unrecognized fossil calibrations

[Yantao Liu]

Hi all

I'm running mcmctree for my tree with 4 fossil calibrations. PAML gives a warning saying that three of them are unrecognized fossil calibrations. Could you please tell me what might be causing this issue?

unrecognized fossil calibration: >2.51

unrecognized fossil calibration: >4.06

unrecognized fossil calibration: >0.65

and the tree file is as follows: 68  1

((((PseHu_SY62,(MoeAp_IMSTJM19,MoeAp_XM01)),((CrySp_Mo29,KwoMa_CBS8507),(NiaVi_CBS119815,SchCo_20R7F01))),((CysSl_IMSTJM16,CysSl_I2R3),(BasSp_IMSTJM26,(LeuSc_PYCC4405,((RhoDi_IMSTJM28,RhoDi_TRY71),(RhoSp_ETNP2018,(RhoMu_IMSTJM29,(RhoMu_5031920B,(RhoMu_B1,RhoMu_CYJ03)))))))))'>2.51',(((YarKe_JCM14894,YarLi_NCIM3590),(LacMe_CBS8951,(MetAu_UFMGCMY6158,DebHa_J6))),(((CadMa_Mo12,CalMa_TRa3180A),((LinTh_JK4322,ZalMa_ATCC34329),(CorMa_CBS119819,((PurLi_FDZ8Y1,(TriSi_GHSJ1,(ParTo_FJIIL10SWP1,(HypSp_ML197S3,ParAl_IMSTJM11)))),((SarKi_IMSTJM17,SarKi_ZJ1),(AcrSp_FKIIL8BKP5,(AcrEg_IMSTJM10,(EmeAt_TS7,EmeCl_MUM1933))))))))'<5.14',((((ExoDe_IMSTJM18,ExoDe_NIHUT8656),(ExoXe_IMSTJM14,ExoXe_IMSTJM23)),((AspAf_CMG70,(AspSp_Z5,AspSy_BOBA1)),(PenSt_P2648,(PenBi_A30,(PenPa_SPGF1,PenPa_SPGF15))))),((((HorWe_IMSTJM27,HorWe_IMSTJM25),(ClaCo_601,ClaHa_TM138)),(AurPu_EXF150,(AurMe_EXF924,(AurMe_EXF3233,AurMe_IMSTJM9)))),(DecGa_P77,(ParSa_CAAAGB01,((AltAl_IMSTJM5,AltAl_PF1),(AltAl_IMSTJM6,(AltAl_IMSTJM3,(AltAl_IMSTJM4,(AltAl_IMSTJM2,(AltAl_IMSTJM1,AltAl_IMSTJM7)))))))))'>0.65'))'>4.06'));

[Sandra AC]

Hi there,

Thanks for your message! I have created a dummy alignment file based on the taxa you have in your Newick tree file, added a dummy root age constraint in your current Newick tree file (e.g., 'B(6.00, 6.30)'; you do not have a root age constraint in your Newick tree file at the moment and, given that you have not share your control file, I am specified this via variable `RootAge` instead), and run MCMCtree with a dummy control file (i.e., I do not know which control file you are using, and so I just specified random settings for the priors). Unfortunately, I cannot reproduce your error; MCMCtree runs without problems, printing out the following when reading the node age constraints in the tree file:

```
Fossil calibration information used.
Node  69:   B (  6.0000,  6.3000,  0.0250,  0.0250 )    # NOTE: this is the dummy root age constraint I added, you may have another
Node  70:   L (  2.5100,  0.1000,  1.0000,  0.0250 )
Node  92:   L (  4.0600,  0.1000,  1.0000,  0.0250 )
Node  93:   U (  5.1400,  0.0250 )
Node 119:   L (  0.6500,  0.1000,  1.0000,  0.0250 )
```

Which PAML version are you using? What settings have you specified in your control file? If you attach your control file, alignment file, and tree file, I can troubleshoot what my be going wrong.

All the best,
Sandy