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Table 1 Parameter Estimates of Codon-Substitution Evolutionary Models for MnCHS and MnSTS family

From: Evolutionary and functional analysis of mulberry type III polyketide synthases

Model Proportion of sites dN/dS ratios Likelihood
lnL P-value
Other specie sequence set
 Branch Model
  MnCHS     ωb = 0.07855
STS + CHSL + oCHS
ωf = 0.09698
MnCHS
  −22140.77149 0.1418015
(MnCHS V.S M0)
  MnSTS     ωb = 0.07363
CHS + CHSL + oSTS
ωf = 0.16568
MnSTS
  −22122.54872 5.192e-010
(MnSTS V.S M0)
  oCHS     ωb = 0.09719
STS + CHSL + MnCHS
ωf = 0.03729
oCHS
  −22110.96154 3.886e-015
(oCHS V.S M0)
  oSTS     ωb = 0.07264
CHS + CHSL + MnSTS
ωf = 0.11261
oSTS
  −22132.52527 1.570e-005
(oSTS V.S M0)
  MnCHS&MnSTS     ωb = 0.07079
CHSL + oCHS + oSTS
ωf = 0.09885
MnCHS
ωf = 0.16602
MnSTS
−22119.93911 3.595e-011
(MnCHS&MnSTS V.S M0)
3.652e-003
(MnCHS&MnSTS V.S MnCHS-MnSTS)
  MnCHS-MnSTS     ωb = 0.07047
CHSL + oCHS + oSTS
ωf = 0.13084
MnCHS-MnSTS
  −22124.16361 2.721e-009 (MnCHS-MnSTS V.S M0)
  M0     ω0 = 0.08027    −22141.85065  
 Clade Model C
  MnCHS&MnSTS p0 = 0.51866 p1 = 0.01377 p2 = 0.46757 ω0b = 0.02173
CHSL + oCHS + oSTS
ω0f1 = 0.02173
MnCHS
ω0f2 = 0.02173
MnSTS
ω1b = 1.00000
CHSL + oCHS + oSTS
ω1f1 = 1.00000
MnCHS
ω1f2 = 1.00000
MnSTS
ω2b = 0.13114
CHSL + oCHS + oSTS
ω2f1 = 0.17857
MnCHS
ω2f2 = 0.28333
MnSTS
−21704.83735 1.321e-006
(MnCHS&MnSTS V.S M2a_rel)
  MnCHS&oCHS p0 = 0.46637 p1 = 0.01890 p2 = 0.51473 ω0b = 0.02016
CHSL + STS
ω0f1 = 0.02016
MnCHS
ω0f2 = 0.02016
oCHS
ω1b = 1.00000
CHSL + STS
ω1f1 = 1.00000
MnCHS
ω1f2 = 1.00000
oCHS
ω2b = 0.16234
CHSL + STS
ω2f1 = 0.15212
MnCHS
ω2f2 = 0.06353
oCHS
−21695.89064 1.719E-10
  MnSTS&oSTS p0 = 0.47783 p1 = 0.01786 p2 = 0.50430 ω0b = 0.01889
CHSL + CHS
ω0f1 = 0.01889
MnSTS
ω0f2 = 0.01889
oSTS
ω1b = 1.00000
CHSL + CHS
ω1f1 = 1.00000
MnSTS
ω1f2 = 1.00000
oSTS
ω2b = 0.11003
CHSL + CHS
ω2f1 = 0.26885
MnSTS
ω2f2 = 0.19651
oSTS
−21693.48253 1.547E-11
  M2a_rel        −21718.37459  
 Branch Site Model
  MnCHS p0 = 0.91716 p1 = 0.02414 p2a = 0.05719
p2b = 0.00151
ω0b = 0.07409
STS + CHSL + oCHS
ω0f = 0.05519
MnCHS
ω1b = 1.00000
STS + CHSL + oCHS
ω1f = 1.00000
MnCHS
ω2ab = 0.07409
STS + CHSL + oCHS
ω2bb,2af,2bf = 1
STS + CHSL + oCHS + MnCHS
−22057.84405 1
  MnCHS(NULL)         
  MnSTS p0 = 0.84795 p1 = 0.02220 p2a = 0.12654
p2b = 0.00331
ω0b = 0.07147
CHS + CHSL + oSTS
ω0f = 0.07147
MnSTS
ω1b = 1.00000
CHS + CHSL + oSTS
ω1f = 1.00000
MnSTS
ω2ab = 0.07147
CHS + CHSL + oSTS
ω2bb,2af,2bf = 1
CHS + CHSL + oSTS + MnSTS
−22040.53516 1
  MnSTS(NULL)        −22040.53516  
Mulberry sequence set
 Branch Model
  MnCHS     ωb = 0.1264 background ωf = 0.0689 MnCHS   −9890.922495 1.721E-05
(MnCHS V.S M0)
  MnSTS     ωb = 0.0775 background ωf = 0.1630 MnSTS   −9888.008106 8.220E-07
(MnSTS V.S M0)
  MnCHS&MnSTS     ωb = 0.09237
MnPKS + MnCHSL
ωf = 0.07027
MnCHS
ωf = 0.16132
MnSTS
−9886.659146 2.032e-007
(MnCHS&MnSTS V.S M0)
2.290e-007
(MnCHS&MnSTS V.S MnCHS-MnSTS)
  MnCHS-MnSTS     ωb = 0.09240
MnPKS + MnCHSL
ωf = 0.10035
MnCHS-MnSTS
  −9900.044736 0.630413825 (MnCHS-MnSTS V.S M0)
  M0     ω0 = 0.0982    −9900.160494  
 Clade Model C
  MnCHS&MnSTS p0 = 0.45899 p1 = 0.02581 p2 = 0.51519 ω0b = 0.02006
MnCHSL + MnPKS
ω0f1 = 0.02006
MnSTS
ω0f2 = 0.02006
MnCHS
ω1b = 1.00000
MnCHSL + MnPKS
ω1f1 = 1.00000
MnSTS
ω1f2 = 1.00000
MnCHS
ω2b = 0.13883
MnCHSL + MnPKS
ω2f1 = 0.28349
MnSTS
ω2f2 = 0.12011
MnCHS
−9734.263087 1.063e-005
(MnCHS&MnSTS V.S M2a_rel)
  M2a_rel        −9745.715191  
 Branch Site Model
  MnCHS p0 = 0.89947 p1 = 0.05549 p2a = 0.04242
p2b = 0.00262
ω0b = 0.07834 background
ω0f = 0.07834
MnCHS
ω1b = 1.00000 background
ω1f = 1.00000
MnCHS
ω2ab = 0.07834 background
ω2bb,2af,2bf = 1 background
MnCHS,MnCHS
−9829.594816 1 (MnCHS V.S MnCHS(NULL))
  MnCHS(NULL)        −9829.594816  
  MnSTS p0 = 0.81332 p1 = 0.04954 p2a = 0.12927
p2b = 0.00787
ω0b = 0.06667 background
ω0f = 0.06667
MnSTS
ω1b = 1.00000 background
ω1f = 1.00000
MnSTS
ω2ab = 0.06667 background
ω2bb,2af,2bf = 1 background
MnSTS,MnSTS
−9813.87732 1
(MnSTS V.S MnSTS(NULL))
  MnSTS(NULL)        −9813.87732  
  MnCHS-A p0 = 0.84861 p1 = 0.06802 p2a = 0.07719
p2b = 0.00619
ω0b = 0.05978
MnCHSL + MnSTS
ω0f = 0.05978
MnCHS-A
ω1b = 1.00000
MnCHSL + MnSTS
ω1f = 1.00000
MnCHS-A
ω2ab = 0.05978
MnCHSL + MnSTS
ω2bb = 1,
MnCHSL + MnSTS
ω2af,2bf = 999.00000
MnCHS-A,MnCHS-A
−8214.284472 3.626E-06
(MnCHS-A V.S MnCHS-A(NULL))
  MnCHS-A(NULL) p0 = 0.83646 p1 = 0.06502 p2a = 0.09141
p2b = 0.00711
ω0b = 0.05774
MnCHSL + MnSTS
ω0f = 0.05774
MnCHS-A
ω1b = 1.00000
MnCHSL + MnSTS
ω1f = 1.00000
MnCHS-A
ω2ab = 0.05774
MnCHSL + MnSTS
ω2bb,2af,2bf = 1
MnCHSL + MnSTS,
MnCHS-A,MnCHS-A
−8225.011056  
  MnSTS-A p0 = 0.83361 p1 = 0.06959 p2a = 0.08934
p2b = 0.00746
ω0b = 0.05962
MnCHSL + MnCHS
ω0f = 0.05962
MnSTS-A
ω1b = 1.00000
MnCHSL + MnCHS
ω1f = 1.00000
MnSTS-A
ω2ab = 0.05962
MnCHSL + MnCHS
ω2bb = 1,
MnCHSL + MnCHS
ω2af,2bf = 210.99468
MnSTS-A,MnSTS-A
−8219.791085 3.684E-02
(MnSTS-A V.S MnSTS-A(NULL))
  MnSTS-A(NULL) p0 = 0.81036 p1 = 0.06741 p2a = 0.11285
p2b = 0.00939
ω0b = 0.05731
MnCHSL + MnCHS
ω0f = 0.05731 MnSTS-A
ω1b = 1.00000
MnCHSL + MnCHS
ω1f = 1.00000
MnSTS-A
ω2ab = 0.05731
MnCHSL + MnCHS
ω2bb,2af,2bf = 1
MnCHSL + MnCHS,
MnSTS-A,MnSTS-A
−8221.968483  
  1. The LTR tests are as follow: Branch Modle, One ratio Model 0 vs.Two ratio Model 2. Clade Modle C, M2a_rel vs. CmC. Branch Site Modle, Model A null (w is fixed as 1) vs. Model A. w = dN/dS. b = background; f = foreground; o = other; p0, p1, p2 = proportion of sites with dN/dS ratios = w0, w1, w2, respectively. lnL = ln of the likelihood; P-value = p-value of the likelihood ratio test