Estimating population structure in diploids with multilocus dominant DNA markers.

Lev Zhivotovsky

Molecular Ecology (1999) 8(6): 907-913.

For reprint send email to: Lev Zhivotovsky

Abstract

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 locus, with a band and with no band. The latter one represents null-homozygotes with unamplified, recessive null-alleles. The frequency of a null-allele can be estimated by taking the square root of the fraction of individuals with no band. Lynch and Milligan (1994) have suggested a modified procedure that reduces bias introduced by the square-root transform. However, the procedure recommends to ignore those samples in which less than four null-homozygotes are observed. This may lead to significant bias in estimates of genetic diversity. In this study, I introduce a Bayesian approach to estimation of null-allele frequencies for dominant DNA markers. It follows from computer 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.

Keywords: Bayesian, bias, dominant, marker, RAPD, recessive.

by Alfred E. Szmidt