With the development of the technique of autoradiography by Howard and Pelc (16 ), the mammalian cel

Two techniques have been described that use the polymerase chain reaction (PCR) to amplify many arbitrary regions of a genome simultaneously. Regions amplified by these techniques are generally polymorphic among closely related species and are beginning to be used in molecular taxonomy. In this chapter I discuss the positive and negative aspects of using arbitrary regions for taxonomy and describe strategies to adopt in overcoming some of their major disadvantages. I discuss how to set up a dataset of arbitrarily primed polymorphisms (APP) and demonstrate how cluster analysis of this dataset can be used to test marker specificity. Once an APP dataset is established, cluster analysis provides a simple means to routinely identify field collected specimens.