21 nucleotides sites detected within 1086 bp fragment of cytochrome b were belonging to 16 haplotypes. Nucleotide diversity and haplotype diversity were obtained (Tab 1). Among these 6 groups, Jiagnjin nucleotide diversity was the highest and the lowest was from Juexi. Zhuyangxi population had the highest haplotype diversity and the lowest was from Juexi.
Tab 1 Polymorphic site, number of haplotypes, haplotype diversity and nucleotide diversity of L. nigricauda mtDNA cyt b
Populations
|
Polymorphic sites
|
number of haplotypes
|
Nucleotide diversity
|
haplotype diversity
|
Gaochang
|
8
|
4
|
0.00046
|
0.18145
|
Jiagnjin
|
7
|
2
|
0.00258
|
0.40000
|
Juexi
|
0
|
1
|
0.00000
|
0.00000
|
Nancong
|
4
|
5
|
0.00029
|
0.29892
|
Shuifu
|
12
|
6
|
0.00067
|
0.28409
|
Zhuyangxi
|
10
|
6
|
0.00200
|
0.40215
|
Total
|
21
|
16
|
0.00087
|
0.26858
|
Geographical distribution of haplotypes showed that haplotypes H_1 had the largest amount in L. nigricauda, and distributed in 6 geographical populations. Shuifu haplotypes were six, and Zhuyangxi population with the same. Juexi had only one haplotype. Besides, there were 13 unique haplotypes distributed in five populations (Table 2).
Table 2. Geographical distribution of L. nigricauda haplotypes based on the seqence of cyt b
Haplotype
|
Juexi
|
Gaochang
|
Jiangjing
|
Shuifu
|
Zhuyangxi
|
Nancong
|
Total
|
H_1
|
13
|
29
|
4
|
28
|
24
|
26
|
124
|
H_2
|
|
1
|
|
|
|
|
1
|
H_3
|
|
1
|
|
|
2
|
|
3
|
H_4
|
|
1
|
|
|
|
|
1
|
H_5
|
|
|
1
|
1
|
2
|
|
4
|
H_6
|
|
|
|
|
|
2
|
1
|
H_7
|
|
|
|
|
|
1
|
1
|
H_8
|
|
|
|
|
|
1
|
1
|
H_9
|
|
|
|
|
|
1
|
1
|
H_10
|
|
|
|
1
|
|
|
1
|
H_11
|
|
|
|
1
|
|
|
1
|
H_12
|
|
|
|
1
|
|
|
1
|
H_13
|
|
|
|
1
|
|
|
1
|
H_14
|
|
|
|
|
1
|
|
1
|
H_15
|
|
|
|
|
1
|
|
1
|
H_16
|
|
|
|
|
1
|
|
1
|
Haplotype network analysis showed that H_1 might be the ancestral haplotype for its central position in the haplotype network and the highest haplotype frequency in each population. H_15, H_5, H_16 and H_2 belonged to secondary haplotypes. And there were some haplotype communications among 6 populations. For instance, a certain degree of haplotype communication was generated among Shuifu/Jiangjin populations and Gaochang/Zhu Yangxi populations. In totally, the haplotype network demonstrated some corresponding relationship between geographical information and haplotype distribution.
2. The molecular variance analysis
Analysis of molecule variance (AMOVA) showed that the FST was 0.05519(0.05<FST<0.15, P<0.02). It was indicated that an initial genetic differentiation existed between the populations, the effect of genetic differentiation among them was not significant. Analysis of the percentage of variance displayed these were 5.52% of the variation within populations, and 94.48% were from among populations. It demonstrated that genetic variance mainly came from among populations, and only 5.52% of variance came from within populations (Tab.3). This result was in accordance with the value of FST mentioned above.
Tab.3 The AMOVA analysis of L. nigricauda between and in populations based on cyt b
Source of variation
|
d.f.
|
Sum of squares
|
Variance components
|
Percentage Of variation
|
Within populations
|
5
|
5.518
|
0.02739 Va
|
5.52
|
Among populations
|
139
|
65.186
|
0.46896 Vb
|
94.48
|
Total
|
144
|
70.703
|
0.49635
|
|
In addition, by analysing the pairwise value of FST and genetic distance from 6 populations, FST showed a direct connection with genetic distance. It infeded that the mainstream populations (Jiang Jin and Zhu Yangxi) of the upper Yangtze River had preliminary genetic differentiation with tributary (Nan Cong, Gao Chang, Jue Xi and Shui Fu).