Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints

The relevance of using dominant random amplified polymorphic DNA (RAPD) fin gerprints for estimating population differentiation was investigated when t ypically small population sample sizes were used. Haploid sexual tissues we re first used to determine genotypes at RAPD loci for 75 eastern white pine s (Pinus strobus L.) representing five populations. Dominant RAPD fingerpri nts were then inferred from genotypic data for each individual at each locu s, and gene diversity estimates from both sources of data were compared. Ge notypic information at RAPD loci indicated little or no differentiation amo ng populations, similar to allozyme loci. However, estimates of population differentiation derived from dominant RAPD fingerprints according to variou s common methods of analysis were generally inflated, especially when all f ragments were considered. Simulations showed that an increase in loci sampl ing and population sample sizes did not significantly alleviate the biases observed.