Analyses for Study

Analyses

Analysis 1

Analysis details

Name

Input data 1 Input object(s) Cylindrocarpon-like Fig2_his3_MAFFT

Analysis step Fig. 2 - MrBayes -- Step details Name Notes Software used Name Version URL Description Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands BEGIN MRBAYES; [Dont ask if we want to continue after the run has stopped, and dont ask if its OK to overwrite files. ] log start filename=Fig2histone.log; Set autoclose=yes nowarn=yes; [* Define the outgroup (one taxon)] outgroup CBS_112679; outgroup CBS_112613; [* Define a number of character sets. Can be used later.] CHARSET His3 = 1-427; [* Define one way of partitioning the data. Can be used later.] [The rest of the commands are specific settings for a particular run of the MCMC] [* Set a partitioning schema for the following MCMC, using the predefined partitioning schema] prset applyto=(all) ratepr=variable; [* Specify the likelihood part of the model] lset applyto=(1) nst=6 rates=invgamma; [GTR + I + gamma] [* Specify the prior for the model parameters] [* Specify the prior for the model parameters] [ Prset statefreqpr=Dirichlet(1,1,1,1);] [Enable the site-specific model. Should be combined with the unlink command.] Prset applyto=(all) ratepr=variable; [* Allow the parameters to be partition specific, by unlinking them from each other.] Unlink shape=(all) statefreq=(all) tratio=(all) revmat=(all) pinvar=(all); [ Unlink shape=(all) statefreq=(all) tratio=(all) revmat=(all) pinvar=(all) brlens=(all) topology=(all); ] mcmcp ngen=10000000 nruns=2 nchains=4 temp=0.2; mcmcp mcmcdiagn=yes diagnfreq=1000 stoprule=yes stopval=0.01; mcmcp printfreq=100 samplefreq=100; help lset; help mcmc; mcmc; sump relburnin=yes burninfrac=0.25; sumt relburnin=yes burninfrac=0.25 Showtreeprobs=yes Conformat=simple; log stop;

Output data 2 Output object(s) con 50 majrule_his3_Fig2 Fig. 2

Input data 1 Input object(s) Cylindrocarpon-like Fig2_his3_MAFFT

Analysis step Fig. 2 - RaxML -- Step details Name Software used Name Version URL Description Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstop_ 1000 bootstrap_seed_ true bootstrap_seed_val_ 12345 convergence_criterion_ false datatype_ dna disable_ratehet_ false disable_seqcheck_ false dna_gtrcat_ GTRCAT intermediate_treefiles_ false mesquite_output_ false mlsearch_ true more_memory_ false no_bfgs_ false number_cats_ 25 outgroup_ CBS_112613,CBS_112679 outsuffix_ result parsimony_seed_val_ 12345 printbrlength_ false provide_parsimony_seed_ true rearrangement_yes_ false runtime_ 0.25 specify_bootstraps_ true use_apobootstopping_ false

Output data 1 Output object(s) Fig. 2

Analysis 2

Analysis details

Name

Input data 5 Input object(s) Cylindrocarpon-like Fig3_his3_Mafft Cylindrocarpon-like Fig3_ITS_Mafft Cylindrocarpon-like Fig3_ITS_Mafft+Fig3_tub2_Mafft+Fig3_his3_Mafft+Fig3_tef1_Mafft Cylindrocarpon-like Fig3_tub2_Mafft Cylindrocarpon-likeFig3_tef1_Mafft

Analysis step Fig. 3 - MrBayes -- Step details Name Software used Name Version URL Description Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [Beginning of the MRBAYES block. All text within this block (except comments) are treated as potential commands, just as if they where typed on the command line.] BEGIN MRBAYES; [Don't ask if we want to continue after the run has stopped, and don't ask if it's OK to overwrite files. ] log start filename=Fig3_concatenado.log; Set autoclose=yes nowarn=yes; [* Define the outgroup (one taxon)] outgroup CBS_112613; outgroup CBS_112679; [* Define a number of character sets. Can be used later.] CHARSET ITS = 1-515; CHARSET tub = 516-1058; CHARSET H3 = 1059-1485; CHARSET TEF = 1486-1939; [* Define one way of partitioning the data. Can be used later.] partition genes = 4: ITS, tub, H3, TEF; [The rest of the commands are specific settings for a particular run of the MCMC] [* Set a partitioning schema for the following MCMC, using the predefined partitioning schema] prset applyto=(all) ratepr=variable; set partition = genes; [* Specify the likelihood part of the model] lset applyto=(1,3) nst=6 rates=invgamma; [GTR + I + gamma] lset applyto=(2,4) nst=6 rates=gamma; [# GTR + gamma] [* Specify the prior for the model parameters] [ Prset statefreqpr=Dirichlet(1,1,1,1);] [Enable the site-specific model. Should be combined with the unlink command.] Prset applyto=(all) ratepr=variable; [* Allow the parameters to be partition specific, by unlinking them from each other.] Unlink shape=(all) statefreq=(all) tratio=(all) revmat=(all) pinvar=(all); mcmcp ngen=10000000 nruns=2 nchains=4 temp=0.2; mcmcp mcmcdiagn=yes diagnfreq=1000 stoprule=yes stopval=0.01; mcmcp printfreq=100 samplefreq=100; help lset; help mcmc; mcmc; sump relburnin=yes burninfrac=0.25; sumt relburnin=yes burninfrac=0.25 Showtreeprobs=yes Conformat=simple; log stop;

Output data 5 Output object(s) Fig. 3 Fig. 3 Fig. 3 Fig. 3 Fig. 3

Analysis 3

Analysis details

Name

Input data 5 Input object(s) Cylindrocarpon-like Fig3_his3_Mafft Cylindrocarpon-like Fig3_ITS_Mafft Cylindrocarpon-like Fig3_ITS_Mafft+Fig3_tub2_Mafft+Fig3_his3_Mafft+Fig3_tef1_Mafft Cylindrocarpon-like Fig3_tub2_Mafft Cylindrocarpon-likeFig3_tef1_Mafft

Analysis step Fig. 3 - RaXML -- Step details Name Software used Name Version URL Description Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands RAxML-HPC2 on XSEDE - Parameters bootstop_ 1000 bootstrap_seed_ true bootstrap_seed_val_ 12345 convergence_criterion_ false datatype_ dna disable_ratehet_ false disable_seqcheck_ false dna_gtrcat_ GTRCAT estimate_perpartbrlen_ false intermediate_treefiles_ false mesquite_output_ false mlsearch_ true more_memory_ false no_bfgs_ false number_cats_ 25 outgroup_ CBS_112613,CBS_112679 outsuffix_ concatenado parsimony_seed_val_ 12345 printbrlength_ false provide_parsimony_seed_ true rearrangement_yes_ false runtime_ 0.25 specify_bootstraps_ true use_apobootstopping_ false Parameter 'partition_' DNA, ITS = 1-515 DNA, tub = 516-1058 DNA, H3 = 1059-1485 DNA, TEF = 1486-1939

Output data 5 Output object(s) Fig. 3 Fig. 3 Fig. 3 Fig. 3 Fig. 3