Biodiv Sci ›› 2018, Vol. 26 ›› Issue (12): 1289-1295. DOI: 10.17520/biods.2018121
• Original Papers: Animal Diversity • Previous Articles Next Articles
Jiping Yang1, Ce Li1,2, Weitao Chen1, Yuefei Li1, Xinhui Li1,*()
Received:
2018-04-16
Accepted:
2018-04-16
Online:
2018-12-20
Published:
2019-02-11
Contact:
Li Xinhui
About author:
# 同等贡献作者 Contributed equally to this work
Jiping Yang, Ce Li, Weitao Chen, Yuefei Li, Xinhui Li. Genetic diversity and population demographic history of Ochetobius elongatus in the middle and lower reaches of the Xijiang River[J]. Biodiv Sci, 2018, 26(12): 1289-1295.
采样点 Sample site | 采样日期 Sampling time | 样本量 Sample size | 经度 Longitude | 纬度 Latitude |
---|---|---|---|---|
广西桂平 Guiping | 2017.09 | 1 | 110°05°54.78°° E | 23°24°08.25°° N |
广西梧州 Wuzhou | 2017.09 | 1 | 111°17°15.32°° E | 23°28°07.94°° N |
广东肇庆 Zhaoqing | 2011.05 | 22 | 112°23°40.13°° E | 23°05°06.24°° N |
广东肇庆 Zhaoqing | 2013.05 | 28 | 112°23°40.13°° E | 23°05°06.24°° N |
Table 1 Sample information of the present study
采样点 Sample site | 采样日期 Sampling time | 样本量 Sample size | 经度 Longitude | 纬度 Latitude |
---|---|---|---|---|
广西桂平 Guiping | 2017.09 | 1 | 110°05°54.78°° E | 23°24°08.25°° N |
广西梧州 Wuzhou | 2017.09 | 1 | 111°17°15.32°° E | 23°28°07.94°° N |
广东肇庆 Zhaoqing | 2011.05 | 22 | 112°23°40.13°° E | 23°05°06.24°° N |
广东肇庆 Zhaoqing | 2013.05 | 28 | 112°23°40.13°° E | 23°05°06.24°° N |
引物名 Primer | 引物序列 Primer sequence (5′-3′) | 退火温度 Annealed temperature (℃) | 参考文献 Reference | |
---|---|---|---|---|
Cytb | L14724 | GACTTGAAA AACCACCGTTG | 58-64 | Xiao et al, 2001 |
H15915 | CTCCGATCTCCGGATTACAAGAC | |||
ND2 | AFND2L | AAGCTYTYGGGCCCATACC | 58 | 黎瑞宝, 2013① |
AFND2R | TCCYGCTTAGGGCTTTGAAGG | |||
myh6 | myh6_F459 | CATMTTYTCCATCTCAGATAATGC | 53 | Chen et al, 2008 |
myh6_R1325 | ATTCTCACCACCATCCAGTTGAA | |||
RAG2 | RAG2-f2a | AARCGCTCMTGTCCMACTGG | 55 | Lovejoy & Collette, 2001 |
RAG2-R6a | TGRTCCARGCAGAAGTACTTG |
Table 2 Primer information used in the present study
引物名 Primer | 引物序列 Primer sequence (5′-3′) | 退火温度 Annealed temperature (℃) | 参考文献 Reference | |
---|---|---|---|---|
Cytb | L14724 | GACTTGAAA AACCACCGTTG | 58-64 | Xiao et al, 2001 |
H15915 | CTCCGATCTCCGGATTACAAGAC | |||
ND2 | AFND2L | AAGCTYTYGGGCCCATACC | 58 | 黎瑞宝, 2013① |
AFND2R | TCCYGCTTAGGGCTTTGAAGG | |||
myh6 | myh6_F459 | CATMTTYTCCATCTCAGATAATGC | 53 | Chen et al, 2008 |
myh6_R1325 | ATTCTCACCACCATCCAGTTGAA | |||
RAG2 | RAG2-f2a | AARCGCTCMTGTCCMACTGG | 55 | Lovejoy & Collette, 2001 |
RAG2-R6a | TGRTCCARGCAGAAGTACTTG |
单倍型数/个体数 Number of haplotype/ sample size | 单倍型多态性 Haplotype diversity | 近期核苷酸多态性 Current nucleotide diversity (θπ, %) | 历史核苷酸多态性 Historical nucleotide diversity (θw, %) | Tajima’s D 检验 Tajima’s D test | Fu’s Fs检验 Fu’s Fs test | 最优模型 Optimal model | |
---|---|---|---|---|---|---|---|
Cytb | 13/52 | 0.784 | 0.197 | 0.470 | -1.83** | -5.43** | HKY+I |
ND2 | 17/52 | 0.869 | 0.239 | 0.272 | -0.35 | -8.16*** | F81+I+G |
Cytb + ND2 | 26/52 | 0.940 | 0.219 | 0.366 | -1.33 | -14.54*** | - |
myh6 | 2/52 | 0.462 | 0.060 | 0.029 | - | - | HKY |
RAG2 | 3/52 | 0.147 | 0.022 | 0.077 | - | - | F81 |
myh6 + RAG2 | 5/52 | 0.546 | 0.040 | 0.055 | - | - | - |
Table 3 Genetic diversity indices, neutrality tests and optimal nucleotide substitution model of Ochetobius elongatus
单倍型数/个体数 Number of haplotype/ sample size | 单倍型多态性 Haplotype diversity | 近期核苷酸多态性 Current nucleotide diversity (θπ, %) | 历史核苷酸多态性 Historical nucleotide diversity (θw, %) | Tajima’s D 检验 Tajima’s D test | Fu’s Fs检验 Fu’s Fs test | 最优模型 Optimal model | |
---|---|---|---|---|---|---|---|
Cytb | 13/52 | 0.784 | 0.197 | 0.470 | -1.83** | -5.43** | HKY+I |
ND2 | 17/52 | 0.869 | 0.239 | 0.272 | -0.35 | -8.16*** | F81+I+G |
Cytb + ND2 | 26/52 | 0.940 | 0.219 | 0.366 | -1.33 | -14.54*** | - |
myh6 | 2/52 | 0.462 | 0.060 | 0.029 | - | - | HKY |
RAG2 | 3/52 | 0.147 | 0.022 | 0.077 | - | - | F81 |
myh6 + RAG2 | 5/52 | 0.546 | 0.040 | 0.055 | - | - | - |
Fig. 2 Mismatch distribution analysis based on different genes and gene groups. Red and purple lines represent observed value and expected values, respectively.
Fig. 3 Extended Bayesian Skyline plots. Black lines represent mean values of effective population size, gray lines represent median values of effective population size, and dashed lines represent 95% confidence interval of effective population size.
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