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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%
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BMC Molecular Biology

ISSN: 1471-2199

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