Table 1 Positively selected genes detected based on the PAML branch-site model. For convenience, only the ω values of foreground branches are shown. Only the positively selected sites with a high posterior probability support (> 0.900) are shown
From: Widespread nocturnality of living birds stemming from their common ancestor
Branches/Genes | Parameter estimates | 2∆L | df | P-value | Corrected P-value | Positively selected sites |
|---|---|---|---|---|---|---|
(A) | ||||||
GRK1 | p0 = 0.929 p1 = 0.051 p2a = 0.017 p2b = 0.000 | 22.82 | 1 | 1.778E-06 | 2.489E-05 | 182 S, 269 E |
ω0 = 0.038 ω1 = 1.000 ω2a = 999.000 ω2b = 999.000 |  |  |  |  |  | |
RCVRN | p0 = 0.915 p1 = 0.022 p2a = 0.060 p2b = 0.001 | 4.46 | 1 | 0.034 | 0.612 | 5 K, 19 T, 37 R |
ω0 = 0.019 ω1 = 1.000 ω2a = 28.660 ω2b = 28.660 |  |  |  |  |  | |
(B) | ||||||
GRK1 | p0 = 0.902 p1 = 0.050 p2a = 0.044 p2b = 0.002 | 5.71 | 1 | 0.016 | 0.224 | 9 K, 25 K, 252 N, 316 I |
ω0 = 0.038 ω1 = 1.000 ω2a = 11.732 ω2b = 11.732 |  |  |  |  |  | |
(C) | ||||||
LWS | p0 = 0.898 p1 = 0.091 p2a = 0.008 p2b = 0.000 | 7.09 | 1 | 0.007 | 0.112 | 70 S, 254 S |
ω0 = 0.036 ω1 = 1.000 ω2a = 40.133 ω2b = 40.133 |  |  |  |  |  | |
(D) | ||||||
SWS1 | p0 = 0.948 p1 = 0.010 p2a = 0.040 p2b = 0.000 | 4.55 | 1 | 0.032 | 0.512 | 78 T |
ω0 = 0.023 ω1 = 1.000 ω2a = 10.955 ω2b = 10.955 |  |  |  |  |  | |
(E) | ||||||
GUCY2D | p0 = 0.906 p1 = 0.089 p2a = 0.003 p2b = 0.000 | 6.03 | 1 | 0.014 | 0.126 | 459 F, 565 K |
ω0 = 0.046 ω1 = 1.000 ω2a = 302.150 ω2b = 302.150 |  |  |  |  |  | |
(F) | ||||||
GUCY2D | p0 = 0.905 p1 = 0.089 p2a = 0.004 p2b = 0.000 | 5.68 | 1 | 0.017 | 0.153 | 69 K, 161 D |
ω0 = 0.046 ω1 = 1.000 ω2a = 50.303 ω2b = 50.303 |  |  |  |  |  | |
(G) | ||||||
CNGB1 | p0 = 0.896 p1 = 0.087 p2a = 0.014 p2b = 0.001 | 3.83 | 1 | 0.050 | 1.150 | 346 N, 475 G |
ω0 = 0.047 ω1 = 1.000 ω2a = 6.517 ω2b = 6.517 |  |  |  |  |  | |
LWS | p0 = 0.877 p1 = 0.090 p2a = 0.028 p2b = 0.002 | 16.28 | 1 | 5.439E-05 | 8.702E-04 | 126 K, 130 R, 237 H |
ω0 = 0.036 ω1 = 1.000 ω2a = 67.591 ω2b = 67.591 |  |  |  |  |  | |
SWS2 | p0 = 0.824 p1 = 0.125 p2a = 0.042 p2b = 0.006 | 10.94 | 1 | 0.000 | 0.013 | 18 A, 42 K, 43 A |
ω0 = 0.038 ω1 = 1.000 ω2a = 237.344 ω2b = 237.344 |  |  |  |  |  | |
(H) | ||||||
GRK1 | p0 = 0.878 p1 = 0.047 p2a = 0.070 p2b = 0.003 | 13.14 | 1 | 0.000 | 0.004 | 2 L, 9 K, 14 E, 16 C, 25 K, 29 N, 33 N, 44 E |
ω0 = 0.037 ω1 = 1.000 ω2a = 15.634 ω2b = 15.634 |  |  |  |  | 197 E, 250 R, 289 A, 292 T, 303 K, 306 Y | |
GUCY2D | p0 = 0.903 p1 = 0.088 p2a = 0.006 p2b = 0.000 | 8.35 | 1 | 0.003 | 0.027 | 175 G |
ω0 = 0.046 ω1 = 1.000 ω2a = 999.000 ω2b = 999.000 |  |  |  |  |  | |
SLC24A1 | p0 = 0.736 p1 = 0.257 p2a = 0.003 p2b = 0.001 | 4.93 | 1 | 0.026 | 0.520 | 233 I |
ω0 = 0.048 ω1 = 1.000 ω2a = 42.679 ω2b = 42.679 |  |  |  |  |  | |
(I) | ||||||
LWS | p0 = 0.902 p1 = 0.092 p2a = 0.004 p2b = 0.000 | 5.00 | 1 | 0.025 | 0.400 | 97 S |
ω0 = 0.037 ω1 = 1.000 ω2a = 58.101 ω2b = 58.101 |  |  |  |  |  | |
(J) | ||||||
GUCY2F | p0 = 0.770 p1 = 0.228 p2a = 0.001 p2b = 0.000 | 8.15 | 1 | 0.004 | 0.100 | 306 E |
ω0 = 0.063 ω1 = 1.000 ω2a = 244.082 ω2b = 244.082 |  |  |  |  |  | |
LWS | p0 = 0.908 p1 = 0.084 p2a = 0.006 p2b = 0.000 | 4.01 | 1 | 0.045 | 0.720 | 43 K |
ω0 = 0.038 ω1 = 1.000 ω2a = 59.283 ω2b = 59.283 |  |  |  |  |  | |
(K) | ||||||
LWS | p0 = 0.904 p1 = 0.082 p2a = 0.011 p2b = 0.001 | 6.41 | 1 | 0.011 | 0.176 | 42 A, 88 L |
ω0 = 0.038 ω1 = 1.000 ω2a = 213.404 ω2b = 213.404 |  |  |  |  |  | |
RCVRN | p0 = 0.960 p1 = 0.023 p2a = 0.015 p2b = 0.000 | 7.22 | 1 | 0.007 | 0.126 |  |
ω0 = 0.019 ω1 = 1.000 ω2a = 999.000 ω2b = 999.000 |  |  |  |  |  | |