TABLE 4.
Summary of polymorphic sites, nucleotide diversity per site, global rate ratios, and positively/negatively selected codon sitesa
| Species (no. of strains) | Gene | No. of nt | No. of codons | No. (%) of polymorphic sites | Mean nucleotide diversity (π) ± SD | Mean dN/dS (global ω; 95% CI) | No. of sites (%) |
|
|---|---|---|---|---|---|---|---|---|
| Negatively selected | Positively selected | |||||||
| T. vincentii (11) | flaA | 1,062 | 353 | 19 (1.79) | 0.006 ± 0.0010 | 0.103 (0.032–0.239) | 1 (0.28) | 0 |
| recA | 1,326 | 441 | 24 (1.71) | 0.004 ± 0.0005 | 0.060 (0.019–0.139) | 0 | 0 | |
| pyrH | 687 | 228 | 106 (14.60) | 0.031 ± 0.0194 | 0.067 (0.042–0.102) | 0 | 0 | |
| 16S | 1,450 | NA | 6 (0.41) | 0.001 ± 0.0004 | NA | NA | NA | |
| T. medium (1) | flaA | 1,068 | 355 | NA | NA | NA | NA | NA |
| recA | 1,362 | 453 | NA | NA | NA | NA | NA | |
| pyrH | 687 | 228 | NA | NA | NA | NA | NA | |
| 16S | 1,450 | NA | NA | NA | NA | NA | NA | |
| T. sinensis (4) | flaA | 1,059 | 352 | 5 (0.47) | 0.003 ± 0.0008 | 0.058 (0.003–0.257) | 0 | 0 |
| recA | 1,338 | 445 | 50 (3.57) | 0.019 ± 0.0066 | 0.052 (0.019–0.112) | 0 | 0 | |
| pyrH | 687 | 228 | 23 (3.17) | 0.017 ± 0.0051 | 0.183 (0.078–0.357) | 0 | 0 | |
| 16S | 1,450 | NA | 0 (0.00) | 0.000 ± 0.0000 | NA | NA | NA | |
| Treponema sp. IB (3) | flaA | 1,068 | 355 | 5 (0.47) | 0.003 ± 0.0010 | 0.074 (0.004–0.328) | 0 | 0 |
| recA | 1,368 | 455 | 124 (8.85) | 0.061 ± 0.0282 | 0.052 (0.019–0.112) | 0 | 0 | |
| pyrH | 687 | 228 | 0 (0.00) | 0.000 ± 0.0000 | 0.001 (0.00–10000) | 0 | 0 | |
| 16S | 1,450 | NA | 6 (0.41) | 0.003 ± 0.0008 | NA | NA | NA | |
| Treponema sp. IC (4) | flaA | 1,065 | 354 | 6 (0.56) | 0.003 ± 0.0006 | 0.148 (0.025–0.456) | 0 | 0 |
| recA | 1,350 | 449 | 40 (2.86) | 0.016 ± 0.0043 | 0.108 (0.052–0.195) | 0 | 0 | |
| pyrH | 687 | 228 | 10 (1.38) | 0.009 ± 0.0021 | 0.061 (0.102–0.190) | 1 (0.44) | 0 | |
| 16S | 1,450 | NA | 4 (0.28) | 0.001 ± 0.0006 | NA | NA | NA | |
| T. denticola (41) | flaA | 1,050 | 349 | 218 (20.76) | 0.029 ± 0.0070 | 0.121 (0.097–0.149) | 13 (3.71) | 0 |
| recA | 1,245 | 414 | 185 (13.20) | 0.035 ± 0.0030 | 0.094 (0.076–0.115) | 58 (13.98) | 1 | |
| pyrH | 696 | 231 | 149 (20.52) | 0.031 ± 0.0067 | 0.082 (0.061–0.106) | 31 (13.36) | 0 | |
| 16S | 1,450 | NA | 25 (1.72) | 0.003 ± 0.0005 | NA | NA | NA | |
| T. putidum (7) | flaA | 1,050 | 349 | 2 (0.19) | 0.001 ± 0.0002 | 0.00 (0.00–0.263) | 0 | 0 |
| recA | 1,245 | 414 | 154 (10.99) | 0.058 ± 0.0064 | 0.122 (0.091–0.160) | 9 (2.17) | 0 | |
| pyrH | 696 | 231 | 3 (0.41) | 0.001 ± 0.0004 | NA | 0 | 0 | |
| 16S | 1,450 | NA | 20 (1.38) | 0.005 ± 0.0016 | NA | NA | NA | |
a
NA, not applicable; nt, nucleotides; 95% CI, 95% confidence interval.