88 
Fishery Bulletin 108(1 ) 
Table 1 
Collection location, date of collection, and number of Atlantic menhaden (Brevoortia tyrannus) and Gulf menhaden (B. patronus) 
analyzed in this study and range of sample fork lengths. For all collections outside the Chesapeake Bay, young-of-the-year (YOY) 
and yearling samples are pooled. 
Collection 
Location 
Date 
n 
Fork length (mm) 
New England 2006 
Gloucester, MA 
Aug. 2006 
25 
43-58 
New England 2007 
Gloucester, MA 
Aug. 2007 
25 
34-64 
Mid-Atlantic 2006 
Pennsville, NJ 
Aug. 2006 
27 
61-110 
Mid-Atlantic 2007 
Oakwood Beach, NJ 
June 2007 
25 
77-190 
Chesapeake Bay YOY 2006 
Gloucester Point, VA 
May 2006 
25 
27-67 
Chesapeake Bay yearling 2006 
Gloucester Point, VA 
Aug. 2006 
18 
120-200 
Chesapeake Bay YOY (early) 2007 
Gloucester Point, VA 
May 2007 
25 
34-84 
Chesapeake Bay YOY (late) 2007 
Gloucester Point, VA 
Aug. 2007 
31 
35-99 
Chesapeake Bay yearling 2007 
Gloucester Point, VA 
June 2007 
18 
114-184 
U.S. South Atlantic 2006 
Beaufort, SC 
Aug. 2006 
28 
41-113 
U.S. South Atlantic 2007 
Beaufort, SC 
April 2007 
41 
28-181 
Gulf menhaden 2006 
Galveston, TX 
Oct. 2006 
25 
not recorded 
Gulf menhaden 2007 
Cameron, LA 
Oct. 2007 
25 
52-91 
In this study, analyses of sequence data from the 
mitochondrial cytochrome c oxidase subunit I (COI) 
gene region and allele frequencies of seven nuclear mi- 
crosatellite loci were used to investigate the genetic 
relationships of Atlantic and Gulf menhaden, the stock 
structure of Atlantic menhaden, and to evaluate the 
potential for loss of unique genetic variation resulting 
from “localized depletion” of Atlantic menhaden within 
the Chesapeake Bay region. 
90°W 80°W 70°W 
Figure 1 
Map of ranges of Atlantic menhaden ( Brevoortia tyrannus) 
and Gulf menhaden ( B . patronus) and the approximate 
location of sites sampled in 2006-2007 for the analysis 
of stock structure in Atlantic menhaden. 
Materials and methods 
Sample collection 
Young-of-the-year (YOY) and yearling 
Atlantic menhaden were sampled from New 
England (MA), the U.S. mid-Atlantic (NJ), 
Chesapeake Bay (VA), and the U.S. South 
Atlantic (SC) in 2006 and 2007, and YOY 
Gulf menhaden were sampled from the Gulf 
of Mexico in 2006 and 2007 (Table 1; Fig. 1). 
For all collections outside the Chesapeake 
Bay, samples of YOY and yearling Atlantic 
menhaden were pooled. For Chesapeake Bay 
collections, scales were aged from a sub- 
sample of 20% of individuals taken in 2007 
and length was used as a surrogate for the 
remaining samples (where fish less than 100 
mm fork length were considered YOY and 
fish greater than 100 mm fork length were 
considered yearling). The younger cohorts 
were sampled because they are less likely 
to have migrated far from where they were 
spawned. Local experts identified menha- 
den on the basis of morphological characters 
and capture location. Muscle tissue samples 
were taken from each individual and either 
frozen or stored in DMSO buffer (Seutin et 
al., 1991) at room temperature. Voucher spec- 
imens were retained from all U.S. Atlantic 
