TreeBASE Search-Analyses for study 18227

@ARTICLE{TreeBASE2Ref25063, author = {Cesar Castellanos and Royce A.D. Steeves and Anne Bruneau and Gwilym P. Lewis}, title = {A settled sub-family for the Orphan tree: The phylogenetic position of the endemic Colombian genus Orphanodendron in the Leguminosae}, year = {2016}, keywords = {Colombia, Fabaceae, genistoid clade, matK, Papilionoideae, phylogenetic analysis. }, doi = {}, url = {}, pmid = {}, journal = {Brittonia}, volume = {}, number = {}, pages = {}, abstract = {Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support (0.6 posterior probability) for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus. } }

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Analyses for Study 18227

Citation title: "A settled sub-family for the Orphan tree: The phylogenetic position of the endemic Colombian genus Orphanodendron in the Leguminosae".

Study name: "A settled sub-family for the Orphan tree: The phylogenetic position of the endemic Colombian genus Orphanodendron in the Leguminosae".

This study is part of submission 18227 (Status: Published).

Analyses

Analysis 1

Analysis details

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1 Input object(s)

Analysis step

matK Maximum Parsimony of 674 taxa --

Step details

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begin pauprat; dimensions nchar=1803; set nreps=200; set seed=0; set pct=20; set wtmode=uniform; set terse; startcmd "[!************************************]"; startcmd "[! ******** PAUP* Ratchet ****** ]"; startcmd "[! Derek S. Sikes & Paul O. Lewis ]"; startcmd "[! University of Connecticut ]"; startcmd "[! March, 2000 ]"; startcmd "[! Based on Kevin Nixon's Parsimony ]"; startcmd "[! Ratchet as described in: Nixon, ]"; startcmd "[! K. C. 1999. The Parsimony Ratchet ]"; startcmd "[! a new method for rapid parsimony ]"; startcmd "[! analysis. Cladistics 15: 407-414. ]"; startcmd "[!**********************************]"; startcmd "[exe infile.nex]"; startcmd "log file=paupratchet.log"; startcmd "set increase=auto"; startcmd "hs status=no nrep=1 swap=tbr start=stepwise addseq=random nchuck=1 chuckscore=1"; startcmd "savetrees file=mydata.tre replace"; startcmd "savetrees file=mydata.tmp replace"; paupcmd "pset mstaxa=uncertain"; paupcmd "hsearch status=no start=1 swap=tbr multrees=no "; paupcmd "outgroup Polygala_californica_AY386842"; normcmd "savetrees file=mydata.tmp replace"; normcmd "gettrees file=mydata.tre mode=7"; normcmd "savetrees file=mydata.tre replace"; normcmd "gettrees file=mydata.tmp mode=3 warntree=no"; normcmd "time"; stopcmd "gettrees file=mydata.tre mode=3"; stopcmd "pscores all"; stopcmd "time"; stopcmd "log stop"; stopcmd "[!*******************************]"; stopcmd "[! THIS SEARCH IS COMPLETE ]"; stopcmd "[! A LOG FILE HAS BEEN WRITTEN ]"; stopcmd "[! AND ALL TREES HAVE BEEN SAVED. ]"; stopcmd "[! IT IS OK TO QUIT PAUP* ]"; stopcmd "[!*********************************]"; stopcmd "filter best=yes permdel=yes"; stopcmd "savetrees file=pauprat.best.tre"; stopcmd "[quit]"; write file=ratchet.nex replace; end;

Output data

1 Output object(s)

Analysis 2

Analysis details

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1 Input object(s)

Analysis step

matK and trnL-F combined Bayesian analysis of Genistoid s.l. Papilionoid legumes --

Step details

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begin mrbayes; outgroup Panurea_longifolia; set precision = 15; set seed=1116355510; set swapseed=1116355510; set scientific=Yes; set autoclose=yes; set nowarnings=yes; charset matK = 1-1611; charset trnL = 1612-2393; partition genes = 2: matK,trnL; set partition = genes; [!MrBayes settings for the best-fit model (GTR+G) selected by hLRT and AiC in MrModeltest 2.3 for matK] lset applyto= (1) nst=6 rates=gamma; Prset applyto= (1) statefreqpr=dirichlet(1,1,1,1); [!MrBayes settings for the best-fit model (GTR+G) selected by hLRT and AiC in MrModeltest 2.3 for trnL] lset applyto= (2) nst=6 rates=gamma; Prset applyto= (2) statefreqpr=dirichlet(1,1,1,1); unlink revmat=(all) statefreq=(all) shape=(all) pinvar=(all); prset ratepr=variable; mcmc ngen=10000000 filename=infile.nex nruns=2 nchains=4 temp=0.200 swapfreq=1 nswaps=1 samplefreq=1000 mcmcdiagn=Yes minpartfreq=0.1 allchains=No relburnin=Yes burninfrac=0.25 stoprule=No starttree=random stopval=0.01 Savebrlens=Yes nperts=0 Ordertaxa=Yes; sump relburnin=Yes burninfrac=0.25 nruns=2 outputname=sumpoutput.out; sumt relburnin=Yes burninfrac=0.25 nruns=2 ntrees=1 minpartfreq=0.05 contype=Halfcompat conformat=simple; end;

Output data

1 Output object(s)

Analysis 3

Analysis details

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1 Input object(s)

Analysis step

ITS Bayesian analysis of Genistoid s.l. Papillionoid legumes --

Step details

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begin mrbayes; outgroup Ormosia_amazonica_EF457724; set precision = 15; set seed=1116355510; set swapseed=1116355510; set scientific=Yes; set autoclose=yes; set nowarnings=yes; [!MrBayes settings for the best-fit model (GTR+I+G) selected by hLRT and AiC in MrModeltest 2.3] Lset nst=6 rates=invgamma; Prset statefreqpr=dirichlet(1,1,1,1); mcmc ngen=10000000 filename=infile.nex nruns=2 nchains=4 temp=0.200 swapfreq=1 nswaps=1 samplefreq=1000 mcmcdiagn=Yes minpartfreq=0.1 allchains=No relburnin=Yes burninfrac=0.25 stoprule=No starttree=random stopval=0.01 Savebrlens=Yes nperts=0 Ordertaxa=Yes; sump relburnin=Yes burninfrac=0.25 nruns=2 outputname=sumpoutput.out; sumt relburnin=Yes burninfrac=0.25 nruns=2 ntrees=1 minpartfreq=0.05 contype=Halfcompat conformat=simple; end;

Output data