Assessing the limits of random amplified polymorphic DNAs (RAPDs) in seaweed biogeography

As judged by comparison with other molecular data sets, random amplified polymorphic DNA (RAPD) data are robust in identifying large-scale biogeographic populations that range from hundreds to thousands of kilometers apart. As the geographical scale is shifted downward, however, RAPD data often fail. This is because RAPD data are inherently ''noisy'' as a result of technical artifacts and reproducibility problems associated with non-independence of bands, ''missing'' bands, and the presence of de novo bands, all of which contribute to scoring errors in the data set. To estimate the contribution of these error factors in algal phylogeographic studies, segregation of RAPD bands in tetrasphorophytic and gametophytic parents, their natural and synthetic offspring, and self-cycled tetrasporophytes were compared in Lophocladia trichoclados (Mertens in C. Agardh) Schmitz and to a limited extent in Digenea simplex (Wulfen) C. Agardh. Wide-ranging biogeographic populations of D. simplex were compared as were mixed populations of tetrasporophytes and gametophytes. Results show that nested priming can lead to some nonindependence of bands but that this probably does not significantly contribute to scoring error. Southern analysis using individual RAPD bands as probes revealed that up to 16% of visually nondetectable bands are actually present but that the random distribution of the error contributes uniformly across the data set. Non-parental (de novo in offspring) and parental (not present in offspring) bands may contribute substantially to the scoring error in tetrasporophytes, gametophytes, and self-cycled tetrasporophytes. The presence of tetrasporophytes and gametophytes in a sample is not important in large-scale phylogeographic studies but does affect within-clade variation at smaller scales. We conclude that the overall level of error remains roughly constant at probably between 5 and 10%, which is not a problem at large biogeographic scales where the phylogenetic signal is strong. Finally, some unexpectedly large abberations in RAPD banding patterns among life stages in L. trichoclados were observed that cannot be explained by methodological artifacts alone clue to comparisons with synthetic offspring controls. The possibility that carpospore amplification may not always involve a simple mitotic process is discussed.