DOI: 10.5061/dryad.04fj885
title: Data from: A reevaluation of the Andean Genus Petroravenia (Brassicaceae: Thelypodieae) based on morphological and molecular data

description: Abstract Petroravenia was until recently considered as a genus of three
 species (P. eseptata, P. friesii, and P. werdermannii) distributed along
 the Central Andes of Argentina, Bolivia, Chile, and Peru. This genus was
 included in the tribe Thelypodieae and was morphologically characterized
 by being tiny rhizomatous perennial herbs with rosulate leaves, dendritic
 trichomes, capsular silicles, and incumbent cotyledons. However, the
 phylogeny of Petroravenia, and its tribal placement, was never analyzed
 using molecular data. The lack of such studies, as well as the paucity of
 herbarium collections, suggesting that Petroravenia species are vulnerable
 and/or endangered, prompted us to address the molecular phylogeny of this
 genus. For this purpose, we generated comprehensive molecular phylogenies
 using nuclear (ITS) and plastid (trnL-F and trnH-psbA) data, and conducted
 morphological comparisons between these species and their closest related
 taxa. Results from the phylogenetic analyses showed that Petroravenia
 represents a polyphyletic group, with P. eseptata included in tribe
 Halimolobeae, and P. friesii and P. werdermannii placed within tribe
 Eudemeae and related to the genus Alshehbazia. Based on the results
 obtained from morphological and molecular data, we decided herein to
 retain the original circumscription of Petroravenia as monospecific within
 the tribe Halimolobeae and to transfer P. friesii and P. werdermannii to
 the genus Alshehbazia within the tribe Eudemeae. Systematic implications
 of these results are also discussed.
description: Appendix1New sequences of Petroravenia generated for this study. Species, specimen vouchers, and GenBank accession numbers (ITS, trnL-F, trnH-psbA). For sequences downloaded from GenBank, see Appendix 2.Appendix 2Taxa and GenBank accession numbers for the ITS, trnL-F, and trnH-psbA sequences downloaded from GenBank and used in the phylogenetic analyses. New sequences generated for this study are shown in Appendix 1.Appendix2.docxTable S1Table S1. Features of the DNA alignments used in the phylogenetic analyses within Brassicaceae and within tribes Halimolobeae and Eudemeae.TableS1.docxFigure S1Maximum likelihood tree for Brassicaceae generated with RAxML. A, ITS dataset. B, trnL-F dataset. Tribes are indicated to the right of the boxes. Circles on nodes indicate bootstrap support values. The white arrows indicate phylogenetic position of P. friesii and P. werdermanni within the tribe Eudemeae, while black arrow show position of P. eseptata in the tribe Halimolobeae. The vertical line indicates the tribe Thelypodieae, in which Petroravenia is currently included. Units of branch length are proportional to nucleotide substitutions per site.FigS1.pdfFigure S2Maximum likelihood trees for tribes Halimolobeae and Eudemeae generated with RAxML. Tribe Halimolobeae (A–B): A, ITS dataset. B, trnL-F dataset. The black arrow shows the position of P. eseptata within the tribe. Tribe Eudemeae (C–D): C, ITS dataset. D, trnL-F + trnH-psbA (cpDNA) dataset. The grey arrow shows the position of P. friesii and P. werdermanii within the tribe. Numbers on branches correspond to bootstrap support values. Units of branch length are proportional to nucleotide substitutions per site.FigS2.pdfFigure S3Bayesian 50% majority-rule consensus tree for tribes Halimolobeae and Eudemeae from 6002 trees generated by Bayesian inference with MrBayes. Tribe Halimolobeae (A–C): A, ITS dataset. B, trnL-F dataset. C, combined ITS + trnL-F dataset. The black arrow shows the position of P. eseptata within the tribe. Tribe Eudemeae (D–F): D, ITS dataset. E, combined trnL-F + trnH-psbA (cpDNA) dataset. F, combined ITS + cpDNA dataset. The grey arrow shows the position of P. friesii and P. werdermanii within the tribe. Circles on nodes indicate posterior probability values. Units of branch length are proportional to nucleotide substitutions per site.FigS3.pdfBrassicaceae ITS alignmentITS alignment of Brassicaceae dataset.BRASSICACEAE_ITS_alignment.fasBrassicaceae ITS Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for Brassicaceae and the ITS dataset.BRASSICACEAE_ITS_MrBayes.con50.treBrassicaceae ITS Maximum likelihood treeMaximum likelihood tree for Brassicaceae generated with RAxML using the ITS dataset.BRASSICACEAE_ITS_RAxML_bestTree.treBrassicaceae trnL-F alignmenttrnL-F alignment of Brassicaceae dataset.BRASSICACEAE_trnLF_alignment.fasBrassicaceae trnL-F Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for Brassicaceae and the trnL-F dataset.BRASSICACEAE_trnLF_MrBayes.con50.treBrassicaceae trnL-F Maximum likelihood treeMaximum likelihood tree for Brassicaceae generated with RAxML using the trnL-F dataset.BRASSICACEAE_trnLF_RAxML_BestTree.treHalimolobeae ITS alignmentITS alignment of tribe Halimolobeae dataset.HALIMOLOBEAE_ITS_alignment.fasHalimolobeae ITS Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Halimolobeae and the ITS dataset.HALIMOLOBEAE_ITS_MrBayes.con50.treHalimolobeae ITS Maximum likelihood treeMaximum likelihood tree for tribe Halimolobeae generated with RAxML using the ITS dataset.HALIMOLOBEAE_ITS_RAxML_bestTree.treHalimolobeae trnL-F alignmenttrnL-F alignment of tribe Halimolobeae dataset.HALIMOLOBEAE_trnLF_alignment.fasHalimolobeae trnL-F Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Halimolobeae and the trnL-F dataset.HALIMOLOBEAE_trnLF_MrBayes.con50.treHalimolobeae trnL-F Maximum likelihood treeMaximum likelihood tree for tribe Halimolobeae generated with RAxML using the trnL-F dataset.HALIMOLOBEAE_trnLF_RAxML_bestTree.treHalimolobeae ITS+trnL-F Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Halimolobeae and the concatenated ITS+ trnL-F datasetsHALIMOLOBEAE_ITS+trnLF_MrBayes.con50.treHalimolobeae ITS+trnL-F Maximum likelihood treeMaximum likelihood tree for tribe Halimolobeae generated with RAxML using the concatenated ITS+ trnL-F datasets.HALIMOLOBEAE_ITS+trnLF_RAxML_bestTree.treEudemeae ITS alignmentITS alignment of tribe Eudemeae dataset.EUDEMEAE_ITS_alignment.fasEudemeae ITS Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the ITS dataset.EUDEMEAE_ITS_MrBayes.con50.treEudemeae ITS Maximum likelihood treeMaximum likelihood tree for tribe Eudemeae generated with RAxML using the ITS dataset.EUDEMEAE_ITS_RAxML_bestTree.treEudemeae trnL-F alignmenttrnL-F alignment of tribe Eudemeae dataset.EUDEMEAE_trnLF_alignment.fasEudemeae trnL-F Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnL-F dataset.EUDEMEAE_trnLF_MrBayes.con50.treEudemeae trnL-F Maximum likelihood treeMaximum likelihood tree for tribe Eudemeae generated with RAxML using the trnL-F dataset.EUDEMEAE_trnLF_RAxML_bestTree.treEudemeae trnLH-psbA alignmenttrnH-psbA alignment of tribe Eudemeae dataset.EUDEMEAE_trnH_alignment.fasEudemeae trnH-psbA Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnH-psbA dataset.EUDEMEAE_trnH_MrBayes.con50.treEudemeae trnH-psbA Maximum likelihood treeMaximum likelihood tree for tribe Eudemeae generated with RAxML using the trnH-psbA dataset.EUDEMEAE_trnH_RAxML_bestTree.treEudemeae cpDNA Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated cpDNA (trnL-F+trnH-psbA) datasets.EUDEMEAE_cpDNA_MrBayes.con50.treEudemeae cpDNA Maximum likelihood treeMaximum likelihood tree for tribe Eudemeae generated with RAxML using the concatenated cpDNA (trnL-F+trnH) dataset.EUDEMEAE_cpDNA_RAxML_bestTree.treEudemeae ITS+cpDNA Bayesian majority-rule consensus treeBayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated ITS + cpDNA (trnL-F+trnH-psbA) datasets.EUDEMEAE_ITS+cpDNA_MrBayes.con50.treEudemeae ITS+cpDNA Maximum likelihood treeMaximum likelihood tree for tribe Eudemeae generated with RAxML using the concatenated ITS+cpDNA (trnL-F+trnH) datasets.EUDEMEAE_ITS+cpDNA_RAxML_bestTree.tre