Table 4 Summary of PAML results for CYP2J19 across 13 ploceid species including site-specific, clade (“CmC”), branch and branch-site analyses
Model | Parameter estimates | lnL | Model comparison | LRT Statistic | df | p-value | ||||
|---|---|---|---|---|---|---|---|---|---|---|
M0 | ω0 = 0.241 | − 2591.727 | ||||||||
M1a | ω0 = 0.024 p0 = 0.782 | |||||||||
ω1 = 1.000 p1 = 0.218 | − 2587.623 | |||||||||
M2a | ω0 = 0.176 p0 = 0.985 | |||||||||
ω1 = 1.000 p1 = 0.000 ω2 = 5.935 p2 = 0.015 | − 2586.444 | M1a vs. M2a | 2.358 | 2 | 0.308 | |||||
M7 | p = 0.005 q = 0.019 | −2587.657 | ||||||||
M8 | p0 = 0.985 (p1 = 0.015) | |||||||||
p = 21.271 q = 99.000 ωs = 5.960 | − 2586.447 | M7 vs. M8 | 2.422 | 2 | 0.298 | |||||
M2a_rel a | ω0 = 0.176 p0 = 0.985 ω1 = 1.000 p1 = 0.000 ω2 = 5.935 p2 = 0.015 | − 2586.444 | ||||||||
CmC a | ω0 = 0.091 p0 = 0.913 ω1 = 1.000 p1 = 0.000 ω2 (#0) = 1.101 p2 = 0.087 ω2 (#1) = 3.393 | − 2585.570 | M2a_rel vs. CmC | 1.749 | 1 | 0.186 | ||||
2ω branch model a | ω (#0) = 0.165 | |||||||||
ω (#1) = 0.370 | − 2590.044 | M0 vs. 2ω branch model | 3.366 | 1 | 0.067 | |||||
Branch-site Null a | site class | 0 | 1 | 2a | 2b | −2586.422 | ||||
proportion | 0.677 | 0.144 | 0.148 | 0.031 | ||||||
background ω | 0.000 | 1.000 | 0.000 | 1.000 | ||||||
foreground ω | 0.000 | 1.000 | 1.000 | 1.000 | ||||||
Branch-site Alternative Model A a | site class | 0 | 1 | 2a | 2b | −2586.295 | Null vs. Alternative Model A | 0.255 | 1 | 0.613 |
proportion | 0.756 | 0.147 | 0.081 | 0.016 | ||||||
background ω | 0.012 | 1.000 | 0.012 | 1.000 | ||||||
foreground ω | 0.012 | 1.000 | 1.939 | 1.939 | ||||||