Phylogeny and Population Structure
After filtering, we obtained 1,064,089 high-quality SNPs from 80 individuals, 55.604% of which were located upstream and downstream, 17.454% were located in intronic regions, and 7.07% were located in the exonic regions of genes. According to the above SNPs, ML and NJ trees were constructed to infer the phylogenetic relationships amongAquilegia species. Both topologies indicated that different populations of A. viridiflora shared a recently common ancestor with strong support (Figure S1). Therefore, population genetics analysis could be performed subsequently on the 20 populations of A. viridiflora , including 672,439 high-quality SNPs. The individuals ofA. viridiflora were divided into eastern and western lineages, each of which contained two groups. For convenience, the four groups were designated as NE (including the WD, AE, SZ and LF populations), EL (including the LT, YS, MS and TS populations), CN (including the YT, QB, TL and YM populations), and NW (including the XW, HL, HH, HD, YS, SF, ZG and JQ populations) (Figure 2). The NE and EL groups belong to eastern lineages, and the CN and NW groups belong to western lineages.
PCA was performed to determine the grouping of populations, and principal component 1 (PC1) and principal component 2 (PC2) explained 6.61% and 4.04% of the observed variation, respectively (Figure S2A). The groups obtained according to the PCA plot were the same as those indicated in the phylogenetic tree. ADMIXTURE analysis showed that the optimal K value was 4 because K = 4 resulted in the lowest cross-validation error (Figure S2B). Additionally, populations SZ, LT, YM, XW, HL, HH and HD showed multiple ancestral compositions (Figure 2).