Biodiv Sci ›› 2022, Vol. 30 ›› Issue (12): 22224. DOI: 10.17520/biods.2022224
• Original Papers • Previous Articles Next Articles
Qi Zhao1,2, Jibao Jiang1,2, Zenglu Zhang1,2, Qing Jin1,2, Jiali Li1,2, Jiangping Qiu1,2,*()
Received:
2022-04-26
Accepted:
2022-08-30
Online:
2022-12-20
Published:
2022-12-17
Contact:
*E-mail: jpq@sjtu.edu.cn
Qi Zhao, Jibao Jiang, Zenglu Zhang, Qing Jin, Jiali Li, Jiangping Qiu. Species composition and phylogenetic analysis of earthworms on Hainan Island[J]. Biodiv Sci, 2022, 30(12): 22224.
基因 Gene | 整体 Total | 第一位点 1st position of codon | 第二位点 2nd position of codon | 第三位点 3rd position of codon | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
A+T(%) | C+G(%) | (A+T)/(C+G) | A+T(%) | C+G(%) | (A+T)/(C+G) | A+T(%) | C+G (%) | (A+T)/(C+G) | A+T(%) | C+G (%) | (A+T)/(C+G) | |
COI | 59.5 ± 1.4 | 40.5 ± 1.4 | 1.5 ± 0.1 | 44.2 ± 1.3 | 55.8 ± 1.3 | 0.8 ± 0.0 | 56.1 ± 0.2 | 43.9 ± 0.2 | 1.3 ± 0.0 | 78.3 ± 4.0 | 21.7 ± 4.0 | 3.7 ± 1.0 |
COII | 65.4 ± 1.2 | 34.6 ± 1.2 | 1.9 ± 0.1 | 76.6 ± 3.3 | 23.4± 3.3 | 3.4 ± 0.6 | 53.4 ± 1.1 | 46.6 ± 1.1 | 1.1 ± 0.0 | 66.1 ± 0.6 | 33.9 ± 0.6 | 1.9 ± 0.1 |
ND1 | 66.1 ± 1.9 | 33.9 ± 1.9 | 2.0 ± 0.2 | 62.0 ± 0.8 | 38.0 ± 0.8 | 1.6 ± 0.1 | 72.0 ± 3.0 | 28.0 ± 3.0 | 2.6 ± 0.4 | 64.2 ± 3.0 | 35.8 ± 3.0 | 1.8 ± 0.3 |
12S | 71.6 ± 1.0 | 28.4 ± 1.0 | 2.5 ± 0.1 | 74.3 ± 1.5 | ||||||||
16S | 62.2 ± 0.9 | 37.8 ± 0.9 | 1.6 ± 0.1 | 61.3 ± 1.3 | ||||||||
5 genes | 65.7 ± 0.9 | 34.3 ± 0.9 | 1.9 ± 0.1 | 63.3 ± 1.0 |
Table 1 The base composition of 5 genes and combined genes of pheretimoid earthworms in Hainan Island
基因 Gene | 整体 Total | 第一位点 1st position of codon | 第二位点 2nd position of codon | 第三位点 3rd position of codon | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
A+T(%) | C+G(%) | (A+T)/(C+G) | A+T(%) | C+G(%) | (A+T)/(C+G) | A+T(%) | C+G (%) | (A+T)/(C+G) | A+T(%) | C+G (%) | (A+T)/(C+G) | |
COI | 59.5 ± 1.4 | 40.5 ± 1.4 | 1.5 ± 0.1 | 44.2 ± 1.3 | 55.8 ± 1.3 | 0.8 ± 0.0 | 56.1 ± 0.2 | 43.9 ± 0.2 | 1.3 ± 0.0 | 78.3 ± 4.0 | 21.7 ± 4.0 | 3.7 ± 1.0 |
COII | 65.4 ± 1.2 | 34.6 ± 1.2 | 1.9 ± 0.1 | 76.6 ± 3.3 | 23.4± 3.3 | 3.4 ± 0.6 | 53.4 ± 1.1 | 46.6 ± 1.1 | 1.1 ± 0.0 | 66.1 ± 0.6 | 33.9 ± 0.6 | 1.9 ± 0.1 |
ND1 | 66.1 ± 1.9 | 33.9 ± 1.9 | 2.0 ± 0.2 | 62.0 ± 0.8 | 38.0 ± 0.8 | 1.6 ± 0.1 | 72.0 ± 3.0 | 28.0 ± 3.0 | 2.6 ± 0.4 | 64.2 ± 3.0 | 35.8 ± 3.0 | 1.8 ± 0.3 |
12S | 71.6 ± 1.0 | 28.4 ± 1.0 | 2.5 ± 0.1 | 74.3 ± 1.5 | ||||||||
16S | 62.2 ± 0.9 | 37.8 ± 0.9 | 1.6 ± 0.1 | 61.3 ± 1.3 | ||||||||
5 genes | 65.7 ± 0.9 | 34.3 ± 0.9 | 1.9 ± 0.1 | 63.3 ± 1.0 |
水平 Level | 基因 Gene | 遗传距离区间 P-distance (%) | ||
---|---|---|---|---|
平均值 Average | 最大值 Maximum | 最小值 Minimum | ||
物种水平 Species level | COI | 17.91 ± 1.89 | 23.20 ± 1.92 | 4.73 ± 0.92 |
COII | 14.99 ± 1.81 | 20.01 ± 2.09 | 2.09 ± 0.53 | |
12S | 14.42 ± 2.45 | 19.81 ± 1.95 | 1.60 ± 0.44 | |
16S | 6.90 ± 1.77 | 12.68 ± 1.70 | 0.91 ± 0.50 | |
ND1 | 18.90 ± 1.97 | 25.35 ± 2.12 | 6.00 ± 0.86 | |
5 genes | 15.10 ± 1.46 | 18.94 ± 0.76 | 5.84 ± 0.43 | |
亚种水平 Subspecies level | COI | 9.15 ± 2.48 | 15.04 ± 1.71 | 6.31 ± 0.89 |
COII | 6.68 ± 3.18 | 17.52 ± 1.85 | 4.89 ± 0.84 | |
12S | 4.31 ± 1.92 | 11.09 ± 1.11 | 3.24 ± 0.63 | |
16S | 3.47 ± 2.68 | 8.45 ± 1.32 | 0.92 ± 0.49 | |
ND1 | 7.94 ± 2.79 | 16.09 ± 1.56 | 5.72 ± 0.77 | |
5 genes | 6.55 ± 2.22 | 13.74 ± 0.64 | 4.57 ± 0.30 | |
种群水平 Population level | COI | 1.18 ± 1.92 | 7.16 ± 1.05 | 0.00 ± 0.00 |
COII | 1.00 ± 1.52 | 5.36 ± 0.83 | 0.00 ± 0.00 | |
12S | 0.71 ± 1.00 | 3.61 ± 0.68 | 0.00 ± 0.00 | |
16S | 0.83 ± 1.78 | 7.41 ± 1.12 | 0.00 ± 0.00 | |
ND1 | 1.29 ± 2.06 | 8.31 ± 1.12 | 0.00 ± 0.00 | |
5 genes | 1.10 ± 1.49 | 5.10 ± 0.39 | 0.00 ± 0.00 |
Table 2 The genetic distance of 5 genes and combined genes of pheretimoid earthworms in Hainan Island
水平 Level | 基因 Gene | 遗传距离区间 P-distance (%) | ||
---|---|---|---|---|
平均值 Average | 最大值 Maximum | 最小值 Minimum | ||
物种水平 Species level | COI | 17.91 ± 1.89 | 23.20 ± 1.92 | 4.73 ± 0.92 |
COII | 14.99 ± 1.81 | 20.01 ± 2.09 | 2.09 ± 0.53 | |
12S | 14.42 ± 2.45 | 19.81 ± 1.95 | 1.60 ± 0.44 | |
16S | 6.90 ± 1.77 | 12.68 ± 1.70 | 0.91 ± 0.50 | |
ND1 | 18.90 ± 1.97 | 25.35 ± 2.12 | 6.00 ± 0.86 | |
5 genes | 15.10 ± 1.46 | 18.94 ± 0.76 | 5.84 ± 0.43 | |
亚种水平 Subspecies level | COI | 9.15 ± 2.48 | 15.04 ± 1.71 | 6.31 ± 0.89 |
COII | 6.68 ± 3.18 | 17.52 ± 1.85 | 4.89 ± 0.84 | |
12S | 4.31 ± 1.92 | 11.09 ± 1.11 | 3.24 ± 0.63 | |
16S | 3.47 ± 2.68 | 8.45 ± 1.32 | 0.92 ± 0.49 | |
ND1 | 7.94 ± 2.79 | 16.09 ± 1.56 | 5.72 ± 0.77 | |
5 genes | 6.55 ± 2.22 | 13.74 ± 0.64 | 4.57 ± 0.30 | |
种群水平 Population level | COI | 1.18 ± 1.92 | 7.16 ± 1.05 | 0.00 ± 0.00 |
COII | 1.00 ± 1.52 | 5.36 ± 0.83 | 0.00 ± 0.00 | |
12S | 0.71 ± 1.00 | 3.61 ± 0.68 | 0.00 ± 0.00 | |
16S | 0.83 ± 1.78 | 7.41 ± 1.12 | 0.00 ± 0.00 | |
ND1 | 1.29 ± 2.06 | 8.31 ± 1.12 | 0.00 ± 0.00 | |
5 genes | 1.10 ± 1.49 | 5.10 ± 0.39 | 0.00 ± 0.00 |
Fig. 3 Phylogenetic analysis of Hainan pheretimoid earthworms based on the 5 combined genes and their ancestral distribution. The numbers in the node were bootstrap values. The pie charts present the distribution area probabilities with different colors standing for different locations. The scale shows the differentiation time (in millions of years).
节点 Node | 后验分化时间(百万年) Posterior differentiation time (Ma) | 祖先分布区域比例 Ratio of ancestral distribution (%) | |||
---|---|---|---|---|---|
吊罗山 Mt. Diaoluo | 吊罗山和五指山 Mt. Diaoluo and Mt. Wuzhi | 吊罗山和黎母山 Mt. Diaoluo and Mt. Limu | 吊罗山和尖峰岭 Mt. Diaoluo and Jianfengling | ||
1 | 68.26 | 65.28 | 13.92 | 10.79 | 10.01 |
2 | 61.39 | 47.09 | 29.43 | 23.48 | 0 |
3 | 57.05 | 84.04 | 15.96 | 0 | 0 |
4 | 56.12 | 100 | 0 | 0 | 0 |
5 | 53.29 | 100 | 0 | 0 | 0 |
6 | 51.46 | 100 | 0 | 0 | 0 |
Table 3 The posterior differentiation time and ancestral distribution analysis of Hainan pheretimoid earthworms based on the Bayesian loose molecular clock method
节点 Node | 后验分化时间(百万年) Posterior differentiation time (Ma) | 祖先分布区域比例 Ratio of ancestral distribution (%) | |||
---|---|---|---|---|---|
吊罗山 Mt. Diaoluo | 吊罗山和五指山 Mt. Diaoluo and Mt. Wuzhi | 吊罗山和黎母山 Mt. Diaoluo and Mt. Limu | 吊罗山和尖峰岭 Mt. Diaoluo and Jianfengling | ||
1 | 68.26 | 65.28 | 13.92 | 10.79 | 10.01 |
2 | 61.39 | 47.09 | 29.43 | 23.48 | 0 |
3 | 57.05 | 84.04 | 15.96 | 0 | 0 |
4 | 56.12 | 100 | 0 | 0 | 0 |
5 | 53.29 | 100 | 0 | 0 | 0 |
6 | 51.46 | 100 | 0 | 0 | 0 |
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