Interplay between conservatism and divergence in climatic niche evolution of Brassicaceae tribe Eudemeae shaped its distribution across the different environments of the Andes
Creators: name: Salariato, Diego
Publisher: name: figshare
Year: 2022
Subjects: subject: 60302 Biogeography and Phylogeography
subject: FOS: Biological sciences
subject: Botany
subject: Evolutionary Biology
subject: 60310 Plant Systematics and Taxonomy

description: <strong>SUPPORTING INFORMATION</strong> <br> <strong>Figure S1. </strong>Study area and climatic variables used in this study. <strong>A</strong>. Study area defined by a minimum convex polygon enclosing all specimen records of Eudemeae with a 50-km buffer zone. Dots represent specimen records for the tribe. <strong>B</strong>. First four climatic PCs used in this study and projected onto the geographic space, obtained by performing a PCA-env approach using 21 climatic variables (the 19 bioclimatic variables from CHELSA + AI + PET). <strong>C</strong>. Projection of the first four climatic PCs used in this study in the environmental (climate) space. The gray dots represent the background space, while the red dots are associated with the presence of Eudemeae. <br> <strong>Figure S2</strong>. Phylogenetic analyses of Eudemeae using the nrITS and the cpDNA (<em>trnL</em>-<em>F</em>/ <em>trnH</em>-<em>psbA</em>/ <em>rps16</em> intron) datasets. <strong>A</strong>. Maximum clade credibility (MCC) specimen tree estimated from ITS and cpDNA datasets using the multispecies coalescent method implemented in *BEAST 1.8.4, using all accessions as separate OTUs. Values on branches correspond to Bayesian posterior probability (%). <strong>B</strong>. Primary concordance tree from the BUCKy analyses using the 6002 trees from the nrITS and the cpDNA datasets obtained in the MrBayes analyses and under α = 1. Concordance factor values (CF) ≥ 50% are shown on branches. Units of branch length are proportional to the concordance factor. Results from concordance analyses varying the discordance prior (α= 1, 10, 100) had no effect on topology or concordance. <strong>C</strong>. Filtered supernetwork generated in SplitsTree 4.14.8 using 1000 Bayesian posterior trees per each nrITS and cpDNA dataset with the Z-closure algorithm, and filtering the splits to show only those present in a minimum of 30% input trees. The different clades and subclades identified by letters are discussed in the text. <br> <strong>Figure S3. </strong>Delimitation of the main climatic spaces in Eudemeae. To delimit the main climatic spaces (MCSs) of Eudemeae values corresponding to the first four climatic PCs for the occurrence dataset (530 data points) were extracted and utilized to conduct a model-based clustering using finite Gaussian mixture modeling with the R package mclust 5.4.8, with the optimal number of clusters determined using the Bayesian Information Criterion (BIC). <strong>A</strong>. BIC values for different models and numbers of groups. The arrow shows the BIC value for the best-ranked model: VVV (ellipsoidal, varying volume, shape, and orientation) model with 11 groups. Assignment probability of each specimen in the occurrence data set for each MCS. Upper triangles indicate the two main clades of Eudemeae, while lower triangles show genera of the tribe. <br> <strong>Figure S4</strong>. Main climatic spaces (MCSs) delimited for tribe Eudemeae. For delimitation, dimensionality of the environmental space in the study area was first reduced by performing a PCA-env approach, and then values corresponding to the first four PCs for the occurrence dataset (530 data points) were used to conduct a model-based clustering to define the different MCSs (see Materials and Methods). A. Climatic PC values for each delimited MCS of Eudemeae, estimated using the values extracted from the components of the PCA-env (first four components) for the occurrence data. B. Geographic distribution of specimens included in the different MCSs. <br> <strong>Figure S5</strong>. Violin plots of the four climatic PCs for delimited MCSs of Eudemeae. <br> <strong>Figure S6</strong>. Scatterplot between number of dispersal (mean) of each MCS as a source or a sink, and the size of its climatic hypervolume [log10 (x+1) transformed]. Blue line corresponds to the fitted regression line, and shaded area shows 0.95 confidence interval. <br> <strong>Figure S7</strong>. Centroid values (niche position) of each species for the four climatic PCs estimated from their climatic hypervolumes. Species in red belong to clade A, while species in blue are included in clade B. <br> <strong>Table S1</strong>. Specimen occurrence data of tribe Eudemeae compiled for this study. <br> <strong>Table S2.</strong> Features of the DNA alignments used in the phylogenetic analyses within tribe Eudemeae. <br> <strong>Table S3</strong>. Estimated ages (Myr) for nodes of the main lineages within Eudemeae obtained in the species tree analyses and their corresponding support values. <br> <strong>Table S4.</strong> Loadings on the first four components obtained from the principal component analysis (PCA-env) using bioclimatic variables extracted from the study area. <br> <strong>Table S5</strong>. Number of dispersal (range expansion) events between main climatic spaces (MCSs) of Eudemeae estimated using 100 biogeographical stochastic mapping. <br> <strong>Table S6</strong>. Environmental (climatic) niche for each species of the MCC species tree estimated using the first four climatic PCs for each specimen occurrence through n-dimensional hypervolumes. <br> <strong>Appendix S1.</strong> Taxa and GenBank accession numbers for the <em>ITS</em>, <em>trnL</em>-<em>F</em>, <em>trnH</em>-<em>psbA</em>, and <em>rps16</em> intron sequences used in the phylogenetic analyses. <br> <strong>ESI_files.zip</strong> Supporting information files including Supplementary Materials and Methods; ITS, <em>trnl-F</em>, <em>trnH-psbA</em>, and <em>rps16</em> alignments; MCC species tree; occurrence data; matrices used in BioGeoBEARS analyses; distance matrices used in MRM analyses.