Table 1.
Log likelihood and AICc values a for empirical models and the GTR model optimized for exposed and buried sites. The GTR model had the best fit (note bold AICc value).
| Structural Subset | Model | T2 b | T3 b | Cni+Bil c | Cni+Pla c | lnL | AICc |
|---|---|---|---|---|---|---|---|
| Exposed | GTR | 92 | - | - | 98 | −1,212,232.985 | 2,424,956.474 |
| LG | 100 | - | - | 100 | −1,222,489.017 | 2,445,088.162 | |
| WAG | 87 | - | - | 100 | −1,225,898.553 | 2,451,907.235 | |
| VT | 96 | - | - | 98 | −1,225,672.633 | 2,451,455.395 | |
| rtREV | 90 | - | - | 98 | −1,222,733.929 | 2,445,577.986 | |
| JTTDCMUT | 94 | - | - | 98 | −1,229,028.451 | 2,458,167.031 | |
| Buried | GTR | - | 82 | 64 | - | −1,045,694.924 | 2,091,880.072 |
| LG | - | 87 | 62 | - | −1,050,022.577 | 2,100,155.267 | |
| WAG | - | 85 | 58 | - | −1,054,829.256 | 2,109,768.626 | |
| VT | - | 81 | 61 | - | −1,059,148.671 | 2,118,407.455 | |
| rtREV | - | 89 | 52 | - | −1,054,432.123 | 2,108,974.359 | |
| JTTDCMUT | - | 81 | - | 54 | −1,061,103.295 | 2,122,316.704 |
a AICc was calculated using: AICc = 2k − 2(lnL) + (2k2 + 2k) / (n − k − 1) where k is the number of parameters and n is the number of sites. This is the formula for the AICc that is typically used in phylogenetics. b RaxML bootstrap support for T2 or T3. c RAxML bootstrap support for the cnidaria+bilateria clade or the cnidaria + placozoa clade.