Additional file 1 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa
Creators: name: Zhao, Zhongning
name: Heideman, Neil
name: Bester, Phillip
name: Jordaan, Adriaan
name: Hofmeyr, Margaretha D.
Publisher: name: figshare
Year: 2020
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Ecology

description: Additional file 1: Figure S1. The results of the Bayesian clustering analysis with STRUCTURE. The plot shows the values of ΔK calculated according to Evanno et al. [47]. Figure S2. (a) Results of BIC value versus the number of clusters to determine the optimal clustering scheme in the DAPC analyses. (b) The Cross-Validation test results determining the optimal number of PCs retained. Figure S3. The species tree chronograms generated from the BEAST calibration dating analyses, A: mtDNA chronogram, B: mtDNA+nDNA chronogram. The red dots were the five constrained calibration points for calibration dating analyses. Figure S4. The macroevolution cohort matrix for the seven clades of the P. tentorius species complex. BAMM Bayesian diversification rate analysis based on the mean phylorate plot trees, are shown at the top and on the left side of the cohort matrix, for purposes of comparison. The matrix shows pairwise probabilities of two groups sharing the same evolutionary dynamics. The “warm” colours represent high cohort similarities (highest value “1” refers to 100% similarity), whilst, the “cool” colours represent low cohort similarities (lowest value “0” refers to 0% similarity). Figure S5. Visualizing the single-chain MCMC diagnostics for a CoMET analysis with empirically estimated diversification hyperpriors. Blue bars/dots represent passed tests and red bars/dots mean failed tests (failed convergence). Table S3. The node age (Ma) and 95% HPD at each node (see Fig. 5 and Fig. S3) generated from BEAST calibration dating analyses in both gene trees and species trees of the mtDNA and (mtDNA+nDNA) datasets, respectively. Table S4. The independent BioGeoBEARS model test results for the six habitat reconstruction models with consideration of the “founder effect” parameter “J” on geographic regions, biome and topographic barriers datasets. The selected best model of each analysis with its criteria is shown in bold. Table S5. The ANOVA based LRT test results retrieved from the likelihood function models of different scenarios investigated under character dependency analyses BiSSE and MuSSE with different models of regions, biomes and the two sides of the Orange River. “Minimal”: the null model assumed all parameters are equal between different characters states; “all different”: the full parameter model considered lambda, mu and q as different between character states; “free.lambda”: the model considered lambda as different only between different character states, “free.mu”: the model considered only mu as different between different character states, “free.lambda.mu”: the model considered only lambda and mu as differ between different character states, “free.q”: the model considered only q as different between different character states. The best model with its criteria from the LRT test in each analysis is shown in bold. Table S6. The average test AUC criterion under the ROC curve and its standard deviation (SD) generated by ENM analyses for each group [P. t. tentorius (Ptt-A – Ptt-D), P. t. trimeni (Ptr), P. t. verroxii (Pv-A and Pv-B), and the entire P. tentorius species complex] through the given timeline. LIG: Last Interglacial, LGM: Last Glacial Maximum, and MIDH: Middle Holocene. Table S7. The results of the optimization of parameters settings for all ENM analyses across groups (group abbreviations as in Table S6, with All denoting the entire P. tentorius species complex) and timelines. Features: Linear features (L), Quadratic features (Q), Product features (P) and Hinge features (H); RM = Regularization multiplier. LIG: Last Interglacial, LGM: Last Glacial Maximum, and MIDH: Middle Holocene. Table S8. The pairwise results of niche difference analysis between clades (taxon abbreviations the same as group abbreviations in Table S6). The pairwise comparisons showing significant niche differences are in bold, whilst, comparisons without significant niche differences are underlined. Note: If the point estimated value (the matrix at the bottom-left) was lower than the 5% threshold value (the matrix at the top-right), then the niches were significantly different. Table S9. The ENM analyses estimating the area of suitable habitats of the seven clades (group abbreviations as in Table S6), as well as changes in the area of suitable habitats against the timeline (for details about the timeline see the Materials and Methods). The arrow " ↑ " represents increasing area, whilst, " ↓ " indicates decreasing area. Groups currently showing a decrease in the area of suitable habitats or future habitats are given in bold. Table S13. Optimal partition scheme, substitution model, likelihood score (-InL), Gamma shape, proportion of estimated invariable sites for the mtDNA+nDNA based BEAST phylogenetic inference. Table S16. Optimal partition scheme, substitution model, likelihood score (-InL), Gamma shap, and proportion of estimated invariant sites for the BEAST calibration dating analyses. Table S17. The constraint of the five most recent common ancestors used in the BEAST calibration dating analyses for the mtDNA and mtDNA+nDNA datasets.