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Table 2 Results of PAML analyses testing for selection on the three mitochondrial subunits

From: Positive selection on two mitochondrial coding genes and adaptation signals in hares (genus Lepus) from China

Gene Model p Parameter estimates Log likelihood Sites Model comparison p (ΔLRT)
ND4 M0 (one-ratio) 1 ω0 = 0.0372 − 7708.624 M0 vs M1a
M0 vs M3
M1a vs M2a
M7 vs M8
 < 0.001
 < 0.001
 < 0.001
 < 0.001
M1 (neutral) 2 ω0 = 0.0074 p0 = 0.9469 ω1 = 1.000 p1 = 0.0531 − 7645.299
M2 (selection) 4 ω0 = 0.0072 p0 = 0.947 ω1 = 1.0000 p1 = 0.0523 ω2 = 2.1673 p2 = 0.0002 − 7504.371 29
M3 (discrete) 5 ω0 = 0.0063 p0 = 0.9425 ω1 = 0.6554 p1 = 0.0575 ω2 = 217.8820 p2 = 0.0000 − 7497.046
M7 (beta) 2 p = 0.0062 q = 0.005 − 8315.174
M8 (beta&ω) 4 p0 = 0.9658 p = 0.0631 q = 2.7963 (p1 = 0.0342) ω = 1.0000 − 7499.443 29
CytB M0 (one-ratio) 1 ω0 = 0.0320 − 5881.359 M0 vs M1a
M0 vs M3
M1a vs M2a
M7 vs M8
 < 0.001
 < 0.001
 > 0.05
 > 0.05
M1 (neutral) 2 ω0 = 0.0115 p0 = 0.9660 ω1 = 1.000 p1 = 0.0340 − 5774.833
M2 (selection) 4 ω0 = 0.0115 p0 = 0.9660 ω1 = 1.000 p1 = 0.0340 ω2 = 14.7728 p2 = 0.0000 − 5785.211
M3 (discrete) 5 ω0 = 0.0072 p0 = 0.9469 ω1 = 0.4605 p1 = 0.0531 ω2 = 14.1110 p2 = 0.0000 − 5785.565
M7 (beta) 2 p = 0.0165 q = 0.0239 − 5908.619
M8 (beta&ω) 4 p0 = 0.9999 p = 0.0590 q = 1.0510 (p1 = 0.00001) ω = 6.0347 − 5911.451
cox1 M0 (one-ratio) 1 ω0 = 0.0047 − 5912.722 M0 vs M1a
M0 vs M3
M1a vs M2a
M7 vs M8
 > 0.05
 > 0.05
 > 0.05
 < 0.001
M1 (neutral) 2 ω0 = 0.0039 p0 = 0.9974 ω1 = 1.000 p1 = 0.0027 − 5910.938
M2 (selection) 4 ω0 = 0.0039 p0 = 0.9974 ω1 = 1.000 p1 = 0.0026 ω2 = 34.4363 p2 = 0.0000 − 5911.120
M3 (discrete) 5 ω0 = 0.0038 p0 = 0.9966 ω1 = 0.5872 p1 = 0.0034 ω2 = 6.8990 p2 = 0.0000 − 5911.043
M7 (beta) 2 p = 0.0101 q = 0.0086 − 6208.708
M8 (beta&ω) 4 p0 = 0.9999 p = 0.0564 q = 6.7184 (p1 = 0.00001) ω = 6.2162 − 5911.451