生物多样性 ›› 2018, Vol. 26 ›› Issue (12): 1289-1295.DOI: 10.17520/biods.2018121
杨计平1, 李策1,2, 陈蔚涛1, 李跃飞1, 李新辉1,*()
收稿日期:
2018-04-16
接受日期:
2018-04-16
出版日期:
2018-12-20
发布日期:
2019-02-11
通讯作者:
李新辉
作者简介:
# 共同第一作者
基金资助:
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
摘要:
鳤(Ochetobius elongatus)曾经是我国许多河流的重要经济鱼类, 然而由于环境污染和人为干扰等原因, 鳤的资源量萎缩严重, 种群处于极度濒危的境地。目前, 常规采样方法获得鳤样本的难度较大, 致使相关研究难以开展。本研究通过仔鱼采集和成鱼采集的手段, 测定两个线粒体基因和两个核基因, 对西江中下游鳤的遗传多样性和种群动态历史进行研究。结果显示, 西江中下游鳤的遗传多样性处于较低水平并且出现了衰退的迹象, 可能经历了遗传瓶颈效应。此外, 种群动态历史分析发现, 西江中下游鳤在后更新世期间(0.06和0.13百万年前)经历了种群扩张, 刚好处于中更新世(0.78-0.126百万年前)冰期褪去之后, 表明更新世气候的波动影响了西江中下游鳤的种群动态。作为鳤可能的重要产卵场, 西江中下游部分江段可以考虑建立鳤的自然保护区, 用于保育和修复鳤的种质资源。
杨计平, 李策, 陈蔚涛, 李跃飞, 李新辉. 西江中下游鳤的遗传多样性与种群动态历史[J]. 生物多样性, 2018, 26(12): 1289-1295.
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 |
表1 本研究的采样信息
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 |
表2 本研究使用的引物信息
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 |
图1 基于不同基因和基因组合的单倍型/等位基因中介网状图。白色圆圈表示缺失单倍型。
Fig. 1 Median-joining networks of haplotype and allele based on different genes and gene groups. White circles indicate missing haplotype.
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 | - | - | - |
表3 鳤遗传多样性指数、中性检验和最优核苷酸替代模型
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 | - | - | - |
图2 基于不同基因和基因组合的错配分布分析。红色和紫色线条分别表示观测值和期望值。
Fig. 2 Mismatch distribution analysis based on different genes and gene groups. Red and purple lines represent observed value and expected values, respectively.
图3 拓展贝叶斯天际线点图(EBSP)。黑色实线表示有效种群大小的平均值, 灰色实线表示有效种群大小的中位数值, 虚线表示95%置信区间的有效种群大小。
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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