TreeBASE Search-Analyses for study 24522

@ARTICLE{TreeBASE2Ref30131, author = {Pedro W. Crous and Michael J Wingfield and Ratchadawan Cheewangkoon and Angus Carnegie and Treena I Burgess and Bret A. Summerell and Jacqueline Edwards and Paul W.J. Taylor and Johannes (Ewald) Zacharias Groenewald}, title = {Foliar pathogens of eucalypts}, year = {2019}, keywords = {Corymbia, Eucalyptus, Foliar pathogen, New taxa, Taxonomy.}, doi = {10.1016/j.simyco.2019.08.001}, url = {http://www.sciencedirect.com/science/article/pii/S0166061619300090}, pmid = {316367}, journal = {Studies in Mycology}, volume = {94}, number = {}, pages = {125--298}, abstract = {Species of eucalypts are commonly cultivated for solid wood and pulp products. The expansion of commercially managed eucalypt plantations has chiefly been driven by their rapid growth and suitability for propagation across a very wide variety of sites and climatic conditions. Infection of foliar fungal pathogens of eucalypts is resulting in increasingly negative impacts on commercial forest industries globally. To assist in evaluating this threat, the present study provides a global perspective on foliar pathogens of eucalypts. We treat 110 different genera including species associated with foliar disease symptoms of these hosts. The vast majority of these fungi have been grown in axenic culture, and subjected to DNA sequence analysis, resolving their phylogeny. During the course of this study several new genera and species were encountered, and these are described. New genera include: Lembosiniella (L. eucalyptorum on E. dunnii, Australia), Neosonderhenia (N. eucalypti on E. costata, Australia), Neothyriopsis (N. sphaerospora on E. camaldulensis, South Africa), Neotrichosphaeria (N. eucalypticola on E. deglupta, Australia), Nothotrimmatostroma (N. bifarium on E. dalrympleana, Australia), Nowamyces (incl. Nowamycetaceae fam. nov., N. globulus on E. globulus, Australia), and Walkaminomyces (W. medusae on E. alba, Australia). New species include (all from Australia): Disculoides fraxinoides on E. fraxinoides, Elsinoe piperitae on E. piperita, Fusculina regnans on E. regnans, Marthamyces johnstonii on E. dunnii, Neofusicoccum corticosae on E. corticosa, Neotrimmatostroma dalrympleanae on E. dalrympleana, Nowamyces piperitae on E. piperita, Phaeothyriolum dunnii on E. dunnii, Pseudophloeospora eucalyptigena on E. obliqua, Pseudophloeospora jollyi on Eucalyptus sp., Quambalaria tasmaniae on Eucalyptus sp., Q. rugosae on E. rugosa, Sonderhenia radiata on E. radiata, Teratosphaeria pseudonubilosa on E. globulus and Thyrinula dunnii on E. dunnii. A new name is also proposed for Heteroconium eucalypti as Thyrinula uruguayensis on E. dunnii, Uruguay. Although many of these genera and species are commonly associated with disease problems, several appear to be opportunists developing on stressed or dying tissues. For the majority of these fungi, pathogenicity remains to be determined. This represents an important goal for forest pathologists and biologists in the future. Consequently, this study will promote renewed interest in foliar pathogens of eucalypts, leading to investigations that will provide an improved understanding of the biology of these fungi.} }

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Analyses for Study 24522

Citation title: "Foliar pathogens of eucalypts".

Study name: "Foliar pathogens of eucalypts".

This study is part of submission 24522 (Status: Published).

Analyses

Analysis 1

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Blastacervulus/Thyrinula (Fig. 12) parsimony analysis --

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Begin ASSUMPTIONS; charset locus1 = 1-144 147-151 197-296; [CHS] charset locus2 = 791-1320; [ITS] charset locus3 = 1576-2371; [LSU] charset locus4 = 2792-3716; [TEFtwo] charset locus5 = 3898-4316; [TUB] charset combined = locus1 locus2 locus3 locus4 locus5; taxset outgroups = Leptosphaeria_doliolum_CBS_505.75; end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = AulographinaCOMBtrimmedparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = AulographinaCOMBtrimmedparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = AulographinaCOMBtrimmedparsimonybootstrap.tre; Log stop=yes; End;

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1 Output object(s)

Analysis 2

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Disculoides (Fig. 33) parsimony analysis --

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Begin ASSUMPTIONS; charset locus1 = 143-276 323-764; [ITS] charset locus2 = 822-1286; [CAL] charset locus3 = 1858-2379; [TUB] charset combined = locus1 locus2 locus3; taxset outgroups = Harknessia_hawaiiensis_CBS_114811; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; SET CRITERION=distance maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; DSet distance=hky85; NJ breakties=random brlens=yes showtree=yes; Savetrees from=1 to=1 format=nexus brlens=yes maxdecimals=6 file = DisculoidesITScalTUBhky85.tre; Bootstrap nreps=1000 search=nj; Savetrees from=1 to=1 format= nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = DisculoidesITScalTUBhky85bs.tre; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = DisculoidesITScalTUBparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = DisculoidesITScalTUBparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = DisculoidesITScalTUBparsimonybootstrap.tre; Log stop=yes; End;

Output data

1 Output object(s)

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1 Input object(s)

Analysis step

Disculoides (Fig. 33) distance analysis --

Step details

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Begin ASSUMPTIONS; charset locus1 = 143-276 323-764; [ITS] charset locus2 = 822-1286; [CAL] charset locus3 = 1858-2379; [TUB] charset combined = locus1 locus2 locus3; taxset outgroups = Harknessia_hawaiiensis_CBS_114811; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; SET CRITERION=distance maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; DSet distance=hky85; NJ breakties=random brlens=yes showtree=yes; Savetrees from=1 to=1 format=nexus brlens=yes maxdecimals=6 file = DisculoidesITScalTUBhky85.tre; Bootstrap nreps=1000 search=nj; Savetrees from=1 to=1 format= nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = DisculoidesITScalTUBhky85bs.tre; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = DisculoidesITScalTUBparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = DisculoidesITScalTUBparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = DisculoidesITScalTUBparsimonybootstrap.tre; Log stop=yes; End;

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1 Output object(s)

Analysis 3

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1 Input object(s)

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Fusculina (Fig. 40) parsimony analysis --

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Begin ASSUMPTIONS; charset combined = 41-730; taxset outgroups = Delitschia_confertaspora_MF459003.1; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = FusculinaITSparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = FusculinaITSparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = FusculinaITSparsimonybootstrap.tre; Log stop=yes; End;

Output data

1 Output object(s)

Analysis 4

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1 Input object(s)

Analysis step

Capnodiales Overview (Fig. 61) Bayesian analysis --

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BEGIN mrbayes; [This block sets up several different partitions that could be used in the analysis of this dataset] outgroup Elsinoe_jasminicola_KX886997.1; [replace fungusX with your outgroup taxon] [When defining your charsets below, the characters must follow each other directly, e.g. 1-300, 301-500, 501-600 and not 5-300, 325-500, 530-600. You will excluded everything you do not want to include in the analysis (e.g. 1-4, 301-324 and 501-529 in the charset excludedcharacters line.] charset locus1 = 1-2650; [replace the xx's with numbers reflecting the character spanning of your gene 1] charset excludedchars = 1-122 904-2650; [list here all of the characters that you do not want to include. e.g. the bits between the loci] exclude excludedchars; partition AllLoci = 1: locus1; log start filename=NowamycesLSUtrimmedMB.log; END; BEGIN mrbayes; [This block defines the models and run parameters used in you actual analysis] set partition= AllLoci; prset statefreqpr=dirichlet(1,1,1,1); lset nst=6 rates=invgamma; unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all); mcmcp ngen=1000000000 nchains=4 printfreq=10 temp=0.25 samplefreq=10 savebrlens=yes stoprule=yes stopval=0.01 filename=NowamycesLSUtrimmedMB; mcmc; sump; sumt; END;

Output data

1 Output object(s)

Analysis 5

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1 Input object(s)

Analysis step

Nowamyces (Fig. 66) parsimony analysis --

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Begin ASSUMPTIONS; charset combined = 63-527; taxset outgroups = Ramularia_endophylla_AY490763.1; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; SET CRITERION=distance maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; DSet distance=hky85; NJ breakties=random brlens=yes showtree=yes; Savetrees from=1 to=1 format=nexus brlens=yes maxdecimals=6 file = NowamycesITShky85.tre; Bootstrap nreps=1000 search=nj; Savetrees from=1 to=1 format= nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = NowamycesITShky85bs.tre; SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = NowamycesITSparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = NowamycesITSparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = NowamycesITSparsimonybootstrap.tre; Log stop=yes; End;

Output data

1 Output object(s)

Analysis 6

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1 Input object(s)

Analysis step

Phaeothyriolum (Fig. 81) parsimony analysis --

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Begin ASSUMPTIONS; charset combined = 114-282 321-736; taxset outgroups = Melanconiella_hyperopta_NR_160258.1; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = PhaeothyriolumITSparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = PhaeothyriolumITSparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = PhaeothyriolumITSparsimonybootstrap.tre; Log stop=yes; End;

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1 Output object(s)

Analysis 7

Analysis details

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1 Input object(s)

Analysis step

Pseudophloeospora (Fig. 89) parsimony analysis --

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Begin ASSUMPTIONS; charset combined = 108-730; taxset outgroups = Discosia_pseudoartocreas_NR_132068.1; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = PseudophloeosporaITSparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = PseudophloeosporaITSparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = PseudophloeosporaITSparsimonybootstrap.tre; Log stop=yes; End;

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1 Output object(s)

Analysis 8

Analysis details

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1 Input object(s)

Analysis step

Quambalaria (Fig. 95) parsimony analysis --

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Begin ASSUMPTIONS; charset combined = 177-757; taxset outgroups = Burgoa_verzuoliana_NR_145334.1; [replace fungus1 to fungusX with your outgroup taxa] end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; [This turns off some user-prompts.] OUTGROUP outgroups/only; exclude 1-./only; include combined/only; [The following will calculate the parsimony trees using 100 random taxon additions] SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = QuambulariaITSparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = QuambulariaITSparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = QuambulariaITSparsimonybootstrap.tre; Log stop=yes; End;

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1 Output object(s)

Analysis 9

Analysis details

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1 Input object(s)

Analysis step

Sonderhenia (Fig. 101) parsimony analysis --

Step details

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Begin ASSUMPTIONS; charset locus1 = 172-658; [ITS] charset locus2 = 763-1296; [ACT] charset locus3 = 1450-1817; [CAL] charset locus4 = 2049-2345; [TUB] charset combined = locus1 locus2 locus3 locus4; taxset outgroups = Cladosporium_allicinum_CBS_177.71; end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; OUTGROUP outgroups/only; exclude 1-./only; include combined/only; SET CRITERION=distance maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; DSet distance=hky85; NJ breakties=random brlens=yes showtree=yes; Savetrees from=1 to=1 format=nexus brlens=yes maxdecimals=6 file = SonderheniaITSACTCALTUBtrimmedhky85.tre; Bootstrap nreps=1000 search=nj; Savetrees from=1 to=1 format= nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedhky85bs.tre; SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = SonderheniaITSACTCALTUBtrimmedparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedparsimonybootstrap.tre; Log stop=yes; End;

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

Sonderhenia (Fig. 101) distance analysis --

Step details

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Begin ASSUMPTIONS; charset locus1 = 172-658; [ITS] charset locus2 = 763-1296; [ACT] charset locus3 = 1450-1817; [CAL] charset locus4 = 2049-2345; [TUB] charset combined = locus1 locus2 locus3 locus4; taxset outgroups = Cladosporium_allicinum_CBS_177.71; end; BEGIN PAUP; LOG start=yes append=yes; set autoclose=yes warnreset=no torder=right; OUTGROUP outgroups/only; exclude 1-./only; include combined/only; SET CRITERION=distance maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; DSet distance=hky85; NJ breakties=random brlens=yes showtree=yes; Savetrees from=1 to=1 format=nexus brlens=yes maxdecimals=6 file = SonderheniaITSACTCALTUBtrimmedhky85.tre; Bootstrap nreps=1000 search=nj; Savetrees from=1 to=1 format= nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedhky85bs.tre; SET CRITERION=parsimony maxtrees=1000 increase=no storebrlens=yes outroot=paraphyl; Pset gapmode=newstate; [alternative: Pset gapmode=missing;] HSEARCH ADDSEQ=random NREPS=100 SWAP=TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format=nexus brlens=yes maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedparsimony.trees; PSCORES 1/TL=yes CI=yes RI=yes RC=yes HI=yes; Contree ALL/strict=yes treefile = SonderheniaITSACTCALTUBtrimmedparsimonycons.tre; Bootstrap nreps=1000 search=heuristic; [Bootstrap nreps=10000000 search=faststep;] Savetrees from=1 to=1 format=nexus brlens=yes savebootp=nodelabels maxdecimals=0 file = SonderheniaITSACTCALTUBtrimmedparsimonybootstrap.tre; Log stop=yes; End;

Output data