DOI: 10.6084/m9.figshare.30734258.v1
title: Phylogenetics, Niche Evolution, and Distribution Dynamics of <i>Isatis</i> Species under Climate Change: Supplementary Figures and Data

description: This dataset contains the supplementary figures and data for the manuscript : "Phylogenetics, Niche Evolution, and Distribution Dynamics of <i>Isatis</i> Species under Climate Change".<b>Fig. 1.</b> Distribution of six <i>Isatis</i> species after screening. Points are coloured by species. The basemap was obtained from the Standard Map Service of the Ministry of Natural Resources, China (Approval No.: GS (2023) 2767).<b>Fig. 2. </b>Parameter optimization of MaxEnt models for <i>I. indigotica</i> and <i>I. costata</i>. Panel (A) shows the parameter optimization results for <i>I. indigotica</i>, and Panel (B) shows those for <i>I. costata</i>.<b>Fig. 3.</b> Permutation importance (%) of core environmental drivers for the six <i>Isatis</i> species. The results are based on permutation importance analysis from the MaxEnt models. Only variables that achieved an importance ≥10% in at least one species are shown. The colour gradient from blue to red indicates low to high importance.<b>Fig. 4.</b> Response curves of habitat suitability to key environmental variables for representative <i>Isatis</i> species.<b> </b>(A) Response of <i>I. indigotica</i> suitability probability to the August NDVI (NDVI_202008). (B) Response of <i>I. violascens</i> suitability probability to precipitation seasonality (Bio15). (C) Response of <i>I. multicaulis</i> suitability probability to the February maximum temperature (TemMax_02).<b>Fig. 5.</b> Predicted potential distribution of six <i>Isatis</i> species under current climatic conditions. Panels (A) to (F) represent <i>I. indigotica</i>, <i>I. costata</i>, <i>I. violascens</i>, <i>I. minima</i>, <i>I. gymnocarpa</i>, and <i>I. multicaulis</i>, respectively. Habitat suitability is classified into four grades (nonsuitable, low, medium, and high) using the natural breaks (Jenks) method. The basemap was obtained from the Standard Map Service of the Ministry of Natural Resources, China (Approval No.: GS (2023) 2767).<b>Fig. 6.</b> Spatial dynamics of suitable habitats for <i>I. indigotica</i> and <i>I. costata</i> under future climate change scenarios. Projections for the period 2041–2060 are shown for the two climate scenarios. (A) <i>I. indigotica</i> under SSP245, (B) <i>I. indigotica</i> under SSP585, (C) <i>I. costata</i> under SSP245, and (D) <i>I. costata</i> under SSP585. In all panels, 'Stable' indicates areas suitable under both current and future conditions, 'Loss' indicates areas suitable only under current conditions, and 'Gain' indicates areas suitable only under future conditions.<b>Fig. 7. </b>Relationships between phylogenetic distance and niche overlap among the six <i>Isatis</i> species. Each data point represents a pairwise comparison between two species (n = 15 pairs). The solid line indicates the linear regression trend. The Mantel test results revealed no significant correlation between phylogenetic distance and niche overlap (r = -0.236, p = 0.772).<b>Fig. 8.</b> Species richness and co-occurrence patterns of the six <i>Isatis</i> species in China.<b> </b>The map was generated by overlaying the binarized suitable habitat maps of all six species. Colour codes from 0 to 21 represent different combinations of species, ranging from unsuitable habitat (0) to areas suitable for multiple species. A detailed legend explaining all species combinations is provided in Table S5.<b>Fig. 9.</b> Comparison of species richness patterns between different ecological strategy groups.<b> </b>(A) Richness of the <i>I. indigotica–I. costata</i> group (cultivated and a wild relative with a habitat-indicator strategy). (B) Richness of the <i>I. violascens–I. minima</i> group (wild species with a climate-dominated strategy).<b>Fig. S1.</b> Pairwise Pearson correlation matrices of the environmental variables selected for the final species distribution models of the six <i>Isatis</i> species. Panels (A) to (F) represent the correlation matrices for <i>I. indigotica</i>, <i>I. costata</i>, <i>I. violascens</i>, <i>I. minima</i>, <i>I. gymnocarpa</i>, and <i>I. multicaulis</i>, respectively. Variables with |r| &gt; 0.8 were considered highly correlated, and the one with the lowest contribution in the preliminary MaxEnt runs was excluded to mitigate multicollinearity. The specific final variable sets for each species are listed in Table S3.<b>Fig. S2.</b> Phylogenetic tree of the six studied <i>Isatis</i> species inferred from complete chloroplast genomes. The tree was reconstructed using the maximum likelihood method. The numbers at the nodes represent bootstrap support values from 1000 replicates. The scale bar indicates the number of substitutions per site.<b>Fig. S3.</b> Predicted potential distributions of six <i>Isatis</i> species under the future SSP245 scenario (2041–2060).<b> </b>Panels (A) to (F) represent <i>I. indigotica</i>, <i>I. costata</i>, <i>I. violascens</i>, <i>I. minima</i>, <i>I. gymnocarpa</i>, and <i>I. multicaulis</i>, respectively. Habitat suitability is classified into four grades (nonsuitable, low, medium, and high) using the natural breaks method.<b>Fig. S4.</b> Predicted potential distributions of six <i>Isatis</i> species under the future SSP585 scenario (2041–2060).<b> </b>Panels (A) to (F) represent <i>I. indigotica</i>, <i>I. costata</i>, <i>I. violascens</i>, <i>I. minima</i>, <i>I. gymnocarpa</i>, and <i>I. multicaulis</i>, respectively. Habitat suitability is classified into four grades (nonsuitable, low, medium, and high) using the natural breaks method.<br>