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Table 4 Summary of PAML results for CYP2J19 across 13 ploceid species including site-specific, clade (“CmC”), branch and branch-site analyses

From: Evolution of CYP2J19, a gene involved in colour vision and red coloration in birds: positive selection in the face of conservation and pleiotropy

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
  1. aBranch partitions for Clade model C, Branch and Branch-site models: #1 = the two clades containing ketocarotenoid species: (E. orix, E. hordeaceus, E. nigroventris and E. ardens) and (F. madagascariensis, Q. erythrops and Q. quelea); #0 = all other lineages