Abstract
Random Amplified Polymorphic DNA (RAPD) data have been increasingly used in studies on population and conservation genetics. Analysis of molecular variance (AMOVA) has become one of the important methods utilized in analysis of population genetic structure. Currently, WINAMOVA is the most popular software that is used for AMOVA analysis, and often runs together with RAPDistance, a software to calculate genetic distances. However,cautions should be taken when AMOVA analysis is used to process the RAPD data because of the dominant characteristic of RAPD marker and the limitation of RAPDistance. In this paper, we briefly introduce the principle and algorithm of AMOVA analysis and describe a new program, DCFA, that substitutes for RAPDistance. We also illustrate the processes of running the programs DCFA and WINAMOVA. In addition, we analyze eight Oryza rufipogon populations as an example to demonstrate how to process RAPD data with AMOVA, and discuss the results in light of population genetic structure. Finally, based on the comparison of four commonly used distance coefficients, we suggest that the coefficients of Euclidean squared distance and NEI LI rather than JACCARD are suitable for analysis of molecular variance.
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