FIGURE LEGENDS

Figure 1. Sampling localities and population genetic structure of the Aquilegia viridifloracomplex. A. Geographical distributions of the sampled A. viridiflora complex, where colors in circles distinguish groups. The genetic structure showed ADMIXTURE proportions of genetic clusters for each individual of the four lineages at the best K value (K = 4), and each bar represents an individual. The scale in the figure is 1:20,000,000, B. Population genetic structure inferred by ADMIXTURE when K= 3-5, C. phylogenetic relationships of A. viridiflora complex according to the maximum likelihood (ML) method, and blue, red, light green and orange represent the NE, EL, CN and NW lineages, respectively. The asterisk indicates that the bootstrap value is 100.
Figure 2. A. NeighborNet diagram based on genome, B. nucleotide diversity (θπ) ofA. viridiflora complex.
Figure 3. Demographic history of Aquilegia viridiflora complex and population genetic analysis. A. Results for the D-statistics. The solid red dot represents that the absolute value of Z-scores is greater than 3, and the hollow red dot represents that the absolute value of Z-scores is less than 3, B. ancestral population sizes, population divergence times, and migration rates were assessed by fastimcoal2, C. pairwise FST and DXY between different groups, D. LD decay of the four lineages of A. viridiflora complex. Except that the difference between the two groups marked in the figure is not significant, there is a significant difference between any other two groups.
Figure 4. Genomic regions with signals of selection and adaptation to local environmental conditions. A. Bayescan results for genome-wide scans to detect outlier SNPs based on locus-specific FST values. Red dots represent qval less than 0.05 and indicated the SNPs under the positive selection, B. relationship of genetic distance and geographical distance, C. outlier SNPs associated with bioclimate factors. The red dots indicate that the SNP in the sliding window was selected by the environment; gray dots represent other regions in the genome. The map shows the spatial variation in different bioclimate factors.