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A Genealogical Interpretation of Principal Components Analysis 英文参考文献
AGenealogicalInterpretationofPrincipalComponents
Analysis
GilMcVean*
DepartmentofStatistics,UniversityofOxford,Oxford,UnitedKingdom
Abstract
Principalcomponentsanalysis,PCA,isastatisticalmethodcommonlyusedinpopulationgeneticstoidentifystructurein
the distribution of genetic variation across geographical location and ethnic background. However, while the methodis
oftenusedtoinformabouthistoricaldemographicprocesses,littleisknownabouttherelationshipbetweenfundamental
demographicparametersandtheprojectionofsamplesontotheprimaryaxes.HereIshowthatforSNPdatatheprojection
ofsamplesontotheprincipalcomponentscanbeobtaineddirectlyfromconsideringtheaveragecoalescenttimesbetween
pairs of haploid genomes. The result provides a framework for interpreting PCA projections in terms of underlying
processes,includingmigration,geographicalisolation,andadmixture.IalsodemonstratealinkbetweenPCAandWright’s
FST 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.
Citation:McVeanG(2009)AGenealogicalInterpretationofPrincipalComponentsAnalysis.PLoSGenet5(10):e1000686.doi:10.1371/journal.pgen.1000686
Editor:MollyPrzeworski,UniversityofChicago,UnitedStatesofAmerica
ReceivedJune2,2009;AcceptedSeptember16,2009;PublishedOctober16,2009
Copyright: ? 2009 Gil McVean. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.
Funding:TheworkwassupportedbytheLeverhulmeTrust(www.leverhulme.ac.uk)andtheHFSP(;grantno.RGP0054/2006).Thefundershadno
roleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript.
CompetingInterests:Theauthorhasdeclaredthatnocompetinginterestsexist.
*E-mail:mcvean@stats.ox.ac.uk
Introduction
samplesontoase
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