Amplified fragment length polymorphisms and microsatellites: a phylogenetic perspective.

Abstract

Harris (1999a) reviewed the use of randomly amplified polymorphic DNA (RAPD) markers in systematic studies. RAPD techniques were embraced due to the relatively high levels of polymorphism they revealed and their low cost compared to other techniques, such as allozymes and restriction fragment length polymorphisms (RFLPs; FranciscoOrtega et al., 1993). Previously a lack of variation had been a considerable problem for many population studies. For example, in Red Pine (Pinus resinosa Ait.; Pinaceae) allozyme studies revealed no isozyme diversity (Fowler and Morris, 1977; Simon et al., 1986), but RAPD markers revealed diversity amongst red pines (De Verno and Mosseler, 1997). Two new marker methodologies appear to be supplanting RAPD analyses; Amplified Fragment Length Polymorphisms (AFLPs) and Simple Sequence Repeats (SSRs; microsatellites). This paper reviews these two techniques, the basis of the polymorphisms they identify; their advantages and disadvantages; their methods of analysis and their applicability to systematic studies.