Molecular markers derived from PCR amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. RAPDs, AFLPs, and ISSR polymorphisms allow analysis of species for which prior 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 Fst from dominant markers. In contrast to existing alternatives, we do not assume prior knowledge of the degree of within-population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy-Winberg proportions. Our estimate of Fst 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 Fst. Moreover, some information about the degree of within population inbreeding (Fis) is available from data sets with a large number of loci and populations. We illustrate the method with reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.
Holsinger, Kent E.; Lewis, Paul O.; and Dey, Dipak, "A Bayesian approach to inferring population structure from dominant markers" (2002). EEB Articles. 1.