32 
Fishery Bulletin 1 12(1) 
Table 7 
Summary of analysis of molecular variance (AMOVA) indicating partitioning of genetic variation on 
the basis of our 2008 (top) and 2009 (bottom) sample collections of Cobia ( Rachycentron canadum) in 
South Carolina. df=degrees of freedom. 
Collection 
year 
Source of variation 
df 
Sum of 
squares 
Variance 
component 
Percentage 
of variation 
P-value 
2008 
Among populations 
3 
973 
1.6 
1.6 
<0.0001 
Within populations 
594 
56,980 
95.9 
98.4 
Total 
597 
57,953 
97.5 
2009 
Among populations 
2 
473 
1.1 
1.2 
<0.0001 
Within populations 
437 
37,760 
86.4 
98.8 
Total 
439 
38,233 
87.5 
diversity. Inbreeding was low (P>0.21; Fig<0.07) in all 
collection locations. 
Discussion 
In recent years, SCDNR has expanded the use of ge- 
netic tools to identify many types of stocked fish, spe- 
cifically Red Drum (Sciaenops ocellatus), Striped Bass 
( Morone saxatilis), and Spotted Seatrout ( Cynoscion 
nebulosus), and to characterize their genetic popula- 
tion structure. These tools create permanently identifi- 
able tags with the use of microsatellite markers that 
are useful for genetically characterizing fish popula- 
tions. South Carolina’s Cobia research program is the 
first to begin rigorously evaluating U.S. populations 
from a genetic perspective. On the basis of our U.S. 
collections of Cobias encountered along the south At- 
lantic coast, tests of both genotypic distributions and 
pairwise hierarchical Rst statistics indicate that the 
offshore groups are genetically homogenous, a finding 
Table 8 
Results of the genotypic distribution (P-values below di- 
agonal) and Rgx pair-wise (above diagonal) comparisons 
of locations from the 2009 sample collections of Cobia 
( Rachycentron canadum). Collection locations were off- 
shore North Carolina (NCoff), offshore South Carolina 
(SCoff), and inshore South Carolina (SC). Bold type in- 
dicates statistical significance following Bonferroni cor- 
rection (critical jP=0.017). 
NCoff SCoff SC 
NC 0 ff - 0.006 0.017 
SC 0 ff 0.529 - 0.018 
SC <0.001 <0.001 
that is consistent with Hrincevich’s (1993) findings. 
However, the detection of the two genetically distinct 
inshore aggregations (SC and VA) is new information 
in our understanding of Cobia life history. Although 
a significant degree of genetic isolation was detected 
among these inshore aggregations and the offshore 
group, the low Pgx statistics and the mixed ancestry 
patterns indicate that a low level of gene flow does 
occur. 
We recognize that population structure can be easily 
masked by a mixed stock effect, whereby gene flow is 
limited among population groups by different spawn- 
ing behaviors, yet intermingling occurs outside of the 
spawning period. For example, if populations of fish 
spawn in unique locations but intermingle and migrate 
with other populations during the nonspawning season, 
the composition of nonspawning breeding stocks would 
appear to be homogenous in terms of allele frequency 
distributions, whereas gene flow would be restricted 
to individuals spawning at each unique spawning site. 
Only sampling of spawning individuals at each unique 
spawning site would reveal the true genetic structure. 
Although we have temporally limited our sampling to 
the spawning period of Cobia, it is possible that the lack 
of detected genetic differences between the VA inshore 
aggregation and the NC offshore samples is due to con- 
founding effects of the potential migration patterns of 
Cobia. In a migrating species, the logistics of sampling 
individuals in one location without resampling from 
the same group in another location is challenging. Al- 
though temporally limiting sampling can lessen the 
confounding effects of such migrations on evaluations 
of population genetics, in the case of Cobias, the lim- 
ited period of accessibility for sampling coincides with 
both their spawning season as well as their proposed 
northward migration. Therefore, although our sampling 
was temporally limited, it is possible that VA individu- 
als were present among the Cobias collected offshore of 
NC as they were completing their migration to the VA 
inshore aggregation. 
