Table 3.
Nucleotide diversity observed within the Aeromonas strains characterized in this studya
| Locus or concatenated sequence for cluster | Fragment size (bp) | No. of alleles | G+C content | No. (%) of polymorphic sites | No. of parsimony informative sites | Synonymous changes | Nonsynonymous changes | Ks | Ka | Tajima's D test | θ | π |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus (avg values) | ||||||||||||
| gyrB | 477 | 81 | 0.596 | 140 (29.3) | 96 | 174 | 9 | 0.23873 | 0.00474 | −1.10866 | 0.057 | 0.053 |
| groL | 510 | 89 | 0.584 | 199 (39) | 145 | 176 | 21 | 0.40048 | 0.01206 | −0.58984 | 0.094 | 0.083 |
| gltA | 495 | 84 | 0.603 | 150 (30.3) | 126 | 156 | 15 | 0.31618 | 0.01663 | −0.33598 | 0.080 | 0.072 |
| metG | 504 | 83 | 0.576 | 178 (35.3) | 143 | 137 | 15 | 0.35801 | 0.01965 | −0.61507 | 0.084 | 0.075 |
| ppsA | 537 | 88 | 0.637 | 233 (43.3) | 171 | 176 | 25 | 0.40523 | 0.01801 | −0.94769 | 0.098 | 0.086 |
| recA | 561 | 87 | 0.595 | 176 (31.3) | 136 | 194 | 9 | 0.24533 | 0.00443 | −1.01709 | 0.058 | 0.054 |
| Concatenated sequence | 3,084 | 89 | 0.599 | 1,073 (34.7) | 807 | 1,013 | 91 | 0.25229 | 0.01233 | −0.84311 | 0.078 | 0.070 |
| Concatenated sequence for: | ||||||||||||
| A. salmonicida-A. bestiarumb | 3,084 | 12 | 0.601 | 395 (12.8) | 250 | 382 | 38 | 0.16307 | 0.00709 | −0.09657 | 0.048 | 0.045 |
| A. veroniic | 3,084 | 35 | 0.598 | 571 (18.5) | 337 | 572 | 73 | 0.12883 | 0.00275 | −1.38050 | 0.035 | 0.033 |
| A. allosaccharophila | 3,084 | 3 | 0.598 | 68 (2.2) | 0 | 59 | 10 | 0.05092 | 0.00315 | 0.015 | 0.015 | |
| A. schubertiid | 3,084 | 2 | 0.619 | 399 (13) | 0 | 307 | 92 | 0.38629 | 0.04596 | 0.156 | 0.129 | |
| A. enteropelogenes | 3,084 | 2 | 0.607 | 99 (3.2) | 0 | 99 | 3 | 0.12679 | 0.00171 | 0.033 | 0.032 | |
| A. sobria | 3,084 | 27 | 0.589 | 394 (12.7) | 258 | 377 | 28 | 0.10795 | 0.00219 | −0.92751 | 0.029 | 0.028 |
| A. hydrophila | 3,084 | 4 | 0.617 | 115 (3.7) | 24 | 114 | 2 | 0.08056 | 0.00043 | −0.23817 | 0.020 | 0.020 |
| A. media-A. caviaee | 3,084 | 7 | 0.619 | 414 (13.4) | 145 | 384 | 48 | 0.18365 | 0.00951 | −0.86238 | 0.056 | 0.052 |
a
π, nucleotide diversity per site; θ, average number of nucleotide differences per site; Ks, number of synonymous changes per synonymous site; Ka, number of nonsynonymous changes per nonsynonymous site.
b
This group also includes DSM 19604, type strain of A. popoffii.
c
This group also includes CECT 4228, type strain of A. jandaei.
d
This group also includes DSM 17534, type strain of A. eucrenophila.
e
This group also includes DSM 11577, type strain of A. encheleia.