Arbitrarily amplified DNA markers as characters for phylogenetic inference

The ease with which arbitrarily amplified dominant (AAD) markers such as RAPD, AFLP and ISSR could be used to generate vast quantities of data led to their rapid application addressing a diverse range of biological questions. The most significant uses of AAD markers remain in genetic mapping, diagnostic fingerprinting and in the study of genetic structure within and between populations of individual species. AAD markers may also be utilised for phylogenetics and systematics, but have commonly been used inappropriately in such analyses due primarily to poor consideration of potential homoplasy. This review discusses the properties of AAD markers (including potential artefacts) that relate to their interpretation as characters for phylogenetic and systematic analysis. Although useful markers are those for which heritability and homology have been demonstrated, this is rarely done because it is potentially time consuming and expensive. A consequence of this is that homology, appropriate taxonomic level, and the resolving capacities of commonly employed hierarchical analyses are often not addressed. A pragmatic approach suggests that tangible monomorphism (e.g. 20%) across all taxa studied should be a minimum requirement before AAD markers could be considered for phylogenetic analyses. This would help to prevent comparison of taxa that are too divergent. Rather than being transferable across widely diverged taxa, AAD polymorphisms can provide useful discriminatory information for phylogenetic and systematic studies of closely related species and non-reticulating, subspecific lineages. Below these levels of taxon divergence, population genetic effects may swamp hierarchical signal in the data, while at greater levels of divergence, homoplasy is likely to be significant.