Table 3.
Comparison of performance of data partitions under maximum parsimony and in a Bayesian framework
| mtCOI | mtLSU | wg | mtCOI+mtLSU | mtCOI+wg | mtLSU+wg | mtCOI+mtLSU+wg | |
|---|---|---|---|---|---|---|---|
| Total Characters | 498 | 506 | 472 | 1004 | 970 | 978 | 1476 |
| Variable (%) | 173 (34.74) | 110 (21.74) | 145 (30.72) | 283 (28.19) | 328 (32.78) | 255 (26.07) | 428 (29.0) |
| Maximum Parsimony | |||||||
| Uninformative characters | 12 | 55 | 41 | 67 | 53 | 96 | 108 |
| Informative characters (%) | 161 (32.33) | 55 (10.87) | 104 (22.03) | 216 (21.51) | 265 (27.32) | 159 (16.26) | 320 (21.68) |
| Consistency Index CI | 0.2819 | 0.6543 | 0.6822 | 0.3373 | 0.3553 | 0.6528 | 0.3911 |
| Retention Index RI | 0.6246 | 0.7833 | 0.9085 | 0.6384 | 0.7035 | 0.8671 | 0.7078 |
| Rescaled consistency index RC | 0.1761 | 0.5125 | 0.6197 | 0.2153 | 0.2499 | 0.5660 | 0.2768 |
| Tree length | 965 | 188 | 258 | 1171 | 1261 | 458 | 1460 |
| No mp trees | 16 | 416 | 64 | 16 | 25 | 128 | 2 |
| Polyspecific nodes bootstrap ≥70 | 6 | 2 | 11 | 7 | 9 | 11 | 13 |
| Bayesian/MCMC | |||||||
| Selected model under hLRT | GTR+I+G | K81uf+I+G | TrN+G | GTR+I+G/K81uf+I+G | GTR+I+G/TrN+G | K81uf+I+G/TrN+G | GTR+I+G/K81uf+I+G/TrN+G |
| Polyspecific nodes pp ≥0.95 | 6 | 4 | 14 | 9 | 16 | 15 | 18 |
| Average distance between runs | 0.007708 | 0.026674 | 0.007544 | 0.016278 | 0.004448 | 0.011423 | 0.002051 |
| Log likelihood | −4635.113 | −1912.363 | −2346.681 | −6627.26 | −7158,902 | −4417.382 | −9156.271 |
| Tree length | 6.369 | 6.734 | 9.43 | 2.995 | 3.252 | 6.224 | 2.303 |
| Model parameter rate of change A/C | 0.0192 | 0.02339 | 0.04757 | 0.02699 | 0.03718 | 0.03693 | 0.03958 |
| Model parameter rate of change A/G | 0.448 | 0.731 | 0.312 | 0.412 | 0.238 | 0.381 | 0.273 |
| Model parameter rate of change A/T | 0.03424 | 0.03627 | 0.07971 | 0.04833 | 0.07508 | 0.102 | 0.06585 |
| Model parameter rate of change G/C | 0.03807 | 0.0803 | 0.07486 | 0.03345 | 0.04837 | 0.114 | 0.06314 |
| Model parameter rate of change C/T | 0.449 | 0.113 | 0.413 | 0.463 | 0.584 | 0.315 | 0.538 |
| Model parameter rate of change G/T | 0.01256 | 0.01591 | 0.07246 | 0.01619 | 0.01704 | 0.05166 | 0.0203 |
| Stationary nucleotide frequency of A | 0.355 | 0.411 | 0.234 | 0.356 | 0.279 | 0.322 | 0.32 |
| Stationary nucleotide frequency of C | 0.203 | 0.076 | 0.323 | 0.165 | 0.253 | 0.2 | 0.195 |
| Stationary nucleotide frequency of G | 0.082 | 0.097 | 0.268 | 0.104 | 0.189 | 0.193 | 0.164 |
| Stationary nucleotide frequency of T | 0.361 | 0.416 | 0.175 | 0.374 | 0.279 | 0.284 | 0.321 |
| Shape parameter α for gamma distribution of rate variation. | 0.911 | 0.129 | 0.119 | 0.169 | 0.499 | 0.144 | 0.229 |
| Proportion of invariable sites | 0.579 | 0.783 | 0.312 | 0.146 | 0.476 | 0.324 | 0.291 |