COMPUTING GENETIC SIMILARITY COEFFICIENTS FROM RAPD DATA - CORRECTINGFOR THE EFFECTS OF PCR ARTIFACTS CAUSED BY VARIATION IN EXPERIMENTAL CONDITIONS

The production of informative random amplified polymorphic DNA (RAPD) markers using PCR and a single primer is often accompanied by the gene ration of artifactual (noninformative) bands as well. When RAPD data a re used to compute genetic similarity coefficients, these artifacts (f alse positives, false negatives, or both) can cause large biases in th e numerical values of the coefficients. As a result, some workers have been reluctant to use RAPD markers in the estimation of genetic simil arities. Artifactual bands are of two types: those caused by variation in experimental conditions, and those caused by characteristics of th e DNA to be amplified. A procedure is described that allows for correc tion of the bias caused by the first type of artifact, providing that replicate DNA sampler have been extracted, amplified, and scored. The resulting data are used to obtain an estimate of the proportion of fal se-positive and false-negatives bands. These values are then used to c orrect the bias in the computed similarity coefficients. Two examples are given, one In which bias correction is critical to the results, an d one In which it is less important. The maximum percent bias, compute d from the estimated proportions of false positives and false negative s in tile RAPD data set, Is proposed as a criterion for determining wh ether bias correction of the similarity coefficients is required or no t. Although all reasonable efforts should be made to optimize PCR prot ocols to eliminate artifactual bands, when this is not possible, the m ethods described allow RAPD markers to compute genetic similarities re liably and accurately, even when artifactual bands resulting from vari ation in experimental conditions are present.