A genealogical interpretation of principal components analysis.

Journal article

Principal components analysis, PCA, is a statistical method commonly used in population genetics to identify structure in the distribution of genetic variation across geographical location and ethnic background. However, while the method is often used to inform about historical demographic processes, little is known about the relationship between fundamental demographic parameters and the projection of samples onto the primary axes. Here I show that for SNP data the projection of samples onto the principal components can be obtained directly from considering the average coalescent times between pairs of haploid genomes. The result provides a framework for interpreting PCA projections in terms of underlying processes, including migration, geographical isolation, and admixture. I also demonstrate a link between PCA and Wrightandapos;s f_ST and show that SNP ascertainment has a largely simple and predictable effect on the projection of samples. Using examples from human genetics, I discuss the application of these results to empirical data and the implications for inference.

Authors: McVean, G

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Public Library of Science
• Journal: PLoS genetics
• Volume: 5
• Issue: 10
• Article number: e1000686
• Publication date: 2009-10-01
• DOI: 10.1371/journal.pgen.1000686
• EISSN: 1553-7404
• ISSN: 1553-7390
• Language: English
• Keywords: Genealogy and Heraldry; Principal Component Analysis; Genetics, Population; Polymorphism, Single Nucleotide; Humans