DOI: 10.5061/dryad.n24q8
title: Data from: Reinstatement of the Southern Andean genus Stenodraba (Brassicaceae) based on molecular data and insights from its environmental and geographic distribution

description: Stenodraba (Brassicaceae) included a group of eight species distributed
 along the Andes of South-Central Argentina and Chile. All of its species
 were subsequently transferred to other genera and are currently treated in
 Pennellia (Tribe Halimolobeae) and Weberbauera (Tribe Thelypodieae).
 However, the phylogeny of Stenodraba and its tribal placement were never
 analyzed using molecular data. The lack of such studies, as well as
 paucity of herbarium collections suggesting that some species are
 vulnerable and/or endangered, prompted us to address the molecular
 phylogeny of Stenodraba. For this purpose, we generated comprehensive
 molecular phylogenies using nuclear (ITS) and plastid (trnL-F and
 trnH-psbA) data, and conducted different niche comparisons in the
 environmental and geographic space using climate data processed both by
 ordination and species distribution modelling (SDM) techniques. The
 results demonstrated that Stenodraba belongs to the South American tribe
 Eudemeae and is related to the genera Aschersoniodoxa, Brayopsis,
 Dactylocardamum, and Eudema. Stenodraba species formed two, strongly
 supported clades, and although molecular data did not recover monophyly of
 the genus, this hypothesis was not significantly rejected. The main clades
 were differentiated in their climatic niches (both in the environmental
 and geographical spaces), and niche overlap was greater within than
 between clades. Systematic implications, including a key distinguishing
 Stenodraba from the remaining genera of Eudemeae and a synopsis of its
 species, are also provided.
description: Appendix1APPENDIX 1. New sequences generated for this study. Species, specimen voucher, and Genbank accession numbers (ITS, trnL-F, trnH-psbA). For sequences download from the GenBank see APPENDIX 2.Appendix2APPENDIX 2. Taxa 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.Supplementary_TableS1TableS1. Species ocurrence data of Stenodraba used in the niche analysesSupplementary_TableS2TABLE S2. Features of the DNA regions included in the phylogenetic analyses within Eudemeae.Supplementary_TableS3TABLE S3. Loadings on the first two components obtained from the principal component analysis (PCA-env) using bioclimatic variables extracted from the study area (50 km-buffered minimum convex polygon enclosing the Stenodraba species distribution).Supplementary_TableS4TABLE S4. Number of ocurrences (n), area under the receiver operating characteristic curve (AUC), variable contribution (%), and permutation importance (%) obtained in the MAXENT modeling for each Stenodraba clade. Variable contributions to overall performance greater than 25% are indicated in bold. BIO3: Isothermality, BIO4: Temperature Seasonality, BIO8: Mean Temperature of Wettest Quarter, BIO12: Annual Precipitation, BIO15: Precipitation Seasonality.Supplementary_FIGS1FIG. S1. Bayesian 50% majority-rule consensus tree from 3,002 trees generated by Bayesian inference with MrBayes for Brassicaceae. A. ITS dataset. B. trnL-F dataset. Tribes are indicated to the right of the boxes. Thick branches indicate &gt;0.90 Bayesian posterior probability. The white arrows indicate phylogenetic position of Stenodraba, while black arrows show the position of Pennellia (tribe Halimolobeae) and Weberbauera (tribe Thelypodieae) .Supplementary_FIGS2FIG. S2. Phylogenetic placement of Stenodraba within tribe Eudemeae, and including indel data in the analyses (nucleotide substitution + indel data). A ̶ C. Bayesian 50% majority-rule consensus trees from 6,002 trees generated by Bayesian inference with MrBayes. A. nrITS dataset. B. cpDNA dataset (trnL-F/trnH-psbA). C. Concatenated cpDNA + nrITS dataset (substitution + indel data). Values on branches correspond to Bayesian posterior probability (%). The start indicates the crown node of tribe Eudemeae.Supplementary_FIGS3FIG. S3. Phylogenetic placement of Stenodraba within tribe Eudemeae. A. Maximum clade credibility species tree (MCCT) estimated from nuclear ribosomal ITS and two chloroplast DNA regions (trnL-F, trnH-psbA) using the multispecies coalescent method implemented in *BEAST. Bayesian posterior probability values &gt;50 % are given at each node. B. Filtered supernetwork generated in SplitsTree using 1000 Bayesian posterior trees per each nuclear ITS and plastid (trnL-F/trnH-psbA) dataset, and filtering the splits to show only those present in a minimum of 35% input trees. The start indicate the crown node of tribe Eudemeae.Supplementary_FIGS4FIG. S4. Results from the niche overlap analyses in the space environmental (E) space obtained using the PCA-env method. A. Correlation circle showing the contribution of environmental variables on the first two axes of the PCA-env, and the percentage of inertia explained by the two axes. B ̶ C. Values for the first two principal components obtained in the PCA-env analyses in the studied area. B. Values for the PC1. C. Values for the PC2. Red dots represent specimen records for species included in the clade A (S. imbricatifolia, S. lagunae, S. suffruticosa), while blue dots represent occurrences for species of clade B (S. lechleri, S. parvifolia, S. chillanensis, S. colchaguensis, S. stenophylla).Supplementary_FIGS5FIG. S5. Climatic niches of Stenodraba species in the environmental space produced by the two main axes of the PCA-env. For each species, the gray to black shading represents the grid cell density of the clade occurrence (black being the highest density). The first dashed line represents the 50% of the available environment and the solid line represents the 100 %. A. S. lechleri. B. S. parvifolia. C. S. chillanensis. D. S. colchaguensis. E. S. imbricatifolia. F. S. lagunae. G. S. stenophylla. H. S. suffruticosa.Supplementary_FIGS6FIG. S6. Values of variables that most contribute in the MaxEnt models for clades A and B of Stenodraba along the distribution area. A. BIO3 (Isothermality). B. BIO4 (Temperature Seasonality). C. BIO8 (Mean Temperature of Wettest Quarter). D. BIO12 (Annual Precipitation). E. BIO15 (Precipitation Seasonality). Red and blue dots represent specimen occurrences of clades A and B, respectively, used for the SDM analyses. F. Response curves for variables used in the MaxEnt models of clades A and B. Response curves show the ranges in environmental conditions that are more favorable for the distribution of the species of each clade. The x-axis of the variables represents their ranges for the complete study area, while the y-axis represents the predicted suitability of the focus variable when all of the other variables are set to their average. Red line represents the mean response while blue shaded area represents ± 1 standard deviation.Supplementary_FIGS7FIG. S7. Stenodraba species. A. Stenodraba chillanensis (Zuloaga 15235, SI), habit. B. Stenodraba colchaguensis (Zuloaga 12539, SI), habit. C-D. Stenodraba parvifolia (Zuloaga 15583, SI). C. Habit. D. flowers. Photographs by: A, C, D, D. Salariato; B, C. Zannotii.ITS alignment BRASSICACEAEITS alignment of Brassicaceae dataset for family-level analyses.ITS_BRASSICACEAE.fastrnL-F alignment BRASSICACEAEtrnL-F alignment of Brassicaceae dataset for family-level analyses.trnL-F_BRASSICACEAE.fasMaximum likelihood tree ITS BRASSICACEAEMaximum likelihood tree for Brassicaceae generated with RAxML using the ITS dataset.BRASSICACEAE_ML_ITS.treMaximum likelihood tree trnL-F BRASSICACEAEMaximum likelihood tree for Brassicaceae generated with RAxML using the trnL-F datasetBRASSICACEAE_ML_trnL-F.treBayesian 50% majority-rule consensus tree ITS BRASSBayesian 50% majority-rule consensus tree from 3002 trees generated by Bayesian inference with MrBayes and using the ITS dataset for BrassicaceaeBRASSICACEAE_BI_ITS.treBayesian 50% majority-rule consensus trees trnL-F BRASSBayesian 50% majority-rule consensus trees from 3002 trees generated by Bayesian inference with MrBayes and using the trnL-F dataset for BrassicaceaeBRASSICACEAE_BI_trnL-F.treITS_EUDEMEAEITS alignment of tribe Eudemeae dataset including Stenodraba accessions.trnL-F_EUDEMEAEtrnL-F alignment of tribe Eudemeae dataset including Stenodraba accessions.trnH-psbA_EUDEMEAEtrnH-psbA alignment of tribe Eudemeae dataset including Stenodraba accessions.ITS_EUDEMEAE_NexusNexus file with the ITS matrix of tribe Eudemeae including Stenodraba accessions.ITS_EUDEMEAE.nextrnL-F_EUDEMEAE_NexusNexus file with the trnL-F matrix of tribe Eudemeae including Stenodraba accessions.trnL-F_EUDEMEAE.nextrnH-psbA_EUDEMEAE_NexusNexus file with the trnH-psbA matrix of tribe Eudemeae including Stenodraba accessions.trnH-psbA_EUDEMEAE.nexRAxML_bestTree.ITSMaximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the ITS dataset.RAxML_bestTree.trnL-FMaximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the trnL-F dataset.RAxML_bestTree.trnH-psbAMaximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the trnH-psbA datasetRAxML_bestTree.cpDNAMaximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the concatenated trnL-F + trnH-psbA datasetsRAxML_bestTree.ITS+cpDNAMaximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the concatenated ITS + trnL-F + trnH-psbA datasetsRAxML_bestTree.ITS_cpDNA.treMrBayes50_ITSBayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the nrITS dataset.BI_ITS.treMrBayes50_trnL-FBayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnL-F dataset.BI_trnL-F.treMrBayes50_trnH-psbABayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnH-psbA dataset.BI_trnH-psbA.treMrBayes50_cpDNABayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated trnLF + trnH-psbA datasets.BI_cpDNA.treMrBayes_ITS+cpDNABayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated ITS+ trnLF + trnH-psbA datasets.BI_ITS+cpDNA.treITS+indel_MrBayesAlignment matrix of ITS sequences for Bayesian inference with MrBayes including indel datacpDNA+indel_MrBayesAlignment matrix of concatenated trnL-F + trnH-psbA datasets for Bayesian inference with MrBayes including indel dataITS+cpDNA+indel_MrBayesAlignment matrix of concatenated ITS + trnL-F + trnH-psbA datasets for Bayesian inference with MrBayes including indel dataMrBayes50tree_ITS+indelBayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the nrITS dataset + Indel data.BI_ITS+indel.treMrBayes50tree_cpDNA+indelBayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated trnLF + trnH-psbA datasets + Indel data.BI_cpDNA+indel.treMrBayes50tree_ITS+cpDNA+indelBayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated ITS+ trnLF + trnH-psbA datasets + Indel data.BI_ITS+cpDNA+indel.trePrimaryConcordanceTree ITSvscpDNA BuckyPrimary concordance tree from the BUCKy analyses using the 6,002 trees from the ITS and the cpDNA datasets obtained in the MrBayes analyses. The discordance parameter (α) was set to 1, 10, and 100, however results from concordance analyses varying the discordance prior (α) had no effect on topology or concordance.PCT_Bucky.trexml BEAST for species tree analysisxml file for species tree analysis under the multispecies coalescent model in BEAST 2.4.4STENO_species.xmlMCC Species Tree BEASTMaximum clade credibility species tree (MCCT) estimated from nuclear ribosomal ITS and two chloroplast DNA regions (trnL-F, trnH-psbA) using the multispecies coalescent method implemented in *BEAST.MCCSpeciesTree.tre