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.
Full Text
The Full Text of this article is available as a PDF (245.4 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Balding D. J., Nichols R. A. A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica. 1995;96(1-2):3–12. doi: 10.1007/BF01441146. [DOI] [PubMed] [Google Scholar]
- Balding D. J., Nichols R. A. DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci Int. 1994 Feb;64(2-3):125–140. doi: 10.1016/0379-0738(94)90222-4. [DOI] [PubMed] [Google Scholar]
- Bowcock A. M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J. R., Cavalli-Sforza L. L. High resolution of human evolutionary trees with polymorphic microsatellites. Nature. 1994 Mar 31;368(6470):455–457. doi: 10.1038/368455a0. [DOI] [PubMed] [Google Scholar]
- Davies N, Villablanca FX, Roderick GK. Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics. Trends Ecol Evol. 1999 Jan;14(1):17–21. doi: 10.1016/s0169-5347(98)01530-4. [DOI] [PubMed] [Google Scholar]
- Ewens W. J., Spielman R. S. The transmission/disequilibrium test: history, subdivision, and admixture. Am J Hum Genet. 1995 Aug;57(2):455–464. [PMC free article] [PubMed] [Google Scholar]
- Goldstein D. B., Pollock D. D. Launching microsatellites: a review of mutation processes and methods of phylogenetic interference. J Hered. 1997 Sep-Oct;88(5):335–342. doi: 10.1093/oxfordjournals.jhered.a023114. [DOI] [PubMed] [Google Scholar]
- Jorde L. B., Bamshad M. J., Watkins W. S., Zenger R., Fraley A. E., Krakowiak P. A., Carpenter K. D., Soodyall H., Jenkins T., Rogers A. R. Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am J Hum Genet. 1995 Sep;57(3):523–538. doi: 10.1002/ajmg.1320570340. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mountain J. L., Cavalli-Sforza L. L. Multilocus genotypes, a tree of individuals, and human evolutionary history. Am J Hum Genet. 1997 Sep;61(3):705–718. doi: 10.1086/515510. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Paetkau D., Calvert W., Stirling I., Strobeck C. Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol. 1995 Jun;4(3):347–354. doi: 10.1111/j.1365-294x.1995.tb00227.x. [DOI] [PubMed] [Google Scholar]
- Parra E. J., Marcini A., Akey J., Martinson J., Batzer M. A., Cooper R., Forrester T., Allison D. B., Deka R., Ferrell R. E. Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet. 1998 Dec;63(6):1839–1851. doi: 10.1086/302148. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pritchard J. K., Rosenberg N. A. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet. 1999 Jul;65(1):220–228. doi: 10.1086/302449. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rannala B., Mountain J. L. Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9197–9201. doi: 10.1073/pnas.94.17.9197. [DOI] [PMC free article] [PubMed] [Google Scholar]