Table 2. Summary of sample sizes and variability in the nine genes in each of the seven collection sites.
| Collection | Gene | N | S | η | H | π | θ | Tajima's D | D ratio (Rep./Silent) |
|---|---|---|---|---|---|---|---|---|---|
| Florida | ace | 49 | 11 | 12 | 11 | 0.0043 | 0.0073 | -1.076 | 0.57 |
| Florida | dhp | 44 | 69 | 100 | 48 | 0.0196 | 0.0593 | -2.23** | 1.33 |
| Florida | trosp | 50 | 19 | 20 | 20 | 0.0056 | 0.0117 | -1.521 | 0.81 |
| Florida | ser | 50 | 65 | 72 | 52 | 0.0143 | 0.0235 | -1.275 | 2.63 |
| Florida | def | 35 | 73 | 80 | 34 | 0.0288 | 0.0402 | -0.961 | 29.36 |
| Florida | hsp | 50 | 31 | 36 | 42 | 0.0137 | 0.0266 | -1.502 | 1.57 |
| Florida | ixo | 48 | 34 | 36 | 42 | 0.0224 | 0.0449 | -1.561 | 1.17 |
| Florida | fer | 49 | 26 | 28 | 38 | 0.0183 | 0.0195 | -0.189 | -1.25 |
| Florida | 16s | 49 | 51 | 54 | 13 | 0.0299 | 0.0351 | -0.511 | |
| Georgia | ace | 45 | 38 | 41 | 32 | 0.0253 | 0.0255 | -0.027 | -0.35 |
| Georgia | dhp | 37 | 24 | 25 | 23 | 0.0072 | 0.0194 | -1.944* | 1.29 |
| Georgia | trosp | 42 | 23 | 23 | 25 | 0.0062 | 0.0140 | -1.687 | 6.4 |
| Georgia | ser | 46 | 49 | 52 | 51 | 0.0129 | 0.0171 | -0.798 | 4.69 |
| Georgia | def | 33 | 92 | 134 | 40 | 0.0480 | 0.0683 | -1.032 | 5.04 |
| Georgia | hsp | 44 | 33 | 39 | 52 | 0.0132 | 0.0296 | -1.758 | 1.18 |
| Georgia | ixo | 45 | 27 | 29 | 25 | 0.0306 | 0.0367 | -0.509 | -7.19 |
| Georgia | fer | 50 | 32 | 39 | 30 | 0.0131 | 0.0270 | -1.601 | 3.42 |
| Georgia | 16s | 47 | 34 | 39 | 21 | 0.0229 | 0.0252 | -0.303 | |
| Mississippi | ace | 44 | 20 | 21 | 15 | 0.0123 | 0.0130 | -0.15 | -0.82 |
| Mississippi | dhp | 42 | 31 | 43 | 33 | 0.0116 | 0.0257 | -1.756 | 1.47 |
| Mississippi | trosp | 43 | 28 | 28 | 19 | 0.0071 | 0.0171 | -1.795* | 0.9 |
| Mississippi | ser | 46 | 63 | 73 | 45 | 0.0120 | 0.0243 | -1.66 | 1.15 |
| Mississippi | def | 33 | 69 | 75 | 27 | 0.0255 | 0.0379 | -1.116 | 2.99 |
| Mississippi | hsp | 50 | 60 | 72 | 59 | 0.0206 | 0.0533 | -1.993* | 1.46 |
| Mississippi | ixo | 37 | 51 | 58 | 48 | 0.0401 | 0.0763 | -1.572 | 1.19 |
| Mississippi | fer | 47 | 49 | 59 | 50 | 0.0200 | 0.0413 | -1.666 | 7.45 |
| Mississippi | 16s | 49 | 57 | 59 | 16 | 0.0238 | 0.0387 | -1.341 | |
| North Carolina | ace | 29 | 33 | 35 | 23 | 0.0252 | 0.0237 | 0.21 | -0.85 |
| North Carolina | dhp | 48 | 38 | 50 | 41 | 0.0179 | 0.0290 | -1.221 | 12.86 |
| North Carolina | trosp | 48 | 22 | 24 | 27 | 0.0072 | 0.0142 | -1.469 | 0.79 |
| North Carolina | ser | 46 | 41 | 42 | 36 | 0.0114 | 0.0138 | -0.557 | 0.63 |
| North Carolina | def | 44 | 99 | 113 | 51 | 0.0407 | 0.0560 | -0.912 | 7.7 |
| North Carolina | hsp | 48 | 23 | 29 | 38 | 0.0093 | 0.0216 | -1.741 | 1.16 |
| North Carolina | ixo | 49 | 29 | 35 | 38 | 0.0203 | 0.0435 | -1.648 | 1.4 |
| North Carolina | fer | 50 | 22 | 28 | 50 | 0.0165 | 0.0194 | -0.449 | -5.79 |
| North Carolina | 16s | 50 | 22 | 24 | 14 | 0.0116 | 0.0153 | -0.799 | |
| Maryland | ace | 50 | 3 | 3 | 3 | 0.0034 | 0.0018 | 1.573 | n.a. |
| Maryland | dhp | 33 | 51 | 53 | 31 | 0.0211 | 0.0331 | -1.215 | 1.66 |
| Maryland | trosp | 46 | 14 | 14 | 13 | 0.0049 | 0.0084 | -1.164 | 1.4 |
| Maryland | ser | 46 | 44 | 45 | 32 | 0.0105 | 0.0148 | -0.93 | 2.14 |
| Maryland | def | 44 | 43 | 43 | 17 | 0.0074 | 0.0201 | -2.009* | n.a. |
| Maryland | hsp | 49 | 34 | 38 | 39 | 0.0139 | 0.0282 | -1.579 | 1.97 |
| Maryland | ixo | 49 | 31 | 40 | 47 | 0.0226 | 0.0497 | -1.71 | 0.67 |
| Maryland | fer | 50 | 19 | 19 | 27 | 0.0099 | 0.0132 | -0.713 | 0.68 |
| Maryland | 16s | 50 | 10 | 10 | 12 | 0.0033 | 0.0064 | -1.39 | |
| New Jersey | ace | 50 | 8 | 9 | 12 | 0.0041 | 0.0054 | -0.595 | -0.01 |
| New Jersey | dhp | 41 | 43 | 45 | 37 | 0.0171 | 0.0272 | -1.198 | 1.02 |
| New Jersey | trosp | 46 | 56 | 63 | 32 | 0.0084 | 0.0374 | -2.514*** | 1.07 |
| New Jersey | ser | 49 | 62 | 67 | 33 | 0.0115 | 0.0220 | -1.552 | 1.05 |
| New Jersey | def | 46 | 22 | 23 | 23 | 0.0040 | 0.0102 | -1.826* | 1.13 |
| New Jersey | hsp | 49 | 46 | 58 | 58 | 0.0185 | 0.0431 | -1.832* | 1.91 |
| New Jersey | ixo | 41 | 29 | 35 | 39 | 0.0307 | 0.0451 | -1.009 | -2.22 |
| New Jersey | fer | 50 | 27 | 29 | 35 | 0.0125 | 0.0201 | -1.143 | 3 |
| New Jersey | 16s | 50 | 8 | 8 | 12 | 0.0033 | .0052 | -0.978 | |
| Wisconsin | ace | 47 | 7 | 7 | 11 | 0.0048 | 0.0043 | 0.311 | -0.66 |
| Wisconsin | dhp | 46 | 54 | 81 | 45 | 0.0183 | 0.0473 | -2.02* | 0.87 |
| Wisconsin | trosp | 46 | 7 | 7 | 8 | 0.0031 | 0.0042 | -0.582 | 1.25 |
| Wisconsin | ser | 46 | 51 | 65 | 52 | 0.0104 | 0.0214 | -1.664 | 1 |
| Wisconsin | def | 40 | 35 | 37 | 31 | 0.0086 | .0169 | -1.56 | -2.28 |
| Wisconsin | hsp | 49 | 35 | 47 | 60 | 0.0125 | 0.0349 | -2.035* | 1.09 |
| Wisconsin | ixo | 49 | 21 | 23 | 23 | 0.0207 | 0.0286 | -0.819 | 1.5 |
| Wisconsin | fer | 44 | 21 | 21 | 30 | 0.0134 | 0.0149 | -0.309 | -3.06 |
| Wisconsin | 16s | 45 | 8 | 8 | 9 | 0.0022 | 0.0052 | -1.623 | |
| All | ace | 314 | 61 | 68 | 81 | 0.0134 | 0.0307 | -1.577 | 0.54 |
| All | dhp | 291 | 110 | 181 | 148 | 0.0166 | 0.0988 | -2.447*** | 1.11 |
| All | trosp | 323 | 95 | 113 | 96 | 0.0098 | 0.0493 | -2.304** | 1.14 |
| All | ser | 329 | 159 | 201 | 238 | 0.0124 | 0.0480 | -2.172** | 1.25 |
| All | def | 275 | 162 | 226 | 168 | 0.0298 | 0.0857 | -1.935* | 1.57 |
| All | hsp | 339 | 100 | 136 | 100 | 0.0148 | 0.0734 | -2.307** | 1.19 |
| All | ixo | 318 | 87 | 122 | 205 | 0.0282 | 0.1112 | -2.155** | 1.61 |
| All | fer | 340 | 78 | 103 | 202 | 0.0172 | 0.0520 | -1.911* | 2.11 |
| All | 16s | 340 | 106 | 116 | 72 | 0.0210 | 0.0531 | -1.813* |
N is number of sequences obtained for each gene in the overall study and in each of the seven collection sites. S is the number of SNPs appearing in more than one sequence and η is the overall number of SNPs (including singletons) while H is the number of unique alleles. π is the average observed number of pairwise differences per nucleotide. θ, calculated from η, is the average expected number of pairwise differences per nucleotide. Tajima’s D is the normalized difference between π and θ. The significance of D is indicated by
*p<0.05
**p<0.01
***p<0.001.
The D ratio is only calculated for exons and is D for replacements substitutions divided by D for silent substitutions.