Table 1. Positively selected genes identified in the four bird taxa.
| Taxa /Genes | Parameter estimates | 2∆L | df | p-value |
|---|---|---|---|---|
| Strigiformes | ||||
| SLC24A1 | ω1 = 999 | 9.17 | 1 | 0.002 |
| LWS | p0 = 0.928 p1 = 0.021 p2a = 0.050 p2b = 0.001 | 17.66 | 1 | 2.647E-05 |
| ω0 = 0.032 ω1 = 1.000 ω2a = 51.224 ω2b = 51.224 | ||||
| SWS2 | p0 = 0.785 p1 = 0.094 p2a = 0.108 p2b = 0.013 | 16.69 | 1 | 4.391E-05 |
| ω0 = 0.041 ω1 = 1.000 ω2a = 29.447 ω2b = 29.447 | ||||
| CNGB1 | p0 = 0.798 p1 = 0.142 p2a = 0.051 p2b = 0.009 | 6.10 | 1 | 0.014 |
| ω0 = 0.042 ω1 = 1.000 ω2a = 5.081 ω2b = 5.081 | ||||
| PCDH15 | p0 = 0.819 p1 = 0.103 p2 = 0.079 | 42.87 | 1 | 5.853E-11 |
| ω0 = 0.032 ω1 = 1.000 ω2 = 2.121 | ||||
| ABCA4 | p0 = 0.784 p1 = 0.102 p2 = 0.115 | 23.57 | 1 | 1.206E-06 |
| ω0 = 0.063 ω1 = 1.000 ω2 = 2.025 | ||||
| SAG | p0 = 0.664 p1 = 0.162 p2 = 0.175 | 16.54 | 1 | 4.759E-05 |
| ω0 = 0.007 ω1 = 1.000 ω2 = 1.933 | ||||
| CNGA1 | p0 = 0.879 p1 = 0.058 p2 = 0.062 | 25.25 | 1 | 5.042E-07 |
| ω0 = 0.017 ω1 = 1.000 ω2 = 1.720 | ||||
| PDE6B | p0 = 0.891 p1 = 0.000 p2 = 0.109 | 6.96 | 1 | 0.008 |
| ω0 = 0.015 ω1 = 1.000 ω2 = 1.374 | ||||
| Falconiformes | ||||
| SLC24A1 | p0 = 0.679 p1 = 0.314 p2a = 0.005 p2b = 0.002 | 7.89 | 1 | 0.005 |
| ω0 = 0.068 ω1 = 1.000 ω2a = 136.369 ω2b = 136.369 | ||||
| GUCY2D | p0 = 0.930 p1 = 0.063 p2a = 0.007 p2b = 0.000 | 4.33 | 1 | 0.037 |
| ω0 = 0.029 ω1 = 1.000 ω2a = 65.241 ω2b = 65.241 | ||||
| GRK1 | p0 = 0.876 p1 = 0.099 p2a = 0.023 p2b = 0.003 | 9.03 | 1 | 0.003 |
| ω0 = 0.029 ω1 = 1.000 ω2a = 36.362 ω2b = 36.362 | ||||
| ARR3 | p0 = 0.937 p1 = 0.049 p2a = 0.013 p2b = 0.001 | 4.87 | 1 | 0.027 |
| ω0 = 0.041 ω1 = 1.000 ω2a = 21.894 ω2b = 21.894 | ||||
| GUCA1A | p0 = 0.913 p1 = 0.000 p2 = 0.087 | 9.86 | 1 | 0.002 |
| ω0 = 0.008 ω1 = 1.000 ω2 = 2.057 | ||||
| GUCY2F | p0 = 0.810 p1 = 0.000 p2 = 0.189 | 11.21 | 1 | 0.001 |
| ω0 = 0.075 ω1 = 1.000 ω2 = 1.903 | ||||
| Accipitriformes | ||||
| CNGB3 | p0=0.818 p1 = 0.180 p2a = 0.002 p2b = 0.000 | 3.97 | 1 | 0.046 |
| ω0 = 0.035 ω1 = 1.000 ω2a = 572.952 ω2b = 572.952 | ||||
| CCDC66 | p0 = 0.649 p1 = 0.305 p2a = 0.032 p2b = 0.015 | 5.08 | 1 | 0.024 |
| ω0 = 0.275 ω1 = 1.000 ω2a = 44.842 ω2b = 44.842 | ||||
| RPGR | p0 = 0.797 p1 = 0.193 p2 = 0.011 | 6.11 | 1 | 0.013 |
| ω0 = 0.064 ω1 = 1.000 ω2 = 17.029 | ||||
| CLN8 | p0 = 0.816 p1 = 0.156 p2 = 0.028 | 6.32 | 1 | 0.012 |
| ω0 = 0.035 ω1 = 1.000 ω2 = 9.626 | ||||
| CNGB3 | p0 = 0.881 p1 = 0.023 p2 = = 0.097 | 9.57 | 1 | 0.002 |
| ω0 = 0.064 ω1 = 1.000 ω2 = 4.375 | ||||
| NXNL2 | p0 = 0.760 p1 = 0.000 p2 = 0.240 | 11.17 | 1 | 0.001 |
| ω0 = 0.012 ω1 = 1.000 ω2 = 2.823 | ||||
| COL2A1 | p0 = 0.891 p1 = 0.000 p2 = 0.109 | 82.40 | 1 | 1.110E-19 |
| ω0 = 0.000 ω1 = 1.000 ω2 = 1.589 | ||||
| Coraciimorphae | ||||
| PDE6H | p0 = 0.843 p1 = 0.077 p2 = 0.080 | 4.86 | 1 | 0.028 |
| ω0 = 0.054 ω1 = 1.000 ω2 = 5.878 | ||||
| PDE6C | p0 = 0.910 p1 = 0.074 p2 = 0.016 | 10.24 | 1 | 0.001 |
| ω0 = 0.035 ω1 = 1.000 ω2 = 4.182 | ||||
With the positive selection analyses, each of the four taxa was respectively treated as the foreground branch or clade while the other three were used as the background one. For convenience, only the ω values for the foreground branches or clades are shown. All the positively selected genes based on the branch model, branch-site model and clade model C are listed (please see Fig. 1 for the genes classes). Note that for the likelihood ratio tests under the clade model C, the M2a_real was used as the null model.
2∆L: twice difference of likelihood values between two nested models; df: degrees of freedom; p: proportion of sites in different site classes. The four site classes (p0, p1, p2a and p2b) of the branch-site model and the three site classes (p0, p1 and p2) of the clade model C are shown.