Anderson and Karel: Limited genetic structure of Brevoortia patronus revealed by microsatellite markers 
77 
Table 2 
Statistics for 19 polymorphic microsatellite loci in Gulf Menhaden (Brevoortia patronus ) col- 
lected throughout the Gulf of Mexico in 2002-04. The statistics include the overall number 
of alleles observed; heterozygosity, both observed ( H 0 ) and expected (H e Y, P-value of Hardy- 
Weinberg equilibrium (HWE) exact tests; null allele presence and frequency; and polymorphic 
information content (PIC). Statistical significance of the HWE P-value (initial a=0.05) was 
assessed before (*) and after (**) sequential Bonferroni correction. Loci in italic type were 
described originally in a study of American Shad ( Alosa sapidissima) (Waters et al., 2000). 
Locus 
Alleles 
H 0 
H e 
HWE (P) 
Null alleles 
Null freq. 
PIC 
Bp003 
15 
0.627 
0.690 
0.227 
no 
na 
0.687 
BpQ17 
10 
0.364 
0.666 
0.000** 
yes 
0.17 
0.664 
Bp039 
7 
0.653 
0.613 
0.081 
no 
na 
0.611 
Bpl21 
15 
0.847 
0.851 
0.794 
no 
na 
0.847 
Bpl55 
16 
0.778 
0.892 
0.017* 
yes 
0.05 
0.888 
Bp221 
17 
0.847 
0.850 
0.663 
no 
na 
0.846 
Bp230 
17 
0.863 
0.908 
0.149 
no 
na 
0.905 
Bp239 
21 
0.838 
0.935 
0.014* 
yes 
0.03 
0.931 
Bp275 
24 
0.763 
0.919 
0.017* 
yes 
0.06 
0.915 
Bp301 
12 
0.414 
0.867 
0.000** 
yes 
0.25 
0.863 
Bp473 
7 
0.615 
0.624 
0.077 
no 
na 
0.622 
Bp489 
6 
0.085 
0.099 
0.213 
no 
na 
0.098 
Bp501 
15 
0.907 
0.883 
0.713 
no 
na 
0.880 
Bp531 
19 
0.915 
0.907 
0.711 
no 
na 
0.903 
AF039657 
15 
0.686 
0.690 
0.916 
no 
na 
0.687 
AF039658 
21 
0.763 
0.868 
0.101 
yes 
0.03 
0.865 
AF039660 
13 
0.271 
0.666 
0.000** 
yes 
0.30 
0.663 
AF039661 
6 
0.102 
0.138 
0.001** 
yes 
0.10 
0.137 
AF049462 
26 
0.831 
0.930 
0.011* 
yes 
0.02 
0.926 
Overall 
14.8 
0.641 
0.737 
— 
— 
— 
— 
Species assignment was carried out with 14 genetic 
loci, excluding the 4 loci that deviated from HWE in 
Gulf Menhaden after Bonferroni adjustment (BP017, 
BP301, AF039660, and AF039661) and also exclud- 
ing the locus that did not amplify a product in spe- 
cies other than Gulf Menhaden (BP155). Ten of the 14 
loci contributed more than 95% to the cumulative lo- 
cus score in species assignment (Table 4). Interestingly, 
the microsatellite that ranked highest in species as- 
signment (AF039657) was initially developed for use in 
American Shad (Waters et ah, 2000). With a stringency 
ofLOD=2, 3 genetic loci were required to accurately as- 
sign all individuals to species. This number increased 
to 6 loci at LOD=3, and all 14 loci at LOD=4. At each 
level of stringency, 100% of individuals were correctly 
assigned to species. 
The Powsim analysis of Gulf Menhaden was conduct- 
ed with 15 loci and excluded the previously mentioned 
loci that deviated from HWE and had high null allele 
frequencies (BP017, BP301, AF039660, and AF039661). 
At an effective population size of 500, significant ge- 
netic divergence among populations was detected in all 
500 simulations after 10 generations of drift (F st =0.01), 
with both sample sizes. At an effective population size 
of 1000 (F st =0.004), significant genetic divergence was 
detected in 91% (454/500) of simulations with a sample 
size of 40 individuals and in 96% (480/500) of simu- 
lations when n- 50. At the lowest level of genetic di- 
vergence (F st =0.001), only 16% (78/500) of simulations 
resulted in a significant genetic divergence result when 
n=40 and 22% (112/500) of simulations had that result 
when n=50. 
Analysis of genetic structure of Gulf Menhaden was 
conducted with the same 15 loci that were used in 
population assignment (excluding HWE deviating loci). 
There was little evidence for significant genetic struc- 
ture among the 4 Gulf Menhaden samples. The Struc- 
ture analysis indicated that K= 1 was the most likely 
number of genetic clusters represented in the sample 
(posterior probability P>0.999). When individual ad- 
mixture scores for levels of K> 1 were examined, all in- 
dividuals were approximately equal admixtures of all 4 
genetic clusters. Such a finding is expected in the case 
of no genetic structure, and in such cases the admix- 
ture summary statistic (a) can vary greatly during the 
course of Structure runs (Pritchard et al., 2000). The 
AMOVA results similarly indicated a lack of genetic 
structure among samples (F st =0.002, P=1.0), but there 
was a small but significant amount of structure among 
individuals within samples (Fi s =0.052, P<0.001). A post 
hoc examination of locus-specific F xs indicated that 6 
loci of the original suite of 15 loci had significantly 
