Table 4.
Parameter Estimates for the Best Trees Under Four Sets of Modeling Assumptions
| Parameter | Model 1 | Model 2 | Model 3 | Model 4 | |
| α | 0.155 ± 0.016 | 0.125 ± 0.015 | 0.051 ± 0.013 | ||
| β | 0.174 ± 0.019 | 0.200 ± 0.021 | 0.217 ± 0.023 | ||
| γ | 0.084 ± 0.007 | 0.071 ± 0.007 | 0.078 ± 0.009 | ||
| δ | 0.080 ± 0.007 | 0.092 ± 0.009 | 0.060 ± 0.009 | ||
| ε | 0.174 ± 0.018 | ||||
| κ | 0.107 ± 0.009 | 0.083 ± 0.008 | 0.117 ± 0.013 | ||
| λ | 0.067 ± 0.006 | 0.086 ± 0.008 | 0.078 ± 0.009 | ||
| ς | 0.134 ± 0.025 | ||||
| u | 0.333 ± 0.023 | ||||
| κ | 0.464 ± 0.077 | ||||
| πA | 0.233 ± 0.013 | 0.202 ± 0.012 | 0.193 ± 0.012 | ||
| πG | 0.316 ± 0.014 | 0.362 ± 0.015 | 0.373 ± 0.015 | ||
| πC | 0.245 ± 0.013 | 0.290 ± 0.014 | 0.297 ± 0.015 | ||
| πT | 0.206 ± 0.012 | 0.141 ± 0.011 | 0.137 ± 0.011 | ||
| Branch 1 | 1 ± 0 | 1 ± 0 | 1 ± 0 | 1 ± 0 | |
| Branch 2 | 0.232 ± 0.047 | 0.234 ± 0.047 | .001 | 0.110 ± 0.044 | |
| Branch 3 | 0.538 ± 0.065 | 0.539 ± 0.065 | 0.544 ± 0.065 | 0.568 ± 0.065 | |
| Branch 4 | 1.650 ± 0.154 | 1.642 ± 0.153 | 1.671 ± 0.155 | 1.690 ± 0.154 | |
| Branch 5 | 0.194 ± 0.052 | 0.188 ± 0.051 | 0.196 ± 0.051 | 0.190 ± 0.050 | |
| Branch 6 | 0.215 ± 0.046 | 0.082 ± 0.050 | |||
| Best tree | topology E | topology E | tree 5 | tree 5 | |
| Iterations | 11 | 11 | 11 | 11 | |
| Max log likelihood | −4606.6 | −4598.2 | −4555.7 | −4536.2 | |
| χ2(df) | 140.8 (7) | 124.0 (6) | 39.0 (2) | ||
