From:Identification and evolution of C4photosynthetic pathway genes in plants
| Test Used | Foregroud branches | Model | ω | LnL | Estimates of parameters | df | P | Positively selected sites under BEB |
|---|---|---|---|---|---|---|---|---|
| Site analysis | – | M0:(one-ratio) | 0.091 | −27,294.09 | ω = 0.091 | – | – | – |
| – | M3:(discrete) | 0.117 | −26,141.38 | p0 = 0.601ω0 = 0.019 | 4 | 0.000(M0 vs M3) | – | |
| p1 = 0.360 ω1 = 0.175 | ||||||||
| p2 = 0.039 ω2 = 1.091 | ||||||||
| Branch analysis | – | M0 | – | −27,294.09 | ω = 0.091 | – | – | – |
| – | a1 | – | −27,286.99 | ω0 = 0.092 ω1 = 0.006 | 1 | < 0.001 | – | |
| – | a2 | – | −27,287.52 | ω0 = 0.092 ω1 = 0.016 | 1 | < 0.001 | – | |
| – | a3 | – | −27,285.91 | ω0 = 0.092 ω1 = 0.018 | 1 | < 0.001 | – | |
| – | a4 | – | −27,292.69 | ω0 = 0.090 ω1 = 0.314 | 1 | 0.095 | – | |
| – | a5 | – | −27,294.06 | ω0 = 0.091 ω1 = 0.085 | 1 | 0.827 | – | |
| – | a6 | – | −27,293.33 | ω0 = 0.090 ω1 = 0.358 | 1 | 0.218 | – | |
| – | a7 | – | −27,292.88 | ω0 = 0.090 ω1 = 0.158 | 1 | 0.121 | – | |
| Branch-site analysis | – | M1 | – | −26,625.07 | p0 = 0.915 p1 = 0.085 | – | – | – |
| a1 | Model A | – | −26,616.55 | p0 = 0.871 p1 = 0.079(p2a + p2b = 0.050) | 2 | 0.0002 (ModelA vs M1) | Prob > 0.6 (178 M, 188Q, 193D, 326E, 330 L, 344 V, 345S, 375 L) | |
| ω2 = 37.078 | ||||||||
| a2 | Model A | – | −26,622.12 | p0 = 0.897 p1 = 0.081 (p2a + p2b = 0.002) | 2 | 0.0520 (ModelA vs M1) | Prob > 0.6 (11 L, 63Da, 94H, 110R, 344 V) | |
| ω2 = 8.513 | ||||||||
| a3 | Model A | – | −26,610.43 | p0 = 0.861 p1 = 0.080 (p2a + p2b = 0.058) | 2 | < 0.0001 (ModelA vs M1) | Prob > 0.6 (11 L, 54Ra, 66Qb, 180 Ma, 188Q, 200Aa, 248P, 273Rb, 274Ia, 275 T, 298 V, 344 V, 367 K, 389S) | |
| ω2 = 152.141 | ||||||||
| a4 | Model A | – | −26,624.28 | p0 = 0.801 p1 = 0.074 (p2a + p2b = 0.11) | 2 | 0.4525 (ModelA vs M1) | Prob > 0.6 (122 V, 174A, 185 M, 220R, 268A) | |
| ω2 = 1.000 | ||||||||
| a5 | Model A | – | −26,619.18 | p0 = 0.902 p1 = 0.083 (p2a + p2b = 0.015) | 2 | 0.0028 (ModelA vs M1) | Prob > 0.6(94Ha, 182A, 196Ha, 269E) | |
| ω2 = 11.724 | ||||||||
| a6 | Model A | – | −26,625.07 | p0 = 0.915 p1 = 0.085 (p2a + p2b = 0.000) | 2 | 1.0000 (ModelA vs M1) | Prob > 0.6 (13H, 201H) | |
| ω2 = 3.081 | ||||||||
| a7 | Model A | – | −26,625.07 | p0 = 0.915 p1 = 0.085 (p2a + p2b = 0.000) | 2 | 1.0000 (ModelA vs M1) | Prob > 0.6 (33 K, 56 L) | |
| ω2 = 1.000 |