Table 2.
Nucleotide properties of used loci and details of phylogenetic analysis.
| Phylogenetic marker | |||||
|---|---|---|---|---|---|
| Parameters | gyrB | recA | toxR | pyrH | Concatenated dataset |
| Fragment characterization | DNA gyrase subunit B | Recombinase A | Cholera toxin transcriptional activator | Uridylate kinase | Not applicable |
| Number of sequences | 555 | 555 | 555 | 555 | 555 |
| Number of characters: total/pars. inform./constant | 487/57/410 | 648/167/477 | 658/140/497 | 477/38/432 | 2270/413/1816 |
| Parameters of MCMC analysis | |||||
| Mean nt frequencies* A/C/G/T | 0.27/0.22/0.26/0.5 | 0.26/0.22/0.27/0.25 | 0.31/0.24/0.21/0.24 | 0.21/0.20/0.30/0.29 | Not applicable |
| Substitution rates* A–C/A–G/A–T/C–G/C–T/G–T | 0.05/0.29/0.08/0.08/0.40/0.10 | 0.05/0.39/0.02/0.14/0.30/0.10 | 0.10/0.37/0.06/0.07/0.29/0.11 | 0.02/0.06/0.05/0.02/0.82/0.03 | Not applicable |
| Number of generations/discarded first generations | 1 000 000/700 | 1 000 000/1000 | 1 000 000/500 | 1 000 000/500 | 10 000 000/700 |
| Total tree length | 63.23 | 62.25 | 62.01 | 60.45 | 62.23 |
| DNA polymorphism analysis and neutrality analysis | |||||
| Number of haplotypes | 170 | 170 | 170 | 170 | 170 |
| Number of sites excluding gaps and missing data | 487 | 648 | 653 | 477 | 2265 |
| Segregation sites/number of mutations | 76/87 | 171/214 | 157/177 | 42/49 | 290/59 |
| Nucleotide diversity, Pi | 0.0242 | 0.02324 | 0.02421 | 0.00906 | 0.851/0.01886 |
| Tajima’s D (NonSyn/Syn/ratio) | –1.47/–0.61/2.41 | –2.27/–1.83/1.24 | –1.95/–1.24/1.54 | –1.076/–1.39/0.772 | Not applicable |
| Tajima’s D test | n.s. (–0.70623, P > 0.1) | –1.905, P < 0.05 | n.s. (–1.56513, P > 0.05) | n.s. (–1.49561, P > 0.1) | |