Table 4. Results of the approximately unbiased (AU), Shimodaira-Hasegawa (SH) and weighted Shimodaira-Hasegawa (wSH) tests for studied data sets and topologies assuming different relationships between three Yellow-headed Amazona lineages: C – Central American, S – South American, NS – Northern South American including A. barbadensis and its relative A. ochrocephala ochrocephala.
| Data set | Selected sites | P-values from AU/SH/wSH tests for topology: | ||
| (S,NS) | (C,NS) | (S,C) | ||
| nd+cox+atp6+81 | all | 0.775/0.763/0.755 | 0.333/0.284/0.450 | 0.212/0.293/0.482 |
| with rates <2 | 0.766/0.823/0.822 | 0.298/0.255/0.382 | 0.071/0.080/0.165 | |
| with rates <1 | 1.000/1.000/1.000 | 1e-04/2e-05/2e-05 | 3e-50/0/0 | |
| with rates <0.5 | 1.000/1.000/1.000 | 1e-09/0/0 | 1e-07/0/0 | |
| with rates <0.1 | 1.000/1.000/1.000 | 1e-07/0/0 | 6e-68/0/0 | |
| nd+cox2 | all | 0.673/0.724/0.715 | 0.537/0.561/0.586 | 0.131/0.390/0.418 |
| with rates <2 | 0.959/0.897/0.898 | 0.064/0.113/0.197 | 0.065/0.112/0.206 | |
| with rates <1 | 0.194/0.330/0.326 | 0.860/0.950/0.904 | 0.148/0.298/0.097 | |
| with rates <0.5 | 5e-04/0.046/3e-04 | 0.940/1.000/0.999 | 0.067/0.116/0.081 | |
| with rates <0.1 | 0.003/0.107/0.006 | 0.997/1.000/1.000 | 6e-55/0/0 | |
| nd+cox+atp6+82 | all | 0.747/0.769/0.758 | 0.418/0.386/0.500 | 0.125/0.293/0.385 |
| with rates <2 | 0.996/0.999/0.998 | 0.004/0.014/0.020 | 5e-08/1e-06/1e-06 | |
| with rates <1 | 0.918/0.939/0.934 | 0.095/0.097/0.166 | 0.007/0.022/0.035 | |
| with rates <0.5 | 0.966/0.979/0.982 | 0.034/0.040/0.070 | 5e-05/3e-04/5e-04 | |
| with rates <0.1 | 0.755/0.838/0.841 | 0.245/0.343/0.400 | 1e-06/1e-04/7e-06 | |
| 12s+16s+cox3 | all | 0.235/0.230/0.414 | 0.239/0.230/0.422 | 0.826/0.775/0.775 |
| with rates <2 | 0.322/0.278/0.503 | 0.347/0.257/0.306 | 0.752/0.731/0.731 | |
| with rates <1 | 0.757/0.952/0.859 | 0.110/0.467/0.153 | 0.330/0.347/0.349 | |
| with rates <0.5 | 0.578/0.725/0.715 | 0.620/0.733/0.742 | 0.154/0.175/0.176 | |
| with rates <0.1 | 0.896/0.935/0.972 | 0.192/0.483/0.288 | 0.028/0.047/0.044 | |
| 12s+16s+cox+cytb4 | all | 0.147/0.394/0.451 | 0.515/0.514/0.565 | 0.670/0.722/0.712 |
| with rates <2 | 0.037/0.353/0.342 | 0.577/0.636/0.642 | 0.613/0.651/0.648 | |
| with rates <1 | 0.127/0.180/0.146 | 0.835/0.922/0.922 | 0.263/0.356/0.330 | |
| with rates <0.5 | 0.002/0.001/0.001 | 0.971/0.994/0.994 | 0.038/0.067/0.061 | |
| with rates <0.1 | 4e-05/0.001/0.001 | 1.000/1.000/1.000 | 7e-93/0/0 | |
1
based on Ribas et al. [14] data set;
2
based on Ribas et al. [14] and modified data set;
3
based on Rusello and Amato [7] and modified data set;
4
similar to the set3 but including also cytochrome b.
The tests were performed for all sites and sites with decreasing substitution rate. P-values of the best tree are underlined whereas those less than 0.05 are in bold.