800 
Abstract .—Three types of genetic 
markers were used to determine ge- 
netic relations among four spawning 
populations of orange roughy off New 
Zealand. Eleven allozyme loci were 
tested in starch and cellulose acetate 
gels. Restriction fragment length poly- 
morphisms 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 haplo- 
types. There was no significant differ- 
ence between the two northern spawn- 
ing populations for any marker, but 
there were significant differences be- 
tween all other pairwise population com- 
parisons with allozymes and RAPD’s, in- 
dicating the presence of three genetic 
stocks. The mtDNA analysis revealed 
less genetic subdivision than did 
allozymes and RAPD’s. 
Manuscript accepted 14 May 1997. 
Fishery Bulletin 95:800-811 (1997). 
A comparison of three genetic methods 
used for stock discrimination of orange 
roughy, Hoplostethus atlanticus: 
allozymes, mitochondrial DNA, and 
random amplified polymorphic DNA 
Peter J. Smith 
Peter G. Benson 
S. Margaret McVeagh 
National Institute of Water and Atmospheric Research Ltd (NIWA) 
PO Box 14,901, Wellington, New Zealand 
E-mail address: p.smith@niwa.cri.nz 
The orange roughy, Hoplostethus 
atlanticus, is a deepwater species 
with wide distribution in the Atlan- 
tic, Indian, and South Pacific 
Oceans. Around New Zealand the 
species supports a fishery which 
peaked at 50,000 tons per annum 
in the mid 1980’s but which has sub- 
sequently declined owing to quota 
restrictions. There are several geo- 
graphically isolated spawning popu- 
lations of orange roughy which are 
the major targets of fishing within 
the New Zealand Exclusive Eco- 
nomic Zone (EEZ). 
A basic prerequisite of fisheries 
management is the identification of 
production units or stocks of a spe- 
cies; inadequate knowledge of stock 
structure may lead to over- or un- 
der-exploitation. Orange roughy 
occur at depths of about 1,000 m 
and therefore tag and release stud- 
ies to estimate movements between 
areas are impracticable. There have 
been several other approaches to 
stock identification of orange 
roughy with differing results. Stud- 
ies of parasite distribution (Lester 
et al., 1988), morphometric charac- 
ters (Linkowski and Liwoch, 1986; 
Haddon and Willis, 1995), and trace 
element composition of otoliths 
(Edmonds et al., 1991) have dem- 
onstrated regional subdivisions in 
Australasian orange roughy. An 
allozyme study revealed a high level 
of genetic variation but only mar- 
ginally significant differences be- 
tween the fishing areas around New 
Zealand (Smith, 1986). Genetic evi- 
dence for discrete stocks off South 
Australia and eastern Australia 
based on an allozyme survey (Black 
and Dixon 1 ) was not supported by 
a larger-scale study (Elliott and 
Ward, 1992). Restriction fragment 
length polymorphism (RFLP) analy- 
ses of mitochondrial (mt)DNA have 
indicated genetic subdivision of or- 
ange roughy around Australia (Smo- 
lenski et al., 1993) and New Zealand 
(Smith et al., 1996). 
The development of the poly- 
merase chain reaction (PCR), which 
amplifies DNA, enables genetic 
analyses to be carried out on small 
tissue samples and provides a range 
of methods for the population biolo- 
1 Black, M., and R I. Dixon. 1989. Pop- 
ulation structure of orange roughy (Hoplo- 
stethus atlanticus) in Australian waters. 
Internal Report, Centre for Marine Sci- 
ence, University of New South Wales, 
Kensington, Australia, 22 p. 
