Table 3 Parameters in the site analysis, branch and branch-site analyses of PPDK
From: Identification and evolution of C4 photosynthetic 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) | 0.1 | −34,454.01 | ω = 0.095 | – | – | – |
– | M3:(discrete) | 0.11 | −32,794.04 | p0 = 0.562 ω0 = 0.009 | 4 | 0.000 (M0 vs M3) | – | |
p1 = 0.302 1 = 0.117 | ||||||||
p2 = 0.136 ω2 = 0.521 | ||||||||
Branch analysis | – | M0 | – | −34,454.01 | ω = 0.095 | – | – | – |
– | a | – | − 34,433.04 | ω0 = 0.0979 ω1 = 0.0006 | 1 | < 0.0001 | – | |
– | b | – | −34,444.44 | ω0 = 0.097 ω1 = 0.024 | 1 | < 0.0001 | – | |
– | c | – | −34,441.56 | ω0 = 0.098 ω1 = 0.026 | 1 | < 0.0001 | – | |
– | d | – | −34,453.87 | ω0 = 0.095 ω1 = 0.078 | 1 | 0.606 | – | |
– | e | – | −34,443.74 | ω0 = 0.093 ω1 = 0.284 | 1 | < 0.0001 | – | |
Branch-site analysis | – | M1 | – | −33,410.98 | p0 = 0.844 p1 = 0.156 | – | – | – |
a | Model A | – | −33,410.98 | p0 = 0.844 p1 = 0.156(p2a + p2b = 0.000) | 2 | 1.0000 (ModelA vs M1) | Prob > 0.6 (257I) | |
ω2 = 1.000 | ||||||||
b | Model A | – | −33,410.98 | p0 = 0.844 p1 = 0.156 (p2a + p2b = 0.000) | 2 | 1.0000 (ModelA vs M1) | Prob > 0.6 (337R) | |
ω2 = 1.000 | ||||||||
c | Model A | – | − 33,410.98 | p0 = 0.844 p1 = 0.156 (p2a + p2b = 0.000) | 2 | 1.0000 (ModelA vs M1) | Prob > 0.6 (NO) | |
ω2 = 1.000 | ||||||||
d | Model A | – | −33,410.98 | p0 = 0.844 p1 = 0.156 (p2a + p2b = 0.000) | 2 | 1.0000 ModelA vs M1) | Prob > 0.6 (NO) | |
ω2 = 1.000 | ||||||||
e | Model A | – | −33,400.15 | p0 = 0.810 p1 = 0.147 (p2a + p2b = 0.044) | 2 | <  0.0001 (ModelA vs M1) | Prob > 0.6 (24 N, 95Aa, 174I, 359A, 459G, 489A, 559Eb, 561G) | |
ω2 = 3.507 |