Smith et a I.: A comparison of three genetic methods for stock discrimination of Hoplostethus atlanticus 
80 i 
gist without need for cloning and sequencing. PCR 
amplification of specific regions of mtDNA and di- 
gestion with restriction enzymes (PCR-RFLP) has 
been used as a fisheries tool for the differentiation of 
various fish species (Chow et al., 1993; Chow and 
Inoue, 1993) and for stock identification of albacore 
tuna (Chow and Ushiama, 1995), anchovies (Bembo 
et al., 1995), and salmonids (Cronin et al., 1993; Hall 
and Nawrocki, 1995; O’Connell et al., 1995; Hansen 
and Loeschcke, 1996). Mitochondrial DNAis mater- 
nally inherited and has a higher evolutionary rate 
relative to protein coding loci (Brown, 1983) and con- 
sequently has become a useful stock discrimination 
tool. 
Random amplified polymorphic DNA (RAPD) uses 
PCR to amplify fragments of DNA with primers with 
random nucleotide sequences (Welsh and McClelland, 
1990; Williams et al., 1990). Most fisheries applications 
of RAPD’s have been at the species level (Dinesh et 
al., 1993; Bardakci and Skibinksi, 1994; Takagi and 
Taniguichi, 1995), although Macaranas et al. (1995) 
used RAPD’s to distinguish populations of the fresh- 
water red claw crayfish, Cherax quadricarinatus, in 
northern Australia, and a population specific RAPD 
marker was found in the marine shrimp Penaeus 
vannamei (Garcia et al., 1996). 
In this paper we used three methods (allozymes, 
mtDNA, and RAPD’s) to determine the genetic rela- 
tions among orange roughy collected from four 
spawning sites off the east and south coasts of New 
Zealand. 
Materials and methods 
Tissue samples were collected on the RV Tangaroa 
from four spawning sites off the east and south coasts 
of New Zealand (Fig. 1). These sites were chosen be- 
cause they are isolated by distances beyond the likely 
limit of larval drift (Zeldis et al., 1994). Each site 
supports significant fisheries, although the Waitaki 
fishery is relatively small and has declined quickly 
since development in the early 1990’s (Annala and 
Sullivan 2 ). Heart, liver, and muscle tissues were dis- 
2 Annala, J. H., and K. J. Sullivan. 1996. Report from the fish- 
ery assessment plenary, April-May 1996: stock assessments and 
yield estimates. Unpubl. Rep., Ministry of Fisheries, Greta 
Point Library, Wellington, New Zealand. 
I' I 1 I 1 I 1 
165” 
i i ,, rn _T i 1 i mvw i ' m, i 1 i 1 i 1 i 1 i 1 n r 1 r 
40° 
T- T —r 
175° W 
45° S 
Pacific Ocean 
k 1 ' 
*i' • 
Puysegur 
Figure 1 
Location of orange roughy spawning sites around New Zealand sampled for genetic analyses. 
The dotted line represents the 1,000-m isobath. 
