Table 3.
Summary of Likelihood Ratio Test (LRTs) for selection tests
| Opsins | Comparisons | 2ΔLn L | Df | P value | Positive Sites |
|---|---|---|---|---|---|
| LWS | Branch Models | ||||
| free model x 1ω | 639 | 146 | <10−5 | – | |
| 2ω x 1ω | 218 | 1 | <10−5 | – | |
| 3ω x 2ω | 27 | 1 | <10−5 | – | |
| 4ω x 3ω | 8 | 1 | 0.006 | – | |
| 4ω (D x N) x 3ω | 1 | 1 | 0.28 | – | |
| Branch-Site Models | |||||
| Model A (diurnal) x null | 45.9 | 2 | <10−5 | 39 L(0.97) 49 V(0.89) 112 L(0.81) 119A(0.99) 165C(0.95) 195S(0.97) 213A(0.99) 276 V(1.0) | |
| Model A (nocturnal) x null | 100.9 | 2 | <10−5 | 39 L(0.94) 119A(0.73) 124A(0.99) 137 V(0.82) 146 V(0.98) 166A(0.99) 199G(1.0) 209I(0.79) 213A(1.0) 218 V(1.0) 221I(0.85) 269 T *(1.0) 270F(0.77) 282A(0.99) 290 L(0.97) | |
| Site Models | |||||
| Model 3 x Model 0 | 726 | 4 | <10−5 | – | |
| Model 2a x Model 1a | 156 | 2 | <10−5 | 39 L(1.0) 49 V(0.95) 104 V(0.99) 112 V(1.0) 119 V(1.0) 124A(0.98) 154 V(1.0) 158 L(0.87) 164S*(0.6) 165C(1.0) 166A(1.0) 195S(0.97) 205 V(0.99) 209I(0.98) 213A(0.99) 218 V(0.94) 228 L(0.87) 269 T*(0.79) 270F(0.7) 290 L(1.0) | |
| Model 8 x Model 7 | 172 | 2 | <10−5 | 39 L(1.0) 45 V(0.99) 49 V(0.99) 81I(0.83) 104 V(1.0) 109 L(0.69) 112 L(1.0) 119A(1.0) 124A(1.0) 137 V(0.88) 146 V(0.96) 154 L(1.0) 158 L(0.98) 164S*(0.98) 165C(1.0) 166A(1.0) 195S(0.99) 198P(0.95) 199G(0.9) 205 V(1.0) 206 V(0.85) 209I(0.99) 213A(1.0) 214I(0.8) 218 V(1.0) 221I(0.97) 228 L(0.99) 269 T *(0.99) 270F(0.99) 276 V(0.87) 287 T(0.9) 317 L(1.0) | |
| RH1 | Branch Models | ||||
| free model x 1ω | 427 | 142 | <10−5 | – | |
| 2ω x 1ω | 121 | 1 | <10−5 | – | |
| 3ω x 2ω | 6 | 1 | 0.015 | – | |
| 4ω x 3ω | 2 | 1 | 0.14 | – | |
| 4ω (D x N) x 3ω | 22 | 1 | <10−5 | – | |
| Branch-Site Models | |||||
| Model A (diurnal) x null | 8.5 | 2 | 0.01 | 155 M(0.99) | |
| Model A (nocturnal) x null | 49.5 | 2 | <10−5 | 159 L(0.9) 213 V(0.7) 214 T(1.0) 292S *(1.0) | |
| Site Models | |||||
| Model 3 x Model 0 | 427 | 4 | <10−5 | – | |
| Model 2a x Model 1a | 29 | 2 | <10−5 | 81 V(0.8) 112 V(0.7) 133 V(0.8) 158S(0.9) 159 L(0.8) 209 L(0.7) 213 V(0.99) 217 T(0.99) 290 V(0.96) 292S*(0.7) 299A*(0.9) | |
| Model 8 x Model 7 | 35 | 2 | <10−5 | 46 L(0.8) 60Y(0.66) 81 V(0.9) 83 N*(0.7) 107 T(0.7) 112 V(0.9) 133 V(0.9) 158S(0.98) 159 L(0.9) 169A(0.6) 173I(0.8) 185S(0.6) 209 L(0.9) 213 V(1.0) 217 T(1.0) 290I(0.99) 292S*(0.9) 299A*(0.97) | |
| SWS1 | Branch Models | ||||
| free model x 1ω | 496 | 150 | <10−5 | – | |
| 2ω x 1ω | 39 | 1 | <10−5 | – | |
| 3ω x 2ω | 12 | 1 | <10−4 | – | |
| 4ω x 3ω | 7 | 1 | 0.01 | – | |
| 4ω (D x N) x 3ω | 8 | 1 | 0.004 | – | |
| Branch-Site Models | |||||
| Model A (diurnal) x null | 46.6 | 2 | <10−5 | 57I(0.97) 86 V*(0.75) 91I(0.97) 118 T*(0.9) 122 L(0.9) 143 L(0.96) 178Y(0.76) 213 L(0.8) 217 T(0.8) 255 V(0.6) 258I(0.6) 282G(1.0) 315A(0.8) | |
| Model A (nocturnal) x null | 21.3 | 2 | <10−5 | 105 L(0.68) 109 V(0.87) 124I(0.9) 137I(0.8) 149 N(0.9) 213 L(0.99) 259G(0.98) | |
| Site Models | |||||
| Model 3 x Model 0 | 437 | 4 | <10−5 | – | |
| Model 2a x Model 1a | 0 | 2 | 1.0 | – | |
| Model 8 x Model 7 | 0 | 2 | 1.0 | – | |
Note – Underlined model fits the data significantly better. Sites inferred to be under positive selection at the 99% level are listed in bold; numbers after each site indicate the posterior probability value
*Known spectral tuning sites. Sites are numbered based on the bovine RH1