3.1 Genetic Diversity and Structure
ITS and five chloroplast fragments (matK , ndhA ,ndhG-I , petB-D , petL-G ) were used to analyze 254 individuals from 31 populations of the nine Notholirion species. The ITS and cpDNA haplotype frequencies of each population are listed in Supplementary Table 4 , and the geographical distributions of haplotypes are shown in Figures 2, 4 . The length of ITS sequence we used in this study was 671 bp containing 60 polymorphic sites. We detected 27 ITS haplotypes (N1–N27), which were species-specific as none were shared by any two species (Figure 3) . Most of the populations have only one or two haplotypes and populations with more than three haplotypes only occurred in N. bulbuliferum . Besides, the total length of the aligned sequences of cpDNA was 2753 bp containing 39 polymorphic sites were recovered with 14 haplotypes. Like ITS haplotypes, all cpDNA haplotypes were spec 09ies-specific in Notholirion(Figure 5) . All the populations have only one or two haplotypes, with only 22.58% of the populations having two haplotypes.
The haplotype diversity (Hd) of ITS ranged from 0.000 to 0.867, and nucleotide diversity (π) ranged from 0.000 to 0.011 across all species (Supplementary Table 4) . Total gene diversity (HT) value was all higher than the average gene diversity within populations (HS) at the level of species and genus. Additionally, the number of substitution types (NST) was higher than interpopulation differentiation (GST), which indicated that a significant phylogeographic structure existed in Notholirion (Table 1). The haplotype diversity (Hd) of cpDNA ranged from 0.000 to 0.800, and nucleotide diversity (π) ranged from 0.000 to 0.004 across all species (Supplementary Table 4) . Like ITShaplotypes, the total gene diversity (HT) value was higher than the average gene diversity within populations (HS), whether at the level of species or genus. Total NST was significantly higher than GST, indicating significant phylogeographic structure in Notholirion (Table 1) .
ITS AMOVA revealed that the primary genetic variation (74.86% - 98.68%) in N. bulbuliferum and N. macrophyllum occurred among populations (Table 2 ). Furthermore, the AMOVA analysis of cpDNA data indicated a genetic differentiation pattern similar to that of ITS , with 93.73% - 98.85% of the total variation distributed among populations (Table 2 ).
Table 1 Genetic diversity and genetic differentiation of three species within