As a few of you may know, one of the hats I wear is that of a theoretical population geneticist. In recent years I've been very interested in developing methods to analyze genetic diversity in geographically structured populations.1 Among the methods I've worked on are those that can be used to make inferences from dominant marker data (e.g., RAPDs, AFLPs, or ISSRs). Paul Lewis and I released Hickory six or seven years ago to make it (relatively) easy for others to apply the methods to their own data.
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)