Table 2.
Properties of Sequence Data Partitions Based on Sequenced Region, Codon Position and Genome Location
| Data set | PIS | Empirical base frequency | Rates | Ts:Tv rate (MP Tv:Ts)a | Shape | Pinvar | ML Model | ||
|---|---|---|---|---|---|---|---|---|---|
| COI 1,2,3 | 165 | A = 0.278 C = 0.146 |
G = 0.174 T = 0.402 |
A-C = 0.000 A-G = 21.995 A-T = 21.885 |
C-G = 0.000 C-T = 72.908 G-T = 1.000 |
2.287 (2:1) |
2.100 | 0.631 | GTR+I+G |
| COI 1,2 | 32 | A = 0.201 C = 0.203 |
G = 0.243 T = 0.353 |
A-C = 0.000 A-G = 3.156 A-T = 4.787 |
C-G = 0.000 C-T = 72.078 G-T = 1.000 |
10.024 (10:1) |
- | 0.867 | GTR+I |
| COI 3 | 133 | A = 0.446 C = 0.071 |
G = 0.031 T = 0.448 |
A-C = 0.0000 A-G = 12.996 A-T = 0.207 |
C-G = 0.000 C-T = 4.894 G-T = 1.000 |
5.275 (5:1) |
0.769 | 0.063 | GTR+I+G |
| COII 1,2,3 | 158 | A = 0.319 C = 0.118 |
G = 0.139 T = 0.424 |
A-C = 7.139 A-G = 24.723 A-T = 16.552 |
C-G = 0.000 C-T = 155.021 G-T = 1.000 |
4.489 (4:1) |
2.676 | 0.647 | GTR+I+G |
| CoII 1,2 | 32 | A = 0.285 C = 0.158 |
G = 0.188 T = 0.370 |
A-C = 8.528 A-G = 10.570 A-T = 0.000 |
C-G = 0.000 C-T = 48.380 G-T = 1.000 |
7.542 (8:1) |
- | 0.873 | GTR+I |
| COII 3 | 126 | A = 0.431 C = 0.083 |
G = 0.025 T = 0.463 |
A-C = 0.4255 A-G = 38.165 A-T = 0.175 |
C-G = 0.000 C-T = 22.982 G-T = 1.000 |
6.592 (6:1) |
0.516 | 0.223 | HKY+G |
| Mt 1,2,3 | 323 | A = 0.295 C = 0.134 |
G = 0.155 T = 0.417 |
A-C = 1.510 A-G = 22.441 A-T = 18.857 |
C-G = 0.000 C-T = 94.312 G-T = 1.000 |
3.045 (3:1) |
2.113 | 0.638 | GTR+I+G |
| Mt 1,2 | 64 | A = 0.239 C = 0.185 |
G = 0.218 T = 0.359 |
A-C = 5.798 A-G = 13.824 A-T = 2.814 |
C-G = 0.000 C-T = 70.327 G-T = 1.000 |
8.718 (9:1) |
- | 0.876 | GTR+I |
| cac | 113 | A = 0.224 C = 0.211 |
G = 0.224 T = 0.341 |
A-C = 4.291 A-G = 9.301 A-T = 1.607 |
C-G = 2.422 C-T = 9.301 G-T = 1.000 |
2.204 (2:1) |
0.629 | 0.455 | TVM+I+G |
| cac 3 | 97 | A = 0.2481 C = 0.251 |
G = 0.277 T = 0.243 |
A-C = 2.416 A-G = 4.943 A-T = 1.835 |
C-G = 1.620 C-T = 4.874 G-T = 1.000 |
2.178 (2:1) |
0.912 | 0.293 | K80+G |
| sc | 235 | A = 0.236 C = 0.337 |
G = 0.252 T = 0.176 |
A-C = 1.000 A-G = 3.329 A-G = 2.094 |
C-G = 2.094 C-T = 4.472 G-T = 1.000 |
1.190 (1:1) |
0.451 | 0.000 | TIM+I+G |
| sc 3 | 127 | A = 0.134 C = 0.134 |
G = 0.134 T = 0.410 |
A-C = 2.142 A-G = 3.837 A-T = 2.040 |
C-G = 0.000 C-T = 72.078 G-T = 1.000 |
1.516 (2:1) |
2.247 | 0.124 | HKY+G |
| Nu | 348 | A = 0.231 C = 0.276 |
G = 0.236 T = 0.257 |
A-C = 1.980 A-G = 5.834 A-G = 1.745 |
C-G = 1.670 C-T = 4.294 G-T = 1.000 |
1.447 (1:1) |
0.285 | 0.000 | TVM+G |
| Nu + mt 1,2,3 | 671 | A = 0.266 C = 0.215 |
G = 0.190 T = 0.329 |
A-C = 2.873 A-G = 11.868 A-G = 8.568 |
C-G = 7.867 C-T = 20.930 G-T = 1.000 |
1.574 2:1 |
1.352 | 0.546 | GTR+I+G |
| Nu + mt 1,2 | 412 | A = 0.235 C = 0.244 |
G = 0.226 T = 0.295 |
A-C = 3.112 A-G = 8.2980 A-G = 1.912 |
C-G = 5.240 C-T = 10.717 G-T = 1.000 |
1.814 (2:1) |
0.898 | 0.582 | GTR+I+G |
Note : Nucleotide composition, transformation rates and models of nucleotide change obtained from the Akaike Information Criterion test as implemented in ModelTest.a Transversions (Tv)/Transitions (Ts) ratios used in differential weighting in the MP analysis. CoI = cytochrome oxidase I; CoII = cytochrome oxidase II, cac = cacophony; sc = scute; Mt = mitochondrial genes; Nu = nuclear genes; PIS = number of parsimony-informative sites; Pinvar = proportion of invariant sites; Shape = shape parameter of the gamma distribution. 1, 2 and 3 indicate first, second and third codon positions, respectively.