804 
Fishery Bulletin 95(4), 1997 
where N e = the effective population size; and 
m = the rate of gene flow per generation. 
It is assumed that m«l and that population differen- 
tiation is due to genetic drift and migration with no selec- 
tion. Gene diversity was corrected to a “true” estimate by 
subtracting the G STnuU due to sampling error, derived 
from a randomization test (Elliott and Ward, 1992). 
mtDIMA Heterogeneity in haplotype frequencies in 
the total data was tested by the x 2 randomization 
test described by Roff and Bentzen (1989) with the 
REAP package (McElroy et al., 1992). This method 
overcomes the problem of a large number of observed 
haplotypes at low frequency, by comparing x 2 values 
in 1,000 random rearrangements of the data. In ad- 
dition the % 2 randomization test was applied to 
pairwise comparisons of all populations to test for 
geographic structure. Probabilities were estimated 
from the number of randomizations that were equal 
to or greater than the observed x 2 value. The propor- 
tion of haplotype variation due to differentiation be- 
tween populations was estimated by G ST from the 
haplotype frequencies, as for allozymes. The num- 
ber of migrants exchanged per generation was esti- 
mated from the relation 
Nrrif = ( 1 /G st - l)/2, 
where m^= female migration, modified to account for 
the maternal inheritance of mtBNA. 
RAPD Standard genetic calculations are not imme- 
diately applicable to RAPD data because the frag- 
ments are dominant: individuals carrying two cop- 
ies of an allele cannot be distinguished from indi- 
viduals carrying one copy of the allele. Black ( 1995) 
has provided a set of programs for analyzing RAPD 
population data but points out that a number of as- 
sumptions have to be made. First, the observed frag- 
ments are dominant alleles and the absent fragments 
are recessive alleles. Second, the genotypes are in 
Hardy- Weinberg equilibrium and each observed poly- 
morphism is biallelic: all the absent observations are 
produced by the same recessive allele and all the 
present observations are produced by a single domi- 
nant allele with or without the recessive allele. Each 
primer was scored for the presence or absence of frag- 
ments in the gel. Each fragment, regardless of primer, 
was treated as an independent locus. In most RAPD 
studies, fragments have been found that vary in 
staining intensity; we scored only fragments that 
were intensely stained, following Black (1993). 
Random amplified polymorphic DNA allele fre- 
quencies were calculated from the presence or ab- 
sence observations with the RAPDBIOS software pro- 
gram (Black, 1995) and then used in the BIOSYS 
software program (Swofford and Selander, 1981) for 
calculation of heterogeneity in allele frequencies as 
for allozyme data. The gene-diversity statistic G gT 
(=F st ) was calculated with the RAPDFST software 
program (Black, 1995); probabilities were calculated 
according to Workman and Niswander (1970). An es- 
timation of the number of migrants exchanged per 
generation, N g m, was estimated as for the allozyme 
data. 
Results 
Allozymes 
Eleven enzyme loci were resolved in the four popu- 
lations and allele frequencies are given in Appendix 
Table 1. Eight loci were sufficiently polymorphic 
(P<0.95) for Hardy- Weinberg tests. One out of a pos- 
sible 32 tests (8 loci x 4 populations) showed a sig- 
nificant departure from Hardy- Weinberg equilibrium 
when a Bonferroni modified probability level was 
applied (Idh-1* Puysegur, % 2 =13.99, 1 df, P<0.001). 
The polymorphic loci were tested with a contin- 
gency x 2 test. There was a significant heterogeneity 
among all four populations at 5 loci, Est-1*, Gpi-2*, 
Idh-1 * , Idh-2*, and Ldh-1* , with a Bonferroni-modi- 
Table 1 
Results of comparisons of allele frequencies at eleven loci 
and mtDNA haplotypes in four populations of orange 
roughy. df = degrees of freedom; P = probability value; and 
G st = gene diversity . * = significant at the 5% level with a 
Bonferroni-modified P for multiple tests. 
Locus 
l 2 
df 
P 
G st 
P 
Cck-1* 
7.93 
6 
0.243 
0.006 
0.277 
Est-1* 
63.09 
12 
<0.001* 
0.030 
<0.001* 
Gpi-1* 
4.70 
9 
0.860 
0.002 
0.889 
Gpi-2* 
25.09 
6 
<0.001* 
0.021 
0.002* 
Idh-1 * 
26.91 
9 
0.001* 
0.026 
<0.001* 
Idh-2* 
46.08 
9 
<0.001* 
0.065 
<0.001* 
Ldh-1* 
19.02 
3 
0.003* 
0.025 
0.004* 
Ldh-2* 
12.09 
6 
0.061 
0.008 
0.153 
Mdh-1* 
11.20 
6 
0.082 
0.012 
0.066 
Mpi-1* 
7.56 
9 
0.581 
0.003 
0.653 
Pgm-1* 
2.58 
6 
0.860 
0.001 
0.839 
all loci 
226.2 
81 
<0.001 
0.020 
<0.001 
mtDNA 
haplotypes 
45.51 
0.001 
0.057 
0.001 
