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 |  |