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1.
Mol Ecol Notes. 2007 Jul 1;7(4):574-578.

Inference of population structure using multilocus genotype data: dominant markers and null alleles.

Abstract

Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.

2.
Genetics. 2003 Aug;164(4):1567-87.

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

Author information

1
Department of Molecular Biology, Max-Planck Institut für Infektionsbiologie, Schumann Strasse 21/22, 10117 Berlin, Germany. falush@mpiib-berlin.mpg.de

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.

PMID:
12930761
PMCID:
PMC1462648
[Indexed for MEDLINE]
Free PMC Article
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3.
Genetics. 2000 Jun;155(2):945-59.

Inference of population structure using multilocus genotype data.

Author information

1
Department of Statistics, University of Oxford, United Kingdom. pritch@tats.ox.ac.uk

Abstract

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.

PMID:
10835412
PMCID:
PMC1461096
[Indexed for MEDLINE]
Free PMC Article
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