  • Female
  • Gene Frequency
  • Genetic Drift
  • Genetic Linkage
  • Genetic Markers
  • Genetics, Population
  • Genotype
  • Helicobacter pylori
  • Humans
  • Male
  • Markov Chains
  • Models, Genetic
  • Monte Carlo Method
  • Recombination, Genetic