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Table 1 Positive selection sites of FPS tested through the site model, branch model and branch-site model

From: Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants

Model Estimate of parameters lnL LRT pairs df 2ΔlnL P value Positive selection sites
Site model
M0:one ratio ω = 0.11676 −30867.39      
M3:discrete p0 = 0.49134, p1 = 0.296497, p2 = 0.21217, ω0 = 0.01740, ω1 = 0.15430, ω2 = 0.50703 −29509.88 M0/M3 3 2715.02 0 none
M1a:neutral p0 = 0.75883, p1 = 0.24117, ω0 = 0.07661, ω1 = 1.00000 −30122.51 M1a/M2a 2 0 1 none
M2a:selection p0 = 0.75883, p1 = 0.15391, p2 = 0.08726, ω0 = 0.07661, ω1 = 1.0000, ω2 = 1.0000 −30122.51      
M7:beta p = 0.37262, q = 1.74173 −29440.75      
M8:beta&ω p0 = 1.0000, p = 0.28555, q = 1.02636, (p1 = 0.00000), ω2 = 2.36785 −34114.08 M7/M8 2 9346.66 0 3D, 7R, 14V, 21N, 25F, 27F, 34W, 47K, 59K, 60L, 65K, 98S, 99S, 181P, 207S, 213K, 233D, 293E, 275F, 286A, 251D, 252I, 270E, 302D, 305A, 309S, 336G, 342Q (all werea)
Branch model
Model 0:(one-ratio) ω = 0.11676 −30867.39 M0/Free model 135 258.64 0 none
Free model ωa = 1.0131, ωb = 1.3249, ωc = 540.6926 −30738.07      
Branch-site model
BSa1 p0 = 0.00006, p1 = 0.00001, p2a = 0.85238, p2b = 0.14755, b:ω0 = 0.07506, ω1 = 1.00000, ω2a = 0.07506, ω2b = 1.00000, f:ω0 = 0.07506, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 −25664.61 BSa1/BSa0-fix 1 10.56 0 98S, 148D, 234D
BSa0_fix p0 = 0.81966, p1 = 0.14204, p2a = 0.03264, p2b = 0.00566, b:ω0 = 0.07521, ω1 = 1.00000, ω2a = 0.07521, ω2b = 1.00000, f:ω0 = 0.07521, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 −25669.89      none
BSb1 p0 = 0.02224, p1 = 0.00386, p2a = 0.82997, p2b = 0.14393, b:ω0 = 0.07528, ω1 = 1.00000, ω2a = 0.07528, ω2b = 1.00000,f:ω0 = 0.07528, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 −25663.83 BSb1/BSb0-fix 1 10.12 0 none
BSb0_fix p0 = 0.10932, p1 = 0.01896, p2a = 0.74286, p2b = 0.12886, b:ω0 = 0.07528, ω1 = 1.00000, ω2a = 0.07528, ω2b = 1.00000, f:ω0 = 0.07528, ω1 = 1.00000, ω2a = 8.15518, ω2b = 8.15518, f:ω0 = 0.07528, ω1 = 1.00000, ω2a = 8.15518, ω2b = 8.15518 −25668.89      
BSc1 p0 = 0.03778, p1 = 0.00655, p2a = 0.81443, p2b = 0.14124, b:ω0 = 0.07526,ω1 = 1.00000,ω2a = 0.07526,ω2b = 1.00000, f:ω0 = 0.07526, ω1 = 1.00000, ω2a = 1.00000, ω2b = 8.15518 −25664.75 BSc1/BSc0-fix 1 9.98 0 none
Sc0_fix p0 = 0.01751, p1 = 0.00303, p2a = 0.83486, p2b = 0.14461, b:ω0 = 0.07526, ω1 = 1.00000, ω2a = 0.07526, ω2b = 1.00000, f:ω0 = 0.07526, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 −25669.74      
  1. Selection analysis by site model was performed using CodeML implemented in PAML. Significant tests at 1% cut off
  2. lnL log-likelihood values, LRT likelihood ratio test, ω2 average dN/dS ratio for sites subject to positive selection, p and q shape parameters for the beta distribution of ω, p0, p1, and p2 proportions of codons subject to purifying selection, neutral evolution, and positive selection, respectively, df degrees of freedom, 2ΔlnL twice the log-likelihood difference of the model compared
  3. a Posterior probability >99%