Genetic Structure
The AMOVA generated the population structure based on both matR and
nad5-1 markers. The results showed that 0.52% and 2.65% of the
variation occurred among groups, 2.98% and 10.41% of the variation
occurred among populations, while 96.50 and 86.95% of the variation
occurred within populations for matR and nad5-1 genes respectively
(Figure 4D, 5D, Supplementary Table S5, 6 ), suggesting
that the variation of the five groups mainly occurred within
populations, and nad5-1 marker supports a stronger population structure.
The higher inter-population variation was detected at the nad5-1 marker,
the comparison of the variation among populations within the groups was:
LN*>SX*>HB*>LN>HB,
which means the SX* group with the highest degree of variation among
populations (left out LN* group) (Figure 5D, Supplementary Table
S6 ).
To reveal the population structure precisely, the NJ tree, PCoA, and
STRUCTURE were obtained from the sequence data of matR and nad5-1
markers (Figures 4, 5 ). Based on the matR marker, the results
of the NJ tree (35 populations, 796 individuals, classified based on
groups) (Figure 4A ) showed 8 similar topologies, and 5 groups
were sorted in a fixed way, suggesting there was a fixed genetic
relationship among the 5 groups, and their ancestral status relationship
was as follows: SX*-HB*-HB-LN*-LN. The dispersion degree of LN
populations in the NJ tree (Figure 4B ) was greater than that of
HB, which indicated that there was higher variation among populations
within the LN group. The discrete distribution of the SX* populations
(Figure 4B ) suggesting there was also a high variation among
populations. The PCoA results (Figure 4C) showed the
distribution of all populations was relatively concentrated, indicating
that the genetic differences of all populations at this locus were
small. The STRUCTURE analysis (Figure 4E ) inferred the optimal
number of the cluster was K=4, we found that the proportions of the four
ancestral components were almost the same in all the populations,
suggesting there was little difference in the genetic background among
all populations at this locus. Based on the nad5-1 marker, the NJ tree
(38 populations, 873 individuals, classified based on groups) showed a
complicated result, and difficult to find some genetic regularity of
five groups (Figure 5A ). NJ trees classified based on STRUCTURE
results (Supplementary Figure 1 ) also showed the same result.
The LN populations were dispersed in four topologies (Figure
5B ), which implies the LN group with a high variation among
populations, was the same as that of matR marker. The high variation
among populations within SX* group could also be reflected in the NJ
tree (Figure 5B ). The PCoA results (Figure 5C ) showed
the distribution of all populations was scattered relatively, indicating
that there was a large genetic difference of all populations at this
locus. The STRUCTURE analysis showed the K=4 (Figure 5C ), which
was the same as that of matR marker, all populations showed higher
heterozygosity in the ancestral component at this locus, suggesting
there was an abundant difference in the genetic variation among all
populations at this locus.