TreeBASE Search-Analyses for study 22022

@ARTICLE{TreeBASE2Ref27961, author = {Beatriz Mora-Sala and Ana Cabral and Maela Leon and Carlos Agusti-Brisach and Josep Armengol and Paloma Abad-Campos}, title = {Survey, Identification and Characterization of cylindrocarpon-like asexual morphs in Spanish forest nurseries}, year = {2018}, keywords = {Pinus, Quercus, Dactylonectria, Ilyonectria, Neonectria, Cylindrodendrum}, doi = {10.1094/PDIS-01-18-0171-RE}, url = { http://apsjournals.apsnet.org/loi/pdis}, pmid = {30189159}, journal = {Plant Disease}, volume = {102}, number = {11}, pages = {2083--2100}, abstract = {Cylindrocarpon-like asexual morphs infect herbaceous and woody plants, mainly in agricultural scenarios, but also in forestry systems. The aim of the present study was to characterize a collection of Cylindrocarpon-like isolates recovered from the roots of a broad range of forest hosts from nurseries showing decline by morphological and molecular studies. Between 2009 and 2012, 17 forest nurseries in Spain were surveyed and a total of 103 Cylindrocarpon-like isolates were obtained. Isolates were identified based on DNA sequences of the partial gene regions histone H3 (his3). For the new species, the internal transcribed spacer and intervening 5.8S nrRNA gene (ITS) region, β-tubulin (tub2), and translation elongation factor 1-α (tef1) were also used to determine their phylogenetic position. Twelve species belonging to the genera Cylindrodendrum, Dactylonectria, and Ilyonectria were identified from damaged roots of 15 different host genera. The species C. alicantinum, D. macrodidyma, D. novozelandica, D. pauciseptata, D. pinicola, D. torresensis, I. capensis, I. cyclaminicola, I. liriodendri, I. pseudodestructans, I. robusta, and I. rufa were identified. In addition, two Dactylonectria species (D. hispanica sp. nov. and D. valentina sp. nov.), one Ilyonectria species (I. ilicicola sp. nov.), and one Neonectria species (N. quercicola sp. nov.) are newly described. The present study demonstrates the prevalence of this fungal group associated with seedlings of diverse hosts showing decline symptoms in forest nurseries in Spain.} }

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Analyses for Study 22022

Citation title: "Survey, Identification and Characterization of cylindrocarpon-like asexual morphs in Spanish forest nurseries".

Study name: "Survey, Identification and Characterization of cylindrocarpon-like asexual morphs in Spanish forest nurseries".

This study is part of submission 22022 (Status: Published).

Analyses

Analysis 1

Analysis details

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Input data

1 Input object(s)

Analysis step

Fig. 2 - MrBayes --

Step details

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Description
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)

Input data

1 Input object(s)

Analysis step

Fig. 2 - RaxML --

Step details

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Software used

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Version
URL
Description
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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)

Analysis 2

Analysis details

Name

Input data

5 Input object(s)

Analysis step

Fig. 3 - MrBayes --

Step details

Name

Software used

Name
Version
URL
Description
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)

Analysis 3

Analysis details

Name

Input data

5 Input object(s)

Analysis step

Fig. 3 - RaXML --

Step details

Name

Software used

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Version
URL
Description
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