RAPDS and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir

Thirty-six nuclear-encoded RAPD loci and 20 allozyme loci were studied to compare levels of diversity and differentiation among populations and races of the widespread North American conifer, Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco]. RAPD assays used diploid seed embryo DNA from 22 to 36 trees in each of six populations that sampled the three major races (two populations per race). A comparable allozyme data set for nearby populations was constructed from a published study. RAPDs of organelle origin were excluded by hybridization of blotted RAPD gels with chloroplast and mitochondrial DNA-enriched probes. RAPD and allozyme markers had similar levels of diversity within populations (H(S) = 0.22±0.03 and 0.16±0.03, respectively) and differentiation among populations (G(ST)=0.34±0.07 and 0.29±0.07, respectively). When the allozyme data set was transformed into dominant, biallelic markers to study how RAPDs may bias diversity estimates, resampling studies showed that simulated H(S) and H(T) were reduced by half regardless of sample size. Because observed diversity for RAPDs was equivalent to, or higher than, that of allozymes, our simulations suggest that RAPD markers may contain substantially higher levels of inherent, but hidden, diversity. In contrast, the simulations showed that estimates of G(ST) using RAPDs should not be significantly biased at the population sizes we employed.