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