Unraveling the effects of climate change on the Patagonian genus Onuris (Brassicaceae: Eudemeae) at different phylogenetic scales

Appendix A Taxa and GenBank accession numbers for the ITS, trnL-F, trnH-psbA, rps16 intron, and trnG intron sequences used in the phylogenetic analyses. For ingroup sequences (Onuris) geographic coordinates and the acronym used in the phylogenetic analysis is also supplied. New sequences generated for this study have underlined accession numbers.

Fig. S1. Study area used in climate niche comparisons, species distribution modeling, and climate change impact assessments. Study area is defined by a minimum convex polygon enclosing all specimen records of Onuris with a 50-km buffer zone. Dots represent specimen records for the genus.

Fig. S2. Axis values for Onuris specimens obtained from linear discriminant analyses (LDA) when climatic niche differentiation was explored using values of the five climatic components for the specimens as predictor, and the different phylogenetic groups as response (i.e., species, ESUs, and lineages). (a) classification by lineages. (b) classification by ESUs. (c) classification by species. (d) performance values of the discriminant models for each phylogenetic category, evaluated with the Accuracy and Cohen's kappa coefficients and leave-one-out cross-validation.

Fig. S3. Results from the species distribution modeling for Onuris species. Predicted suitable climatic conditions (logistic output) for current projections obtained using ensemble of small models (ESM) technique and MaxEnt. OA: O. alismatifolia; OG: O. graminifolia; OH: O. hatcheriana; OP: O. papillosa; OS: O. spegazziniana.

Fig. S4. Suitability change maps (future suitability –current suitability) for each species and SSP. Suitability change values for each species and SPP correspond to the mean obtained by averaging the individual values obtained with the five GCMs assessed (GFDL-ESM4, IPSL-CM6A-LR, MPI-ESM1-2-HR, MRI-ESM2-0, and UKESM1-0-LL). OA: O. alismatifolia; OG: O. graminifolia; OH: O. hatcheriana; OP: O. papillosa; OS: O. spegazziniana.

Fig. S5. Barplots showing for each species the percentage of net change in cell occupancy for the future (% cell gain – % cell loss). Values are mapped on the Onuris MCC species tree. Bars for each species correspond to values recovered for each of the three SSPs evaluated (1-2.6, 3-7.0, 5-8.5) averaged by the five GCMs and the two binarization thresholds used. NL: northern lineage; OA: O. alismatifolia; OG: O. graminifolia; OH: O. hatcheriana; OP: O. papillosa; OS: O. spegazziniana; SL: southern lineage.

Fig. S6. Histograms showing the impact of climate change at the genus level in 5 arc-min cells, and using the MPA90 threshold for binarization. (a) Cell frequency for predicted change in richness (number of species). (b) Cell frequency for predicted change in phylogenetic diversity, estimated with the mean pairwise distance metric (mpd) and the MCC species tree. **: Future _richness/MPD - Current _richness/MPD < 0 at α=0.01 with the paired Wilcoxon Signed Rank Test.

Fig. S7. Correlation plots for shared pattern of local extirpation (cell loss) among Onuris species, estimated in 5 arc-min cells, using the MPA90 threshold for binarization, and captured by unconstrained ordination using a generalized linear latent variable model. Positive correlation is depicted in blue, negative correlation in red, and for each SPP evaluated the UPGMA tree corresponding to this correlation matrix is displayed. OA: O. alismatifolia; OG: O. graminifolia; OH: O. hatcheriana; OP: O. papillosa; OS: O. spegazziniana.

Table S1 Specimen occurrence data for Onuris compiled for this study.

Table S2 Loadings on the first five components obtained from the principal component analysis using bioclimatic variables (PCA-env) extracted from the study area.

Table S3 Features of the DNA alignments used in the phylogenetic analyses.

Table S4 Performance of distribution models (mean ± sd) obtained for Onuris species using the ensemble of small models (ESM) technique and ten cross-validations.

Table S5. Multivariate environmental similarity surface (MESS) analysis to assess the effect of model extrapolation on predictor values that fall outside the calibration range.

Table S6 Variable contribution for distribution models of Onuris species.

Table S7 Loadings on the first two components obtained from the principal component analysis using suitability change obtained for each Onuris species and averaged for the five GCMs evaluated.

ESM1.zip DNA alignments used in phylogenetic analyses.

ESM2.txt Occurrence data used in niche and SDM analyses.