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. Author manuscript; available in PMC: 2016 Mar 14.
Published in final edited form as: Mol Phylogenet Evol. 2007 Nov 21;46(2):776–791. doi: 10.1016/j.ympev.2007.11.003

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