A comparison of three genetic methods used for stock discrimination of orange roughy, Hoplostethus atlanticus: Allozymes, mitochondrial DNA, and random amplified polymorphic DNA

Three types of genetic markers were used to determine genetic relations among four spawning populations of orange roughy (H. atlanticus) off New Zealand. Eleven allozyme loci were tested in starch and cellulose acetate gels. Restriction fragment length polymorphisms were tested in two regions of the mitochondrial DNA amplified with the polymerase chain reaction. Random amplified polymorphic DNA (RAPD) products were generated with 10-base oligonucleotide primers and separated in agarose gels. There was a significant heterogeneity among all four populations, at 5 out of 11 allozyme loci, at 2 of 29 RAPD primer fragments, and in the frequency of mtDNA haplotypes. There was no significant difference between the two northern spawning populations for any marker, but there were significant differences between all other pairwise population comparisons with allozymes and RAPD's, indicating the presence of three genetic stocks. The mtDNA analysis revealed less genetic subdivision than did allozymes and RAPD's.