Comparison of mitochondrial and nuclear DNA analyses of population structure in blacklip abalone Haliotis rubra Leach

Genetic variation in five geographically isolated samples of the blacklip abalone, Haliotis rubra, from south-eastern Australia was examined using two molecular techniques. A restriction fragment length polymorphism (RFLP) analysis using six restriction enzymes on the ND3/COIII region of mitochondrial DNA was compared with five independent nuclear DNA microsatellite loci. The results from both techniques suggest restricted gene flow between blacklip abalone separated by Bass Strait, and homogeneity among geographically isolated samples from around the island of Tasmania. Although both techniques showed similar resolving power, microsatellite DNA analysis is the preferred molecular technique for the fine scale investigation of blacklip abalone population structure because it makes possible the examination of numerous independent loci with potentially high levels of polymorphism. Both sample and locus specific homozygote excesses were recorded for the microsatellite loci. The most likely explanation for the locus specific deviations from Hardy-Weinberg expectations is the presence of null alleles.