Table 2.
Best-fitting models and parameter values for separate (rbcL, 18S, 26S, 5.8S, pgiC, and SQD1), simultaneous nuclear, and simultaneous nuclear + plastid datasets and in this study. “G” = gamma distribution shape parameter (Yang, 1994). “GTR” = general-time-reversible model (Tavaré, 1986). “I” = proportion of invariable sites. “pInv” = proportion of invariable sites. “Simultaneous-1” = 18S + 26S + 5.8S + pgiC + SQD1. “Simultaneous-2” = 18S + 26S + 5.8S + pgiC + SQD1 + rbcL.
| Region | Model (AIC) | Base frequencies |
Substitution model (rate matrix) |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | C | G | T | A–C | A–G | A–T | C–G | C–T | G–T | pInv | G | ||
| rbcL | GTR + I + G | 0.2857 | 0.2433 | 0.2255 | 0.2455 | 0.4631 | 3.9209 | 0.2720 | 0.5053 | 2.4318 | 1.0000 | 0.3140 | 1.0406 |
| 18S | GTR + I + G4 | 0.2781 | 0.2738 | 0.2168 | 0.2313 | 0.6532 | 6.6774 | 1.4011 | 0.3697 | 2.5304 | 1.0000 | 0.6271 | 0.5937 |
| 26S | GTR + I + G | 0.2181 | 0.3153 | 0.2171 | 0.2496 | 0.8700 | 9.0898 | 1.9289 | 0.3311 | 3.0681 | 1.0000 | 0.5842 | 0.7472 |
| 5.8S | TIM2ef + I + G4 | 0.2500 | 0.2500 | 0.2500 | 0.2500 | 1.8204 | 4.9269 | 1.8204 | 1.0000 | 11.7664 | 1.0000 | 0.3311 | 0.5161 |
| pgiC | TVM + I + G4 | 0.2169 | 0.2487 | 0.2353 | 0.2990 | 1.5604 | 8.0577 | 1.8589 | 1.6658 | 8.0577 | 1.0000 | 0.4050 | 1.2491 |
| SQD1 | TIM3+I + G | 0.2077 | 0.2875 | 0.3089 | 0.1959 | 1.3327 | 3.7081 | 1.0000 | 1.3327 | 5.8799 | 1.0000 | 0.4093 | 1.0064 |
| Simultaneous-1 | GTR + F + I + G4 | 0.2410 | 0.2790 | 0.2310 | 0.2480 | 0.9487 | 5.8027 | 1.1042 | 0.8629 | 4.0430 | 1.0000 | 0.5810 | 0.6100 |
| Simultaneous-2 | GTR + I + G4 | 0.2488 | 0.2598 | 0.2411 | 0.2503 | 0.7940 | 5.0369 | 0.7221 | 0.7775 | 3.7732 | 1.0000 | 0.4813 | 0.6299 |