Table 1.
Summary of initial conditions and results obtained in phylogenetic reconstructions and model testing.
| Analysis | Mitochondrial | Nuclear | Combined |
| 129 taxa, 2866 bp | 73 taxa, 978 bp | 73 taxa, 3844 bp | |
| MP | |||
| RA replicates | 100 | 5 | 100 |
| Bootstrap replicates | 1000 (10 RA rep.) | _ | 1000 (10 RA rep.) |
| Optimal trees retained | 8 | >5 × 104 | 36 |
| Optimal tree score (steps) | 11208 | 387 | 9002 |
| Consistency index | 0.188 | 0.749 | 0.25 |
| Consensus type | strict | 50% majority rule | 90% majority rule |
| Initial model (ML and BI) | |||
| Akaike information criterion | GTR+I+Γ | HKY+I+Γ | GTR+I+Γ |
| Number of substitution rate parameters | 6 | 2 | 6 |
| ML – Garli | |||
| Search replicates | 10 | 5 | 10 |
| Automatic termination* (generations) | 1 × 104 | 1 × 104 | 1 × 104 |
| Optimal tree score (lnL) | -52003.50 | -3791.51 | -43666.78 |
| Bootstrap | _ | _ | _ |
| ML – RAxML | |||
| Search replicates | 10 | 5 | 5 |
| Partitions | none | none | none |
| Optimal tree score (lnL) | -52145.37 | -3790.72 | -43726.10 |
| Bootstrap replicates** | 150 | 400 | 200 |
| BI | |||
| Search replicates | 3 | 3 | 3 |
| Partitions | none | none | none |
| Generations | 1 × 107 | 6 × 106 | 6 × 106 |
| Burn-in | 2.5 × 106 | 1.5 × 106 | 1.5 × 106 |
| Post-burn-in trees (combined searches) | ~2.15 × 105 | ~1.35 × 105 | ~1.35 × 105 |
| Mean lnL | -52160 | -4119.14 | -43760 |
| Efective Sample Size (all parameters) | >200 | >200 | >200 |
| Consensus type | 50% majority rule | 50% majority rule | 50% majority rule |
RA, random addition
*genthreshfortopoterm command
**rapid bootstrapping algorithm via automatic termination