ANALYSIS OF POPULATION GENETIC-STRUCTURE WITH RAPD MARKERS

Recent advances in the application of the polymerase chain reaction ma ke it possible to score individuals at a large number of loci. The RAP D (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structu re with RAPD data is hampered by the lack of complete genotypic inform ation resulting from dominance, since this enhances the sampling varia nce associated with single loci as well as induces bias in parameter e stimation. We present estimators for several population-genetic parame ters (gene and genotype frequencies, within- and between-population he terozygosities, degree of inbreeding and population subdivision, and d egree of individual relatedness) along with expressions for their samp ling variances. Although completely unbiased estimators do not appear to be possible with RAPDs, several steps are suggested that will insur e that the bias in parameter estimates is negligible. To achieve the s ame degree of statistical power, on the order of 2 to 10 times more in dividuals need to be sampled per locus when dominant markers are relie d upon, as compared to codominant (RFLP, isozyme) markers. Moreover, t o avoid bias in parameter estimation, the marker alleles for most of t hese loci should be in relatively low frequency. Due to the need for p runing loci with low-frequency null alleles, more loci also need to be sampled with RAPDs than with more conventional markers, and sole prob lems of bias cannot be completely eliminated.