ASSESSING POPULATION GENETIC-STRUCTURE AND VARIABILITY WITH RAPD DATA- APPLICATION TO VACCINIUM MACROCARPON (AMERICAN CRANBERRY)

A method for estimating and comparing population genetic variation usi ng random amplified polymorphic DNA (RAPD) profiling is presented. An analysis of molecular variance (AMOVA) is extended to accomodate pheno typic molecular data in diploid populations in Hardy-Weinberg equilibr ium or with an assumed degree of selfing. We present a two step strate gy: 1) Estimate RAPD site frequencies without preliminary assumptions on the unknown population structure, then perform significance testing for population substructuring. 2) If population structure is evident from the first step, use this data to calculate better estimates for R APD site frequencies and sub-population variance components. A nonpara metric test for the homogeneity of molecular variance (HOMOVA) is also presented. This test was designed to statistically test for differenc es in intrapopulational molecular variances (heteroscedasticity among populations). These theoretical developments are applied to a RAPD dat a set in Vaccinium macrocarpon (American cranberry) using small sample sizes, where a gradient of molecular diversity is found between centr al and marginal populations. The AMOVA and HOMOVA methods provide flex ible population analysis tools when using data from RAPD or other DNA methods that provide many polymorphic markers with or without direct a llelic data.