Development of species- and genome-specific genetic markers by representational difference analysis: Application in systematic and evolutionary research

In the study of biodiversity, it is important to have a reliable system for identification of various genetically distinct units (species, subspecies, etc). One of the most efficient tools available today is the polymerase chain reaction (PCR) with diagnostic primers, that yield a detectable product for one taxon but not for other taxa. Critical to this method is the identification of diagnostic DNA fragments from which primers can be designed. Representational difference analysis (RDA) can reliably isolate DNA fragments that are unique to a specific taxon. In this report, we demonstrate the utility of the technique by development of binary markers that distinguish between two cryptic species of voles (genus Microtus).