TreeBASE Search-Analyses for study 12754

@ARTICLE{TreeBASE2Ref20736, author = {Domingos Ben?cio Oliveira Silva Cardoso and Luciano Paganucci Queiroz and Haroldo Cavalcante de Lima and Elisa Suganuma and Cassio van den Berg and Matthew T. Lavin}, title = {A molecular phylogeny of the Vataireoid legumes underscores floral evolvability that is general to many early-branching papilionoid lineages}, year = {2013}, keywords = {convergence; floral evolution; Leguminosae; morphology; phylogeny; Papilionoideae}, doi = {}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {100}, number = {2}, pages = {403?421}, abstract = {Premise of study: The fused and completely differentiated papilionate floral organs in the neotropical legume trees Vatairea and Vataireopsis were traditionally used in part to ascribe these genera to the tribe Dalbergieae. In contrast, the free and mostly undifferentiated floral parts of Luetzelburgia and Sweetia fit the circumscription of the ?primitive? Sophoreae. Such divergent floral morphologies thought to divide deep phylogenetic lineages indeed may be prone to episodic transformation among close papilionoid relatives. Methods: Parsimony and Bayesian phylogenetic analyses involved nuclear ribosomal ITS/5.8S and six plastid (matK, 3'-trnK, psbA-trnH, trnL intron, rps16, and trnD-T) DNA sequence loci. We sampled 26 out of 27 known species of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis for at least five loci, most represented by multiple conspecific accessions. Outgroups included the Lecointeoid legumes. Parsimony mapping of 30 morphological traits was performed to apomorphically diagnose each genus. Papilionate floral morphology was used in an ancestral state likelihood reconstruction at each node of the Vataireoid clade. Key Results: Analysis of individual and combined data sets strongly resolved the monophyly of each of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis. Vataireopsis was resolved as sister to the rest and the morphologically divergent Luetzelburgia and Vatairea were strongly resolved as sister clades. Floral morphology was generally not a good predictor of phylogenetic relatedness. Conclusions: For the first time, Luetzelburgia, Sweetia, Vatairea, and Vataireopsis are unequivocally resolved as the ?Vataireoid? clade. Fruit and vegetative traits are found to be more phylogenetically conserved than many floral traits. This explains why the identity of the Vataireoids has been overlooked or confused. The evolvability of floral traits may also be a general condition among many of the early-branching papilionoid lineages.} }

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Analyses for Study 12754

Citation title: "A molecular phylogeny of the Vataireoid legumes underscores floral evolvability that is general to many early-branching papilionoid lineages".

Study name: "A molecular phylogeny of the Vataireoid legumes underscores floral evolvability that is general to many early-branching papilionoid lineages".

This study is part of submission 12754 (Status: Published).

Analyses

Analysis 1

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis of the ITS sequence data --

Step details

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Software used

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Description
Algorithm
Commands
begin mrbayes; set autoclose=yes; charset ITS1 = 1-353; charset 58S = 354-520; charset ITS2 = 521-844; partition ITS = 3: ITS1, 58S, ITS2; set partition=ITS; prset ratepr=variable; lset applyto=(1,2,3) nst=6 rates=invgamma; unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all); mcmcp ngen=10000000 printfreq=100 samplefreq=100000 nchains=4 nruns=2 savebrlens=yes; end;

Output data

1 Output object(s)

Analysis 2

Analysis details

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Input data

1 Input object(s)

Analysis step

Parsimony analysis of the total combined data --

Step details

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Software used

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Version
Description
Algorithm
Commands
begin paup; log start=yes file=vat_comb_molecular_log.nex replace; outgroup 1-8; charset morph = 1-30; charset ITS = 31-874; charset matK = 875-2762; charset Kindel = 875-2762; charset trnDT = 2763-4612; charset DTindel = 2763-4612; charset trnL = 4613-5260; charset DTindel = 4613-5260; charset psbA = 5261-5902; charset DTindel = 5261-5902; charset rpS16 = 5903-6966; charset S16indel = 5903-6966; charset molecular = 31-6966; exclude morph; set criterion=parsimony taxlabels=full torder=right maxtrees=10000 increase=no root=outgroup outroot=monophyl storebrlens=yes warnreset=no warntree=no warntsave=no warnroot=no warnredef=no autoclose=yes; hsearch start=stepwise hold=5 addseq=random limitperrep=no usenonmin=yes swap=tbr steepest=yes multrees=yes; describetrees 1/ root=outgroup plot=phylogram apolist=no; savetrees root=yes file=vat_comb_molecular_tre.nex replace format=altnex brlens=yes; contree all/strict=yes semistrict=no majrule=no adam=no root=outgroup treefile=vat_comb_molecular_tre.nex append=yes; bootstrap nreps=10000 grpfreq=no conlevel=50 search=heuristic/ addseq=random nreps=1 swap=TBR steepest=no multrees=no; savetrees from=1 to=1 root=yes file=vat_comb_molecular_tre.nex append=yes format=altnex savebootp=brlens; log stop=yes; End;

Output data

1 Output object(s)

Analysis 3

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis of total combined data --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
begin mrbayes; set autoclose=yes; charset morph = 1-30; charset ITS = 31-874; charset matK = 875-2745; charset Kindel = 2746-2762; charset trnDT = 2763-4544; charset DTindel = 4545-4612; charset trnL = 4613-5243; charset Lindel = 5244-5260; charset psbA = 5261-5901; charset Aindel = 5902-5902; charset rpS16 = 5903-6912; charset S16indel = 6913-6966; partition data = 12: morph, ITS, matK, Kindel, trnDT, DTindel, trnL, Lindel, psbA, Aindel, rpS16, S16indel; set partition = data; prset ratepr=variable; lset applyto=(1,4,6,8,10,12) rates=gamma; lset applyto=(2,5) nst=6 rates=invgamma; lset applyto=(3,7,9,11) nst=6 rates=gamma; unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all); mcmc ngen=10000000 printfreq=100 samplefreq=100000 nchains=4 nruns=2 savebrlens=yes; end;

Output data