TreeBASE Search-Analyses for study 12652

@ARTICLE{TreeBASE2Ref20655, author = {Domingos Ben?cio Oliveira Silva Cardoso and Haroldo Cavalcante de Lima and Rodrigo Sch?tz Rodrigues and Luciano Paganucci Queiroz and R. Toby Pennington and Matthew T. Lavin}, title = {The Bowdichia clade of Genistoid legumes: phylogenetic analysis of combined molecular (ITS, matK and trnL intron) and morphological data and a recircumscription of Diplotropis}, year = {2012}, keywords = {Acosmium; radial flower; Genistoid clade; papilionate flower; Papilionoideae; phylogeny; Sophoreae}, doi = {}, url = {http://}, pmid = {}, journal = {Taxon}, volume = {61}, number = {5}, pages = {1074?1087}, abstract = {The Neotropical Bowdichia clade (Leguminosae, Papilionoideae) comprises four genera, Bowdichia, Diplotropis, Guianodendron, and Leptolobium, which are sister to the core Genistoid clade. Bowdichia and Diplotropis have been treated as a single genus, whereas Guianodendron and Leptolobium have been synonymized with the distantly Dalbergioid genus Acosmium because of shared radial floral symmetry. We combined and analyzed morphological and molecular data including nuclear ribosomal internal transcribed spacer (ITS/5.8S) and two chloroplast (matK and trnL intron) DNA regions in order to evaluate the monophyly of each genus and the Bowdichia clade. A combined parsimony analysis strongly supported the monophyly of Bowdichia, the paraphyly of Diplotropis, and the independent evolution of radial floral symmetry in Guianodendron and Leptolobium. Leptolobium is sister to Bowdichia and Guianodendron is nested within Diplotropis s.l. Diplotropis is here recircumscribed as to encompass the monophyletic sect. Diplotropis and it is suggested that Diplotropis sect. Racemosae deserves segregation into a new genus. Floral symmetry has been given too much emphasis in previous classifications by taxonomists who did not recognize its evolutionary lability, which has resulted in non-monophyletic circumscriptions of genera like Acosmium, Bowdichia and Diplotropis.} }

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Analyses for Study 12652

Citation title: "The Bowdichia clade of Genistoid legumes: phylogenetic analysis of combined molecular (ITS, matK and trnL intron) and morphological data and a recircumscription of Diplotropis".

Study name: "The Bowdichia clade of Genistoid legumes: phylogenetic analysis of combined molecular (ITS, matK and trnL intron) and morphological data and a recircumscription of Diplotropis".

This study is part of submission 12652 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ITS parsimony analysis --

Step details

Name

Software used

Name
Version
Algorithm
Commands
begin paup; log start=yes file=ITS_Bowdichia_clade_parsimony_log.nex replace; outgroup 1-5; 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=simple limitperrep=no usenonmin=yes swap=tbr steepest=yes multrees=yes; describetrees 1/ root=outgroup plot=phylogram apolist=no; savetrees root=yes file=ITS_Bowdichia_clade_parsimony_tre.nex replace format=altnex brlens=yes; contree all/strict=yes semistrict=no majrule=no adam=no root=outgroup treefile=ITS_Bowdichia_clade_parsimony_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=ITS_Bowdichia_clade_parsimony_tre.nex append=yes format=altnex savebootp=brlens; log stop=yes; End;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

2 Input object(s)

Analysis step

Combined parsimony analysis --

Step details

Name
Notes

Software used

Name
Version
Algorithm
Commands
log start=yes file=Bowdichia_clade_comb_parsimony_log.nex replace; outgroup 1-5; 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=simple limitperrep=no usenonmin=yes swap=tbr steepest=yes multrees=yes; describetrees 1/ root=outgroup plot=phylogram apolist=no; savetrees root=yes file=Bowdichia_clade_comb_parsimony_tre.nex replace format=altnex brlens=yes; contree all/strict=yes semistrict=no majrule=no adam=no root=outgroup treefile=Bowdichia_clade_comb_parsimony_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=Bowdichia_clade_comb_parsimony_tre.nex append=yes format=altnex savebootp=brlens; log stop=yes; End;

Output data