Estimating population structure in diploids with multilocus dominant DNA markers

Multilocus DNA markers [random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphism (AFLPs)] are important for population studies because they reveal many polymorphic loci distributed over the genome. The markers are dominant, that is two phenotypes are distinguished at each loc us, with a band and with no band. The latter one represents null-homozygote s with unamplified, recessive null-alleles. The frequency of a null-allele can be estimated by taking the square root of the fraction of individuals w ith no band. Lynch and Milligan (1994) have suggested a modified procedure that reduces bias introduced by the square-root transform. However, the pro cedure recommends to ignore those samples in which fewer than four null-hom ozygotes are observed. This may lead to significant bias in estimates of ge netic diversity. In this study, I introduce a Bayesian approach to estimati on of null-allele frequencies for dominant DNA markers. It follows from com puter simulations and data on two conifer species that the Bayesian method gives nearly unbiased estimates of heterozygosity, genetic distances and F- statistics. The influence of a prior distribution and departure from Hardy- Weinberg proportions on the estimates is also considered.