I recently received an e-mail from Roeland Kindt of the World Agroforestry Centre in Nairobi, Kenya. He and his colleagues have assembled a guide to the use, analysis, and interpretation of dominant marker data, Molecular Markers for Tropical Trees: Statistical Analysis of Dominant Data. It's available for download at http://www.worldagroforestry.org/resources/databases/molecular-markers-for-tropical-trees. If you're working with dominant marker data, I recommend taking a look at it.
1Bruce Weir and I provide an overview of some of the issues involved in an article published in Nature Review Genetics last summer (subscription required)