80 
Fishery Bulletin 1 12(1) 
to managers in assessment of population structure in 
the Gulf Menhaden. An analysis of genetic structure in 
Gulf Menhaden using these loci showed no evidence for 
discreet populations and no evidence for isolation-by- 
distance across a majority of the range of the species 
in the northern Gulf of Mexico. It has long been sus- 
pected that genetic divergence among Gulf Menhaden 
samples throughout the Gulf of Mexico is very low, and, 
therefore, stock assessments have generally assumed 
that the menhaden fishery in the Gulf of Mexico is cen- 
tered upon a single fishery stock. Although the results 
of this study are a compelling validation of that as- 
sumption, the small sample sizes examined here rele- 
gate this finding as preliminary rather than conclusive. 
The power analysis indicated that sample sizes of 50 
or more are necessary to conclusively detect very low 
levels of genetic divergence (F st <0.004) through the 
use of all 15 markers for Gulf Menhaden. 
Although the loci described in this article are poly- 
morphic in other species of Brevoortia, the power of 
these markers for fine-scale population assessments in 
these species was not rigorously tested. The polymor- 
phism exhibited by samples of Gulf Menhaden at these 
loci was not repeated to the same magnitude in other 
congeners. The finding that other Brevoortia species 
exhibit relatively low genetic variation at loci origi- 
nally discovered in Gulf Menhaden is not surprising. 
Ascertainment bias, or decreased genetic variability 
in species that were not directly targeted in the origi- 
nal marker selection process, is a common finding in 
genetic studies of microsatellite loci among closely re- 
lated species (Ellegren et ah, 1997: Hutter et ah, 1998; 
Vowles and Amos, 2005). Both heterozygosity and PIC 
scores were lower in all 3 Brevoortia congeners. 
The ascertainment biases in comparisons that in- 
volve Gulf Menhaden and either Finescale Menha- 
den or Yellowfin Menhaden were more profound than 
were the biases in comparisons between Gulf Menha- 
den and Atlantic Menhaden. In the former 2 compari- 
sons, there were qualitative differences in the median 
PGR fragment lengths in direct comparisons of species 
(Gulf Menhaden generally had longer alleles) and sig- 
nificantly higher genetic variability in the focal spe- 
cies (Gulf Menhaden exhibited higher PIC and H e ). In 
contrast, PCR fragment lengths were generally simi- 
lar between Gulf Menhaden and Atlantic Menhaden, 
although there was a significant difference in //,. and 
PIC. Similar median repeat lengths between Gulf Men- 
haden and Atlantic Menhaden likely reflect a shallow 
evolutionary lineage between these species (Bowen and 
Avise, 1990; Anderson, 2007), in contrast to relatively 
deep taxonomic divergence between Gulf Menhaden 
and both Yellowfin Menhaden and Finescale Menhaden 
(Anderson, 2007). This result not only underscores the 
notion that the loci described here will be useful in fu- 
ture studies of both Gulf Menhaden and Atlantic Men- 
haden but also indicates that the use of loci in studies 
of Yellowfin Menhaden and Finescale Menhaden should 
be undertaken with caution. 
Conclusions 
It has been suggested previously that the main species 
exploited in the menhaden fishery of the Gulf of Mexico 
is the Gulf Menhaden (xAhrenholz, 1981). Because of 
the importance of this fishery in the Gulf of Mexico 
and because of the significance of Gulf Menhaden to 
inshore trophic systems, this finding should be re-as- 
sessed. In particular, the proportional contribution of 
each menhaden species occurring in the Gulf of Mexico 
to the annual catch should be examined through the 
use of a systematic method. Moreover, the presence 
of a single population of Gulf Menhaden throughout 
the Gulf of Mexico has been assumed in recent stock 
assessments, although this assumption has not been 
rigorously tested. The species composition and the 
number of exploited Gulf Menhaden populations can 
be reliably assessed with genetic data. The gene loci 
described in this study can be used to address both of 
these concerns, and they represent an improvement in 
the tools available for examination of the population 
structure of the genus Brevoortia. 
Acknowledgments 
This work was funded by the Texas Parks and Wildlife 
Department, Coastal Fisheries Division (TPWD-CF). 
We wish to thank D. McDonald for helpful comments 
on the first draft. An internal TPWD-CF review was 
conducted by M. Fisher and 3 anonymous reviewers. 
Reference to trade names does not imply endorsement 
by the state of Texas. 
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