Darden et at: Population genetics of Rachycentron canadum 
25 
and only recently has research verified the reproduc- 
tive function of these aggregations through documen- 
tation of the presence of eggs, newly hatched Cobia 
larvae and reproductively mature females within the 
Port Royal Sound and St. Helena Sound estuaries in 
SC (Lefebvre and Denson, 2012). Therefore, the limited 
understanding of Cobia life history provides conflict- 
ing expectations regarding the genetic structure at the 
population level (hereafter ‘population genetic struc- 
ture’). On one hand, their pelagic nature and trans- 
oceanic distribution would indicate a high potential for 
long distance movement and gene flow (i.e., no genetic 
structure expected); conversely, the presence of site- 
specific spawning aggregations might indicate a low 
potential for gene flow (i.e., genetic structure expect- 
ed). Because the foundation for effective management 
of marine fishes is built upon the determination of bio- 
logical population segments, a better understanding of 
Cobia biology and population genetic structure over a 
broad geographic area is necessary. 
Commercial and recreational U.S. harvests of Cobia 
along the middle and south Atlantic have been highly 
variable over time, but generally have been increas- 
ing since 1980 (Atlantic Coastal Cooperative Statistics 
Program, http://www.ACCSP.org). Concurrently, recre- 
ational fishing pressure on Cobias has increased sub- 
stantially in the last decade, especially in areas where 
they exhibit annual inshore aggregations (SC, VA) and 
this pressure has made them susceptible to overfishing 
during a potentially critical life stage. In these areas, 
fishing tournaments focused solely on Cobias are popu- 
lar (McGlade, 2007) and “catch and release” is the ex- 
ception rather than the rule. Therefore, with continued 
increases in human populations in coastal areas and 
subsequent increased fishing pressure on both offshore 
and inshore coastal finfish populations, the South Caro- 
lina Department of Natural Resources (SCDNR) began 
evaluating the feasibility of stocking Cobias as a man- 
agement option. In 2001, the SCDNR began collecting 
Cobias from the wild, developing broodstock condition- 
ing regimes, spawning broodstock in the laboratory, 
and producing juveniles for aquaculture development 
and stock enhancement (Weirich et al., 2004). In addi- 
tion, efforts were made to collect life history informa- 
tion (spawning, growth, and genetics) of the wild popu- 
lations during seasonal migrations. Externally tagged, 
cultured fish were also released into the estuary from 
which the wild broodstock had been collected as a fish- 
eries research tool to monitor movement, determine 
appropriate tag types, identify site fidelity, determine 
growth rates, and verify annulus formation in otoliths. 
In 2007, shortly after Pruett et al. (2005) and Ren- 
shaw et al. (2006) published microsatellite loci for Co- 
bia, we optimized 3 multiplexed microsatellite panels 
of 10 loci to use as genetic tags for stocked fish and 
population genetic analyses. Although the genetic tools 
were not ready for use until 2007, fin clips were avail- 
able from all hatchery broodstock used in the program 
between 2004 and 2007. Here, we present population 
genetic data on the basis of the 2008 and 2009 col- 
lections and recapture data for Cobias collected from 
south Atlantic coastal waters. Specifically, our goals 
are to characterize the genetic structure of the Cobia 
population along the southeast Atlantic coast of the 
United States; determine if population genetic struc- 
ture is detectable on the basis of movement patterns; 
document if any degree of estuarine fidelity occurs in 
Cobias; and evaluate whether genetic data support the 
reproductive role of their seasonal inshore aggrega- 
tions. Because of the general lack of knowledge of their 
biology, we used a multidisciplinary effort over a broad 
geographical area to address current obstacles facing 
management of Cobia. 
Materials and methods 
Broodstock and production 
Broodstock used for the production of all stocked fish 
was collected from the Port Royal Sound estuary (Fig. 
1); the broodstock pool ranged from 9 to 16 individu- 
als per year (Table 1). Spawning occurred at the Ma- 
rine Resources Research Institute in Charleston, SC, 
and Waddell Mariculture Center in Bluffton, SC, and 
all rearing occurred in outdoor nursery ponds at the 
Waddell Mariculture Center. Relatively small numbers 
of fish have been produced and released since 2004; 
2007 represented the largest release with -54,000 fish 
(Table 1). All year classes are identifiable with distinct 
genetic tags (as described later). Genetic tags offer a 
noninvasive, permanent approach that can be applied 
to all sizes of fish, including larvae, and they are identi- 
fiable through parentage analysis. Small juveniles were 
released at approximately 30 days after hatching, large 
juveniles at approximately 90 days after hatching, and 
yearlings the following spring. Yearlings from the 2004 
and 2005 year classes were also individually tagged 
with external tags before release. Either an 89-mm 
or 127-mm nylon dart tag (Hallprint Pty Ltd., 2 Hind- 
marsh Valley, Australia) was inserted into the dorsal 
musculature. All Cobia releases occurred in the Port 
Royal Sound at the Trask boat landing in Bluffton, SC. 
Sampling 
Anal-fin tissue samples were collected from adult Co- 
bias at fishing tournaments, filleted fish carcasses do- 
nated to SCDNR’s freezer program by cooperating an- 
glers, and fish collected by SCDNR personnel during 
the spawning seasons of 2008 and 2009 (April-July). 
Because Cobia is a federally managed species with a 
minimum size limit of 83.8 cm fork length (-93.8 cm 
TL), the species is not expected to recruit to the fishing 
2 Mention of trade names or commercial companies is for iden- 
tification purposes only and does not imply endorsement by 
the National Marine Fisheries Service, NOAA. 
