87 
Abstract — Atlantic menhaden ( Bre - 
voortia tyrannus), through landings, 
support one of the largest commercial 
fisheries in the United States. Recent 
consolidation of the once coast-wide 
reduction fishery to waters within 
and around Chesapeake Bay has 
raised concerns over the possibility 
of the loss of unique genetic variation 
resulting from concentrated fishing 
pressure. To address this question, 
we surveyed variation at the mito- 
chondrial cytochrome c oxidase sub- 
unit I (COI) gene region and seven 
nuclear microsatellite loci to evaluate 
stock structure of Atlantic menhaden. 
Samples were collected from up to 
three cohorts of Atlantic menhaden 
at four geographic locations along the 
U.S. Atlantic coast in 2006 and 2007, 
and from the closely related Gulf men- 
haden (B. patronus) in the Gulf of 
Mexico. Genetic divergence between 
Atlantic menhaden and Gulf menha- 
den, based on the COI gene region 
sequences and microsatellite loci, 
was more characteristic of conspecific 
populations than separate species. 
Hierarchical analyses of molecular 
variance indicated a homogeneous dis- 
tribution of genetic variation within 
Atlantic menhaden. No significant 
variation was found between young- 
of-the-year menhaden (YOY) collected 
early and late in the season within 
Chesapeake Bay, between young-of- 
the-year and yearling menhaden col- 
lected in the Chesapeake Bay during 
the same year, between YOY and year- 
ling menhaden taken in Chesapeake 
Bay in successive years, or among 
combined YOY and yearling Atlan- 
tic menhaden collected in both years 
from the four geographic locations. 
The genetic connectivity between the 
regional collections indicates that the 
concentration of fishing pressure in 
and around Chesapeake Bay will not 
result in a significant loss of unique 
genetic variation. 
Manuscript submitted 23 January 2009. 
Manuscript accepted 3 November 2009. 
Fish. Bull. 108:87-97 (2010). 
The views and opinions expressed 
or implied in this article are those 
of the author (or authors) and do not 
necessarily reflect the position of the 
National Marine Fisheries Service, 
NOAA. 
A molecular genetic investigation 
of the population structure 
of Atlantic menhaden ( Brevoortia tyrannus ) 
Abigail J. Lynch 
Jan R. McDowell (contact author) 
John E. Graves 
Email address for contact author: McDowell@vims.edu 
Virginia Institute of Marine Science 
School of Marine Science 
College of William and Mary 
Rt. 1208 Greate Rd. 
Gloucester Point, Virginia 23062 
Atlantic menhaden (Brevoortia tyran- 
nus) is an ecologically and economi- 
cally important species along the U.S. 
East Coast. As a filter-feeder and 
key prey fish, it provides a critical 
link between primary production and 
larger piscivorous predators, such 
as striped bass (Morone saxatilis), 
bluefish (Pomatomus saltatrix), and 
weakfish ( Cynoscion regalis). The 
commercial fishery for Atlantic men- 
haden consists of a small bait fishery 
and a larger reduction fishery. Of 
the 20 menhaden reduction plants 
(where menhaden are “reduced” to 
meal and oil) that were once oper- 
ating along the U.S. Atlantic coast, 
only the Reedville, Virginia, facility 
is currently active. The concentration 
of fishing effort for Atlantic menha- 
den in and around Chesapeake Bay 
has raised concerns among many 
environmentalists and sport fisher- 
men about the possibility of “localized 
depletion” of Atlantic menhaden in 
the area. A potential consequence of 
localized depletion could be the loss 
of unique genetic variation within 
Atlantic menhaden, if there is spa- 
tial partitioning of genetic variation 
(stock structure) within the species. 
Results of previous analyses of the 
stock structure of Atlantic menha- 
den have been discordant. Two pop- 
ulations of Atlantic menhaden, one 
north and the other south of Long 
Island, New York, were suggested 
on the basis of vertebral counts 
and transferrin allele frequencies 
(Sutherland, 1963; Epperly, 1989). 
Two populations, one north and one 
south of Cape Hatteras, North Caro- 
lina, have also been proposed. This 
division was based on the presence 
of small, sexually mature fish before 
the arrival of the larger, migrating 
fish in North Carolina waters and 
the presence of spawning fish off 
northern Florida in late winter and 
early spring (June and Nicholson, 
1964). One coast-wide population 
has been indicated by tag recovery 
studies (Nicholson, 1978), which have 
shown that Atlantic menhaden of dif- 
fering ages and sizes share the over- 
wintering grounds off Cape Hatteras 
and undergo seasonal migrations and 
that larger fish travel farther north. 
The Atlantic States Marine Fisher- 
ies Commission currently assesses 
Atlantic menhaden as a single coast- 
wide stock. 
In addition to the uncertainty re- 
garding the stock structure of At- 
lantic menhaden, the relationship 
between Atlantic menhaden and 
Gulf menhaden (B. patronus) is not 
well understood. The mean values 
of several of the morphometric and 
meristic characters are significant- 
ly different between the two puta- 
tive species, although the ranges of 
variation are coincident (Dahlberg, 
1970). Similarly, preliminary genetic 
analyses indicate limited divergence 
between the putative species, and 
therefore the use of larger sample 
sizes and additional genetic charac- 
ters have been recommended (Avise 
et al., 1989; Anderson, 2007). 
