Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

Genetics - Tập 164 Số 4 - Trang 1567-1587 - 2003
Daniel Falush1, Matthew Stephens2, Jonathan K. Pritchard3
1Department of Molecular Biology, Max-Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
2Department of Statistics, University of Washington, Seattle, Washington, 98195
3Department of Human Genetics, University of Chicago, Chicago, Illinois 60637

Tóm tắt

Abstract 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.

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Genetics

Tập 164 Số 4

1567-1587

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