Lynch et al.: A genetic investigation of the population structure of Brevoortia tyrannus 
93 
Table 4 
Analysis of molecular variance (AMOVA) among Atlantic menhaden ( Brevoortia tyrannus ) and Gulf menhaden ( B . patronus) 
based on cytochorme c oxidase subunit I (COI) sequence data and seven microsatellite loci (Aal6, Asa2, Asa4, AsaB020, AsaD055, 
AsaC334, SarBH04) grouped by collection time for Chesapeake Bay samples; by age class (following the 2006 year class) for Ches- 
apeake Bay samples; by age class for Chesapeake Bay in 2006 and 2007; by region for all Atlantic coast samples (New England, 
mid-Atlantic, Chesapeake Bay, and U.S. South Atlantic); by region for large-scale samples (New England, mid-Atlantic, Chesa- 
peake Bay, U.S. South Atlantic, and Gulf menhaden); by cytochrome c oxidase subunit I clade for large-scale samples (“Atlantic 
only” clade, “ubiquitous” clade, anomalous samples); and by putative species (Atlantic and Gulf menhaden). The distance meth- 
ods used were pairwise differences (4> S7 .), number of different alleles ( F ST ), and sum of squared allele size differences ( R ST ); all 
with 10,000 permutations. Bolded P-values indicate significance (P<0.05) after Bonferroni correction (initial a=0. 05/2 = 0. 025). 
4>-statistics 
P 
F.ST 
P 
r st 
P 
Grouped by collection time 
between collection times 
-0.0195 
0.587 
0.00096 
0.398 
0.0155 
0.171 
Grouped by age class (in successive years) 
between years 
-0.0364 
0.88 
0.0294 
0.047 
-0.00103 
0.436 
Grouped by age class (within 2006) 
between age classes 
-0.0203 
0.552 
-0.007 
0.732 
-0.0087 
0.52 
Grouped by age class (within 2007) 
between age classes 
-0.0033 
0.382 
0.0099 
0.066 
0.0233 
0.114 
Grouped by region (Atlantic coast only) 
among regions 
-0.0089 
0.920 
0.0037 
0.041 
-0.0053 
0.902 
Grouped by region (large-scaled menhaden combined) 
among regions 
0.0605 
<0.0001 
0.0489 
<0.0001 
0.0403 
<0.0001 
Grouped by COI clade 
among clades 
0.8659 
<0.0001 
0.00379 
0.068 
0.0059 
0.148 
Grouped by putative species (Atlantic and Gulf menhaden) 
between species 
0.176 
<0.0001 
0.128 
<0.0001 
0.102 
<0.0001 
among regions within a species 
-0.00822 
1 
0.0043 
0.0205 
-0.00511 
0.872 
Table 5 
Estimates of pairwise & ST , above diagonal (*), and pairwise ^ST (and R st ), below diagonal, between regional collections of Atlan- 
tic menhaden ( Brevoortia tyrannus) and Gulf menhaden (B. patronus) based on cytochorme c oxidase subunit I (COD sequence 
data and seven microsatellite loci, respectively. Bolded values indicate significance after correction for multiple tests (a=0.05, 
k=3 for comparisons within Atlantic menhaden). 
Collection 
New England 
mid-Atlantic 
Chesapeake Bay 
U.S. South Atlantic 
Gulf 
New England 
* 
-0.006 
-0.004 
-0.005 
0.032 
mid-Atlantic 
0.004 (0.000) 
* 
-0.001 
-0.004 
0.027 
Chesapeake Bay 
0.004 (-0.011) 
0.009 (-0.000) 
* 
- 0.000 
0.048 
U.S. South Atlantic 
-0.006 (-0.012) 
0.010(0.001) 
0.003 (-0.005) 
* 
0.029 
Gulf menhaden 
0.106 (0.080) 
0.157 (0.091) 
0.130 (0.100) 
0.106 (0.073) 
* 
The POWSIM analysis showed that 94.2%, 93.8%, 
and 92.6% of the tests where the N e :t combination led 
to F ST =0.0025 (10,000: 50, 5000: 25, 1000: 5, respec- 
tively), 100% of the tests where the N e :t combination 
led to F st =0.01 (10,000: 201, 5000: 100.5, 1000: 20.1), 
and 100% of the tests where the N e :t combination led 
to F st = 0.05 (10,000: 1025.8, 5000: 512.9, 1000: 102.6) 
were statistically significant, indicating that there was 
sufficient statistical power to detect population differ- 
ences with the set of microsatellite markers and sample 
sizes used in this study. 
Discussion 
The mitochondrial and nuclear markers employed in this 
analysis revealed considerable variation within Atlantic 
menhaden. The seven microsatellite loci surveyed were 
highly variable and the number of alleles per locus and 
average heterozygosities (a = 5-21, H exp = 0.435-0.924) 
were within the range of variation reported for other 
clupeids (a=l-56, H exp =0. 066-0. 98, Brown et al., 2000; 
McPherson et al., 2001; Olsen et al., 2002; Faria et al., 
2004; Anderson and McDonald, 2007; Volk et al., 2007). 
