Phytologia (April 2007) 89(1) 94 USING SEQUENCE INVERTED REPEATS (RAPDs) DATA IN SYSTEMAICS: POTENTIAL, PROBLEMS AND SOLUTIONS

Several cases are presented from Juniperus in which the use of RAPD (Random Amplified Polymorphic DNA = Sequence Inverted Repeats SIRs) have been very concordant with DNA sequence and biogeographic data. The use of the term 'Random' should be discouraged because the method is not 'Random' but depends on numerous inverted sequences found in DNA that accounts for hairpin loops important to define the tertiary structure of RNA and thence enzyme activity and specificity. SIRs (RAPDs) require very precise attention to laboratory procedures. Several suggestions are presented to aid in these procedures. Unlike DNA sequence data, SIRs (RAPDs) data should be analyzed by a multi-variate statistical method such as Principal Components or Principal Coordinates Analysis that can account for variation within taxa and treat this variation as error terms. Running replicates and/or sibs is critical to determine if lab supplies and equipment are operating at the peak efficiency.