78 
Fishery Bulletin 1 12(1) 
Table 3 
Statistics for 19 microsatellite loci examined in Finescale Menhaden ( Brevoortia gunteri), Yellowfin Menha- 
den ( B . smithi ), and Atlantic Menhaden (B. tyrannus) collected throughout the Gulf of Mexico in 2002-04. 
Statistics were determined with Arlequin, vers. 3.5 (Excoffier et al., 2005). Statistics include the number 
of alleles, expected heterozygosity ( H e ), and proportion of simulations that resulted in a more extreme test 
statistic for the Hardy- Weinberg equilibrium (HWE) exact test within samples (equivalent to an exact P- 
value). Statistical significance of the HWE P-value (initial a=0.05) was determined before (*) and after (**) 
sequential Bonferroni adjustment. 
Finescale Menhaden 
Yellowfin Menhaden 
Atlantic Menhaden 
Alleles 
H e 
HWE 
Alleles 
H e 
HWE 
Alleles 
H e 
HWE 
BpOOS 
2 
0.130 
1.000 
1 
0.000 
na 
10 
0.546 
0.622 
Bp017 
2 
0.426 
1.000 
2 
0.193 
1.000 
8 
0.640 
0.073 
Bp039 
4 
0.133 
0.065 
1 
0.000 
na 
5 
0.625 
0.370 
Bpl21 
8 
0.719 
0.341 
5 
0.700 
0.190 
12 
0.825 
0.512 
Bpl55 
0 
0.000 
na 
0 
0.000 
na 
0 
0.000 
na 
Bp221 
5 
0.575 
0.318 
3 
0.323 
0.489 
9 
0.611 
0.363 
Bp230 
7 
0.769 
0.787 
7 
0.693 
0.810 
9 
0.838 
0.000** 
Bp239 
9 
0.862 
0.052 
7 
0.660 
0.696 
17 
0.927 
0.009* 
Bp275 
6 
0.662 
0.091 
3 
0.398 
1.000 
14 
0.890 
0.056 
Bp301 
8 
0.779 
0.286 
10 
0.848 
0.028* 
11 
0.866 
0.010* 
Bp473 
2 
0.130 
1.000 
3 
0.479 
0.720 
4 
0.363 
0.118 
Bp489 
2 
0.045 
1.000 
1 
0.000 
na 
1 
0.000 
na 
Bp5G0 
5 
0.355 
0.201 
1 
0.000 
na 
11 
0.813 
0.034* 
Bp531 
5 
0.593 
0.335 
5 
0.599 
0.386 
11 
0.889 
0.900 
AF039657 
2 
0.045 
1.000 
2 
0.053 
1.000 
12 
0.698 
0.231 
AF039658 
8 
0.791 
0.195 
5 
0.679 
0.199 
11 
0.837 
0.000** 
AF039660 
3 
0.519 
0.000** 
3 
0.280 
1.000 
4 
0.550 
0.000** 
AF039661 
1 
0.000 
na 
2 
0.341 
1.000 
2 
0.068 
1.000 
AF049462 
9 
0.804 
0.620 
7 
0.707 
0.148 
19 
0.937 
0.004* 
Overall 
4.6 
0.439 
- 
3.6 
0.366 
- 
8.9 
0.628 
- 
high values of F [ s ; of these, 4 loci also indicated low 
frequency (/? n <0.10) null alleles. The Mantel test indi- 
cated a lack of correlation between genetic divergence 
and geographic distance (Mantel r=0.415, P=0.131). 
Discussion 
The analysis of population structure in wild species 
can be confounded by a paucity of readily available 
marker loci that are designed for a specific genus or 
species. The genus Brevoortia is one in which previ- 
ous studies have been hindered by loci that lacked ad- 
equate genetic variability (Anderson, 2007; Anderson 
and Karel, 2007; although, see Lynch et al., 2010). The 
stated purpose of this study was to develop more effec- 
tive tools for genetic analysis of Brevoortia spp. that 
could be used in the context of stock assessments. In 
particular, the intended purpose of the additional loci 
was 1) to improve the stock definition of the menhaden 
fishery in the Gulf of Mexico as it pertains to the pro- 
portion of each menhaden species in the annual catch 
and 2) to determine whether multiple populations of 
Gulf Menhaden are exploited in the fishery. Because 
these 2 goals require somewhat different methods, we 
assessed each independently in the context of the mic- 
rosatellite loci described in this study. 
Species identification of individuals that occur with- 
in the Gulf of Mexico menhaden fishery can be chal- 
lenging. Although there are well-described morpho- 
logical differences between Gulf Menhaden, Yellowfin 
Menhaden, and Finescale Menhaden, differences in 
morphological characteristics are subtle and can po- 
tentially lead to inaccurate identification (Dahlberg, 
1970; Anderson and McDonald, 2007). Genetic differen- 
tiation has been equally problematic. Anderson (2007) 
described reciprocal monophyletic mitochondrial DNA 
lineages between Gulf Menhaden and both of its conge- 
ners in the Gulf of Mexico. However, this same mtDNA 
analysis indicated that Finescale Menhaden and Yel- 
lowfin Menhaden could not be reliably distinguished 
with mtDNA. 
Species identification through the use of mtDNA 
loci can be troublesome when closely related species 
are hybridizing, as is the case with Gulf Menhaden and 
Yellowfin Menhaden (Turner, 1969; Dahlberg, 1970; An- 
