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A Bayesian approach to inferring population structure from dominant markers
Author(s) -
Holsinger Kent E.,
Lewis Paul O.,
Dey Dipak K.
Publication year - 2002
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1046/j.1365-294x.2002.01512.x
Subject(s) - biology , inbreeding , population , genetics , evolutionary biology , population genetics , bayes' theorem , bayesian probability , statistics , demography , mathematics , sociology
Molecular markers derived from polymerase chain reaction (PCR) amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. Random amplified polymorphic DNA markers (RAPDs), amplified fragment length polymorphisms (AFLPs) and intersimple sequence repeat (ISSR) polymorphisms allow analysis of species for which previous DNA sequence information is lacking, but dominance makes it impossible to apply standard techniques to calculate F ‐statistics. We describe a Bayesian method that allows direct estimates of F ST from dominant markers. In contrast to existing alternatives, we do not assume previous knowledge of the degree of within‐population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy–Weinberg proportions. Our estimate of F ST incorporates uncertainty about the magnitude of within‐population inbreeding. Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of F ST . Moreover, some information about the degree of within‐population inbreeding ( F IS ) is available from data sets with a large number of loci and populations. We illustrate the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea .