Data from “Molecular data reveal hidden diversity within the central Andean species Weberbauera spathulifolia (Thelypodieae: Brassicaceae)”
Creators: name: Salariato, Diego
Publisher: name: figshare
Year: 2019
Subjects: subject: 60302 Biogeography and Phylogeography
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Botany
subject: Evolutionary Biology
subject: 60310 Plant Systematics and Taxonomy

description: Data from “Molecular data reveal hidden diversity within the central Andean species Weberbauera spathulifolia (Thelypodieae: Brassicaceae)”<br> <b>Figure S1</b>. Distribution map of Weberbauera spathulifolia and delimited area corresponding to the 50 km-buffered minimum convex polygon used in the niche analyses both along the environmental (E) and geographical (G) space. Red and blue dots represent specimens of the northern group (NG) and the southern-central group (SCG) of Weberbauera, respectively.<br><b>Figure S2</b>. Maximum likelihood trees generated with RAxML 8.2.10 showing the phylogenetic placement of Weberbauera spathulifolia. Left, nrITS dataset. Rigth, cpDNA dataset (trnL-F/trnH-psbA). Values on branches correspond to Bootstrap support ≥ 50%. Units of branch length are proportional to nucleotide substitutions per site. NG: northern group of W. spathulifolia, SCG: southern-central group of W. spathulifolia.<br><b>Figure S3</b>. Maximum likelihood tree generated with RAxML 8.2.10 and the concatenated ITS+cpDNA (trnL-F/trnH-psbA) dataset showing the phylogenetic placement of Weberbauera spathulifolia. Values on branches correspond to Bootstrap support values ≥ 50%. Units of branch length are proportional to nucleotide substitutions per site. NG: northern group of W. spathulifolia, SCG: southern-central group of W. spathulifolia.<br><b>Figure S4</b>. Primary concordance tree from the BUCKy analyses using the 6002 trees from the ITS and the cpDNA datasets obtained in the MrBayes analyses and under α = 1. Concordance factor values (CF) ≥ 0.5 are shown on branches. Units of branch length are proportional to the concordance factor. Results from concordance analyses varying the discordance prior (α) had no effect on topology or concordance. NG: northern group of W. spathulifolia, SCG: southern-central group of W. spathulifolia.<br><b>Figure S5</b>. Maximum clade credibility (MCC) species tree estimated from ITS and cpDNA datasets using the multispecies coalescent method implemented in *BEAST 1.8.4 using all accessions as separate OTUs in the species tree in order to compare with results obtained from the concatenated analyses. Values on branches correspond to Bayesian posterior probability (%). NG: northern group of W. spathulifolia, SCG: southern-central group of W. spathulifolia.<br><b>Figure S6</b>. Results from the climatic niche analyses in the space environmental (E) space obtained using the PCA-env method. Left, Correlation circles showing the contribution of environmental variables on the first three axes of the PCA-env and the percentage of inertia explained. Right, PCA-env scatterplots of the first three principal components based on 21 climatic variables for the northern (NG) (blue dots) and southern-central (SCG) (red dots) groups of W. spathulifolia, represented by 41 and 61 occurrences, respectively. A, PC1 vs. PC2; B, PC1 vs. PC3; C, PC2 vs. PC3.<br><b>Figure S7</b>. Climatic niches for groups of Weberbauera spathulifolia produced by the three main axes of the PCA-env. For each group, the gray to black shading represents the grid cell density of the species occurrence (black being the highest density). The dashed line represents 50% of the available environment and the solid line represents 100%.<br><b>Figure S8</b>. Analyses in the geographical (G) space. A, values of variables (first five principal components of the PCA-env) used in the MaxEnt models for northern (NG) and southern-central (SCG) groups of Weberbauera spathulifolia along the study area. Blue and red dots represent specimen occurrences for NG and SCG, respectively. B, response curves for each PC used in the MaxEnt models of NG and SCG groups. Response curves show the ranges in environmental conditions that are more favourable for the distribution of each group. 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.<br><b>Table S1</b>. Specimen occurrence data of Weberbauera spathulifolia used in the niche analyses and geographical range comparisons.<br><b>Table S2</b>. Features of the DNA alignments used in the phylogenetic analyses within tribe Thelypodieae.<br><b>Table S3</b>. Morphological and geographical comparison between specimens from the northern group (NG) (=Weberbauera spathulifolia) and the southern-central group (SCG) (=Weberbauera orophila). For morphological comparison characters were analysed on 32 and 55 specimens of the NG and SCG, respectively. Range/ mean / standard deviation are shown for quantitative characters. For geographical comparisons were studied 41 and 61 specimens of the NG and SCG, respectively. Complete vouchers are given in the Taxonomic Treatment section.<br><b>Table S4</b>. Loadings on the first three components obtained from the principal component analysis (PCA-env) using bioclimatic variables extracted from the study area.<br><b>Table S5</b>. Number of ocurrences (n), area under the receiver operating characteristic curve (AUC), variable contribution (%), permutation importance (%), and Jackknife test obtained in the MAXENT modelling for each group within Weberbauera spathulifolia (NG and SCG).<br><b>ITS.nex</b>. ITS dataset used for phylogenetic analyses in this study.<br><b>trnLF.nex</b>. trnL-F dataset used for phylogenetic analyses in this study.<br><b>trnH.nex</b>. trnH-psbA dataset used for phylogenetic analyses in this study.<br><b>ITS.MrBayes.con50.tre</b>. Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes and the ITS dataset.<br><b>ITS.RAxML.BestTree.tre</b>. Maximum likelihood tree generated with RAxML using the ITS dataset.<br><b>trnLF.MrBayes.con50.tre</b>. Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes and the trnL-F dataset.<br><b>trnLF.RAxML.BestTree.tre</b>. Maximum likelihood tree generated with RAxML using the trnL-F dataset.<br><b>trnH.MrBayes.con50.tre</b>. Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes and the trnH-psbA dataset.<br><b>trnH.RAxML.BestTree.tre</b>. Maximum likelihood tree generated with RAxML using the trnH-psbA dataset.<br><b>cpDNA.MrBayes.con50.tre</b>. Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes the concatenated cpDNA (trnL-F+trnH-psbA) datasets.<br><b>ITS+cpDNA.MrBayes.con50.tre</b>. Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayesand the concatenated ITS + cpDNA (trnL-F+trnH-psbA) datasets.