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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      
  1. Corrected P-value, Bonferroni multiple testing correction, P values are corrected by multiplying them by the number of branches tested of each gene. Significance level is P < 0.05