808 
Fishery Bulletin 95(4), 1997 
Given the technical problems with RAPD’s, we 
would recommend them only when other genetic 
methods have failed to reveal polymorphisms. Tech- 
niques such as PCR-RFLP of mtDNA, or allozymes, 
yielded fewer polymorphisms per unit of laboratory 
time than did RAPD’s but still produced sufficient 
polymorphisms to detect population structure in or- 
ange roughy. Our allozyme data set indicated a 
higher level of genetic subdivision than that found 
with mtDNA in orange roughy. This result is sur- 
prising in view of the relatively higher rate of evolu- 
tion of mtDNA (Brown, 1983), and it is possible that 
other regions of the mitochondrial genome, or use of 
additional restriction enzymes, might reveal more 
genetic variation. Several studies of marine organ- 
isms have detected greater genetic subdivision with 
mtDNA than with allozyme markers (e.g. Reeb and 
Avise, 1990), although there are examples of the re- 
verse in the fisheries literature (Grewe et al., 1994; 
Ward et al., 1994). It is possible that the allozyme 
markers are under selection (Koehn et al., 1980) and 
are responding to short-term population events 
rather than to historical events due to reproductive 
isolation. 
Acknowledgments 
We are grateful to Malcolm Clark and Di Tracey, for 
collection of orange roughy tissues samples, and to 
John Patton and two anonymous referees for con- 
structive comments on the manuscript. This research 
was supported by funds from The Exploratory Fish- 
ing Company (ORH3B) Limited and the New Zealand 
Ministry of Fisheries, project number FBOROl. 
Literature cited 
Bardakci, F., and D. O. F. Skibinski. 
1994. Application of the RAPD technique in tilapia fish: 
species and subspecies identification. Heredity 73:117- 
123. 
Bell, D. A., and D. M. DeMarini. 
1991. Excessive cycling converts PCR products to random 
length higher molecular weight fragments. Nucleic Ac- 
ids Res. 19:5079. 
Bembo, D. G., G. R. Carvalho, M. Snow, N. Cingolani, and 
T. J. Pitcher. 
1995. Stock discrimination of European anchovies, Engrau- 
lis encrasicolus, by means of PCR-amplified mitochondrial 
DNA analysis. Fish. Bull. 94:31-40. 
Black, W. C. 
1993. PCR with arbitrary primers: approach with care. 
Insect Mol. Biol. 2: 1-6. 
1995. FORTRAN programmes for the analysis of RAPD- 
PCR markers in populations. Colorado State Univ., Ft. 
Collins, CO, 6 p. 
Brown, W. M. 
1983. Evolution of animal mitochondrial DNA. In M. Nei, 
R. K. Koehn (eds.), Evolution of genes and proteins, p. 62- 
88. Sinauer, Sunderland. 
Chow, S., M. E. Clarke, and P. J. Walsh. 
1993. PCR-RFLP analysis on thirteen western Atlantic 
snappers (subfamily Lutjanidae): a simple method for spe- 
cies and stock identification. Fish. Bull. 91:619-627. 
Chow, S., and S. Inoue. 
1993. Intra- and interspecific restriction fragment length 
polymorphism in mitochondrial genes of Thunnus tuna 
species. Bull. Nat. Res. Inst. Far Seas Fish. 30: 207-225. 
Chow, S., and H. Ushiama. 
1995. Global population structure of albacore ( Thunnus 
alalunga ) inferred by RFLP analysis of the mitochondrial 
ATPase gene. Mar. Biol. 123: 39-45. 
Cronin, M. A., W. J. Spearman, R. L. Wilmot, J. C. Patton, 
and J. W. Bickham. 
1993. Mitochondrial DNA variation in chinook (Onco- 
rhyncus tshawytscha ) and chum (O. keta ) detected by re- 
striction enzyme analysis of polymerase chain reaction 
(PCR) products. Can. J. Fish. Aquat. Sci. 50:708-715. 
Devos, K. M., and M. D. Gale. 
1992. The use of random amplified DNA markers in 
wheat. Theor. App. Genet. 84:567-572. 
Dinesh, K. R., T. M. Lim, K. L. Chua, W. K. Chan, and 
V. P. E. Phang. 
1993. RAPD analysis; an efficient method of DNA finger- 
printing in fishes. Zool. Sci. 10:849-854. 
Edmonds, J. S., N. Caputi, and M. Morita. 
1991. Stock discrimination by trace element analysis of 
otoliths of orange roughy ( Hoplostethus atlanticus) a deep- 
water marine teleost. Aust. J. Mar. Freshwater Res. 
42:383-389. 
Elliott, N. G., and R. D. Ward. 
1992. Enzyme variation in orange roughy ( Hoplostethus 
atlanticus) samples from southern Australian and New 
Zealand waters. Aust. J. Mar. Freshwater Res. 45:51-67. 
Ellsworth, D. L., K. D. Rittenhouse, and R. L. Honeycutt. 
1993. Artifactual variation in randomly amplified polymor- 
phic DNA (RAPD) banding patterns. BioTechniques 14: 
214-217. 
Ferguson, A. 
1994. Molecular genetics in fisheries: current and future 
perspectives. Rev. Fish Biol. Fish. 4: 379-383. 
Garcia, D. K., and J. A. H. Benzie. 
1995. RAPD markers of potential use in penaeid prawn 
( Penaeus monodon) breeding programs. Aquaculture 
130:137-144. 
Garcia, D. K., A. K. Dhar, and A. Alcivar- Warren. 
1996. Molecular analysis of a RAPD marker (B20) reveals 
two microsatellites and differential mRNA expression in 
Penaeus vannamei . Mol. Mar. Biol. Biotechnol. 5:71—83. 
Grewe, P. M., A. J. Smolenski, and R. D. Ward. 
1994. Mitochondrial DNA diversity in jackass morwong 
( Nemadactylus macropterus : Teleostei) from Australian and 
New Zealand waters. Can. J. Fish. Aquat. Sci. 51:1101- 
1109. 
Haddon, M., and T. J. Willis. 
1995. Morphometric and merisitic comparison of orange 
roughy (Hoplostethus atlanticus'. Trachichthyidae) from the 
Puysegur Bank and Lord Howe Rise, New Zealand, and 
its implications for stock structure. Mar. Biol. (Berl.) 
123:19-27. 
Hall, H. J., and L. W. Nawrocki. 
1995. A rapid method for detecting mitochondrial DNA 
