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 (2018) 西江中下游鳤的遗传多样性与种群动态历史. 生物多样性, 26, 1289-1295. DOI: 10.17520/biods.2018121.
Jiping Yang, Ce Li, Weitao Chen, Yuefei Li, Xinhui Li (2018) Genetic diversity and population demographic history of Ochetobius elongatus in the middle and lower reaches of the Xijiang River. Biodiversity Science, 26, 1289-1295. DOI: 10.17520/biods.2018121.
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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