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Additional file 5: Table S1. The results of neutrality tests (Tajima’s D and Fu’s FS tests) and mismatch distribution analyses.

Additional file 4: Fig. S4. Haplotypes network of Opisthopappus. 47 haplotypes (H1-H47) were detected in O. longilobus and 28 haplotypes (H48-H75) in O. taihangensis. No shared haplotypes were detected between O. longilobus and O. taihangensis. The color of each haplotype corresponded to Fig. 1 The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step.

Additional file 6: Table S2. ANOVA analysis for the nineteen bioclimatic variables grouped by two different species.

Additional file 3: Fig. S3 The Kruskal–Wallis test of the first two principal components and the first two linear discriminants of the genetic variation revealed significant genetic divergence between species but no or little population differentiation within species. (A–D): Comparisons between species. (E–H): Comparisons among populations.

Additional file 2: Fig. S2. Structure analysis from K = 3 to K = 6 for SNP and InDel, respectively.

Additional file 7: Fig. S5. The average temperature of every month (A) and the average precipitation of every month (B) of the studied populations of the distribution of Opisthopappus.

Additional file 8: Table S3. Information of primer pairs.

Additional file 1: Fig. S1. Phylogenetic relationships between O. longilobus and O. taihangensis. (A): Individual ML clustering of Opisthopappus. Blue branches presented individuals of O. longilobus and red branches presented individuals of O. taihangensis. (B): UPGMA clustering for 24 populations of Opisthopappus based on Nei’s genetic distance. Blue for populations of O. longilobus and red for populations of O. taihangensis.

Additional file 4: Figure S3. Correlation between geographic distance and pairwise FST/environmental distance for Ulmus lamellosa. (a), (b): relationship estimated by ITS and (c), (d): relationship estimated by Aat.

Additional file 2: Figure S1. The maximum likelihood tree of single-copy nuclear gene Aat haplotypes.

Additional file 3: Figure S2. Results of Bayesian clustering analysis conducted by STRUCTURE. The clustering patterns of ITS (a) and Aat (b) by three clusters (K = 3). The clustering patterns of Aat (c) by four clusters (K = 4).