生物多样性 ›› 2025, Vol. 33 ›› Issue (1): 24241. DOI: 10.17520/biods.2024241 cstr: 32101.14.biods.2024241
邓洪1,2, 钟占友1,2, 寇春妮2, 朱书礼2, 李跃飞2, 夏雨果2, 武智2, 李捷2,*(), 陈蔚涛2,*(
)(
)
收稿日期:
2024-06-17
接受日期:
2024-08-06
出版日期:
2025-01-20
发布日期:
2024-09-20
通讯作者:
* E-mail: 基金资助:
Hong Deng1,2, Zhanyou Zhong1,2, Chunni Kou2, Shuli Zhu2, Yuefei Li2, Yuguo Xia2, Zhi Wu2, Jie Li2,*(), Weitao Chen2,*(
)(
)
Received:
2024-06-17
Accepted:
2024-08-06
Online:
2025-01-20
Published:
2024-09-20
Contact:
* E-mail: Supported by:
摘要:
斑鳠(Hemibagrus guttatus)被誉为“珠江四大名鱼”之首, 然而在梯级开发、水体污染、过度捕捞等多种因素的影响下, 其野外资源量严重衰退, 并于2021年2月被列为国家二级重点保护野生动物。为了能够有效支撑斑鳠种群的科学管理与保护工作, 本研究在珠江水系和韩江水系19个站位收集了111尾斑鳠样本, 基于线粒体全基因组数据, 综合系统发育、分化时间估算、种群遗传学等多种研究方法开展了遗传多样性、遗传结构与种群历史动态的研究。种群遗传学分析结果显示, 珠江和韩江水系的斑鳠种群均呈现较低水平的核苷酸多样性, 表明斑鳠种群的保护刻不容缓。系统发育分析和单倍型网络图发现, 珠江水系和韩江水系的斑鳠种群分别形成独立的进化谱系, 其中珠江水系的斑鳠种群形成了两个共域分布的亚谱系。分化时间估算发现珠江和韩江两个水系斑鳠种群的分化时间介于0.284-0.401百万年前(Ma), 珠江水系两个亚谱系的分化时间介于0.092-0.132 Ma, 暗示华南地区更新世气候变化可能是斑鳠种群谱系分化的重要驱动因素。种群动态历史分析发现, 斑鳠种群分别在0.072-0.101 Ma和0.024-0.033 Ma期间经历了明显的种群收缩和种群扩张事件, 并支持珠江水系斑鳠种群在0.024-0.032 Ma之间经历了显著的种群扩张, 表明后更新世期间的冰期与间冰期循环引起的海平面波动及末次盛冰期可能对斑鳠种群的分布与有效种群大小造成了显著影响。基于上述研究结果, 建议加强渔政监管力度或者划立保护区, 提升韩江水系斑鳠种群的关注度, 并指出放流前需明晰放流样本的(亚)谱系来源, 避免非本地谱系亲本或者苗种的盲目投放。
邓洪, 钟占友, 寇春妮, 朱书礼, 李跃飞, 夏雨果, 武智, 李捷, 陈蔚涛 (2025) 基于线粒体全基因组揭示斑鳠的种群遗传结构与演化历史. 生物多样性, 33, 24241. DOI: 10.17520/biods.2024241.
Hong Deng, Zhanyou Zhong, Chunni Kou, Shuli Zhu, Yuefei Li, Yuguo Xia, Zhi Wu, Jie Li, Weitao Chen (2025) Population genetic structure and evolutionary history of Hemibagrus guttatus based on mitochondrial genomes. Biodiversity Science, 33, 24241. DOI: 10.17520/biods.2024241.
河流 River | 采集地 Sampling sites | 样本量 Sample size | 经纬度 Locality |
---|---|---|---|
南盘江 Nanpanjiang (NPJ) | 西林 Xiling (XL) | 7 | 24˚39′ N/104˚28′ E |
柳江 Liujiang (LJ) | 宜州 Yizhou (YZ) | 8 | 24˚50′ N/108˚60′ E |
柳江 Liujiang (LJ) | 柳州 Liuzhou (LZZ) | 2 | 24˚31′ N/109˚42′ E |
柳江 Liujiang (LJ) | 柳城 Liucheng (LC) | 8 | 24˚65′ N/109˚26′ E |
桂江 Guijiang (GJ) | 昭平 Zhaoping (ZP) | 2 | 24˚17′ N/110˚80′ E |
桂江 Guijiang (GJ) | 平乐 Pingle (PL) | 4 | 24˚62′ N/110˚62′ E |
东江 Dongjiang (DJ) | 古竹 Guzhu (GZ) | 4 | 23˚51′ N/114˚70′ E |
东江 Dongjiang (DJ) | 惠州 Huizhou (HZ) | 2 | 23˚11′ N/114˚41′ E |
贺江 Hejiang (HEJ) | 南丰 Nanfeng (NF) | 5 | 23˚44′ N/111˚47′ E |
北江 Beijiang (BJ) | 韶关 Shaoguan (SG) | 4 | 24˚81′ N/113˚59′ E |
北江 Beijiang (BJ) | 连州 Lianzhou (LZ) | 8 | 24˚78′ N/112˚37′ E |
北江 Beijiang (BJ) | 西牛 Xiniu (XN) | 14 | 24˚17′ N/113˚11′ E |
红水河 Hongshuihe (HSH) | 都安 Du’an (DA) | 5 | 23˚93′ N/108˚10′ E |
郁江 Yujiang (YJ) | 龙州 Longzhou (LLZ) | 4 | 22˚34′ N/106˚85′ E |
郁江 Yujiang (YJ) | 隆安 Long’an (LA) | 3 | 23˚17′ N/107˚69′ E |
黔江 Qianjiang (QJ) | 桂平 Guiping (GP) | 7 | 23˚39′ N/110˚07′ E |
韩江 Hanjiang (HJ) | 梅州 Meizhou (MZ) | 16 | 24˚29′ N/116˚11′ E |
韩江 Hanjiang (HJ) | 蕉岭 Jiaoling (JL) | 4 | 24˚65′ N/116˚17′ E |
韩江 Hanjiang (HJ) | 上杭 Shanghang (SH) | 4 | 25˚04′ N/116˚42′ E |
总计 Total | 111 |
表1 斑鳠样本采集信息
Table 1 Sampling information of Hemibagrus guttatus samples
河流 River | 采集地 Sampling sites | 样本量 Sample size | 经纬度 Locality |
---|---|---|---|
南盘江 Nanpanjiang (NPJ) | 西林 Xiling (XL) | 7 | 24˚39′ N/104˚28′ E |
柳江 Liujiang (LJ) | 宜州 Yizhou (YZ) | 8 | 24˚50′ N/108˚60′ E |
柳江 Liujiang (LJ) | 柳州 Liuzhou (LZZ) | 2 | 24˚31′ N/109˚42′ E |
柳江 Liujiang (LJ) | 柳城 Liucheng (LC) | 8 | 24˚65′ N/109˚26′ E |
桂江 Guijiang (GJ) | 昭平 Zhaoping (ZP) | 2 | 24˚17′ N/110˚80′ E |
桂江 Guijiang (GJ) | 平乐 Pingle (PL) | 4 | 24˚62′ N/110˚62′ E |
东江 Dongjiang (DJ) | 古竹 Guzhu (GZ) | 4 | 23˚51′ N/114˚70′ E |
东江 Dongjiang (DJ) | 惠州 Huizhou (HZ) | 2 | 23˚11′ N/114˚41′ E |
贺江 Hejiang (HEJ) | 南丰 Nanfeng (NF) | 5 | 23˚44′ N/111˚47′ E |
北江 Beijiang (BJ) | 韶关 Shaoguan (SG) | 4 | 24˚81′ N/113˚59′ E |
北江 Beijiang (BJ) | 连州 Lianzhou (LZ) | 8 | 24˚78′ N/112˚37′ E |
北江 Beijiang (BJ) | 西牛 Xiniu (XN) | 14 | 24˚17′ N/113˚11′ E |
红水河 Hongshuihe (HSH) | 都安 Du’an (DA) | 5 | 23˚93′ N/108˚10′ E |
郁江 Yujiang (YJ) | 龙州 Longzhou (LLZ) | 4 | 22˚34′ N/106˚85′ E |
郁江 Yujiang (YJ) | 隆安 Long’an (LA) | 3 | 23˚17′ N/107˚69′ E |
黔江 Qianjiang (QJ) | 桂平 Guiping (GP) | 7 | 23˚39′ N/110˚07′ E |
韩江 Hanjiang (HJ) | 梅州 Meizhou (MZ) | 16 | 24˚29′ N/116˚11′ E |
韩江 Hanjiang (HJ) | 蕉岭 Jiaoling (JL) | 4 | 24˚65′ N/116˚17′ E |
韩江 Hanjiang (HJ) | 上杭 Shanghang (SH) | 4 | 25˚04′ N/116˚42′ E |
总计 Total | 111 |
图1 斑鳠种群采样点示意图(a)、系统发育树(b)和单倍型网络图(c)。图(a)实心圆表示采样站位, 黑色和蓝色缩写分别表示采样站位和所属江段; 图(b)括号内数值表示分化时间, 斜杠左侧数字表示贝叶斯进化树的后验概率, 斜杠右侧数字表示最大似然树的支持率; 图(c)圆圈大小表示单倍型频率, 数字表示突变步数。谱系Ⅰ-1/2代表不同亚谱系; 种群代号含义见表1。
Fig. 1 Map of sample sites of Hemibagrus guttatus populations (a), phylogenetic tree (b) and haplotype network (c). In Figure a, the solid cycles indicate sample sites; the black and red fonts represent the abbreviations of sample sites and the river sections, respectively. In Figure b, the values in brackets indicate the divergence time, the values at left and right of slash represent the Bayesian posterior probability and support values of Maximum likelihood tree, respectively. In Figure c, the size of circle represents haplotype frequency and the numbers represent mutation steps. Sublineages I-1 and I-2 demarcate distinct evolutionary subdivisions, population codes refer to Table 1.
采样点 Sampling site | 样本大小 Sample size | 单倍型数 Number of haplotype | 单倍型多样性 Haplotype diversity | 核苷酸多样性 Nucleotide diversity | 中性检测 Neutrality test | |
---|---|---|---|---|---|---|
Tajima’s D | Fu’s Fs | |||||
南盘江 NPJ | 7 | 3 | 0.667 (± 0.160) | 0.0004 (± 0.0001) | -0.367 | 3.708 |
柳江 LJ | 18 | 17 | 0.993 (± 0.021) | 0.0018 (± 0.0003) | -0.607 | -2.697 |
桂江 GJ | 6 | 6 | 1.000 (± 0.096) | 0.0005 (± 0.0001) | -0.644 | -1.522 |
东江 DJ | 6 | 6 | 1.000 (± 0.096) | 0.0005 (± 0.0001) | -0.315 | -1.522 |
贺江 HEJ | 5 | 5 | 1.000 (± 0.126) | 0.0006 (± 0.0001) | -0.770 | -0.542 |
北江 BJ | 27 | 15 | 0.942 (± 0.027) | 0.0004 (± 0.0001) | -1.707* | -3.177 |
红水河 HSH | 5 | 5 | 1.000 (± 0.126) | 0.0007 (± 0.0001) | -0.393 | -0.338 |
郁江 YJ | 7 | 7 | 1.000 (± 0.076) | 0.0007 (± 0.0001) | -0.957 | -1.528 |
黔江 QJ | 7 | 7 | 1.000 (± 0.076) | 0.0011 (± 0.0003) | -1.487* | -0.754 |
珠江 ZJ | 87 | 59 | 1.000 (± 0.003) | 0.0011 (± 0.0002) | -0.805 | -0.930 |
韩江 HJ | 24 | 4 | 0.641 (± 0.076) | 0.0002 (± 0.0002) | 1.526 | 3.312 |
总计 Total | 111 | 63 | 1.000 (± 0.003) | 0.002 (± 0.0005) | -0.986 | 2.243 |
表2 斑鳠种群的单倍型数、单倍型多样性、核苷酸多样性及中性检测。种群代号见表1。
Table 2 Detection of number of haplotype, haplotype diversity, nucleotide diversity and neutrality test of Hemibagrus guttatus. Population codes see Table 1.
采样点 Sampling site | 样本大小 Sample size | 单倍型数 Number of haplotype | 单倍型多样性 Haplotype diversity | 核苷酸多样性 Nucleotide diversity | 中性检测 Neutrality test | |
---|---|---|---|---|---|---|
Tajima’s D | Fu’s Fs | |||||
南盘江 NPJ | 7 | 3 | 0.667 (± 0.160) | 0.0004 (± 0.0001) | -0.367 | 3.708 |
柳江 LJ | 18 | 17 | 0.993 (± 0.021) | 0.0018 (± 0.0003) | -0.607 | -2.697 |
桂江 GJ | 6 | 6 | 1.000 (± 0.096) | 0.0005 (± 0.0001) | -0.644 | -1.522 |
东江 DJ | 6 | 6 | 1.000 (± 0.096) | 0.0005 (± 0.0001) | -0.315 | -1.522 |
贺江 HEJ | 5 | 5 | 1.000 (± 0.126) | 0.0006 (± 0.0001) | -0.770 | -0.542 |
北江 BJ | 27 | 15 | 0.942 (± 0.027) | 0.0004 (± 0.0001) | -1.707* | -3.177 |
红水河 HSH | 5 | 5 | 1.000 (± 0.126) | 0.0007 (± 0.0001) | -0.393 | -0.338 |
郁江 YJ | 7 | 7 | 1.000 (± 0.076) | 0.0007 (± 0.0001) | -0.957 | -1.528 |
黔江 QJ | 7 | 7 | 1.000 (± 0.076) | 0.0011 (± 0.0003) | -1.487* | -0.754 |
珠江 ZJ | 87 | 59 | 1.000 (± 0.003) | 0.0011 (± 0.0002) | -0.805 | -0.930 |
韩江 HJ | 24 | 4 | 0.641 (± 0.076) | 0.0002 (± 0.0002) | 1.526 | 3.312 |
总计 Total | 111 | 63 | 1.000 (± 0.003) | 0.002 (± 0.0005) | -0.986 | 2.243 |
韩江 HJ | 南盘江 NPJ | 柳江 LJ | 桂江 GJ | 东江 DJ | 贺江 HEJ | 北江 BJ | 红水河 HSH | 郁江 YJ | 黔江 QJ | |
---|---|---|---|---|---|---|---|---|---|---|
韩江 HJ | 1.01% | 1.03% | 1.01% | 1.01% | 1.02% | 1.13% | 1.02% | 1.02% | 1.01% | |
南盘江 NPJ | 0.978 | 0.13% | 0.04% | 0.05% | 0.04% | 0.20% | 0.05% | 0.06% | 0.07% | |
柳江 LJ | 0.913 | 0.111 | 0.14% | 0.13% | 0.14% | 0.29% | 0.15% | 0.14% | 0.15% | |
桂江 GJ | 0.976 | 0.000 | 0.072 | 0.05% | 0.05% | 0.20% | 0.06% | 0.06% | 0.08% | |
东江 DJ | 0.976 | 0.206 | 0.070 | 0.098 | 0.06% | 0.21% | 0.06% | 0.06% | 0.08% | |
贺江 HEJ | 0.976 | 0.000 | 0.055 | 0.000 | 0.086 | 0.21% | 0.06% | 0.07% | 0.08% | |
北江 BJ | 0.970 | 0.150 | 0.185 | 0.010 | 0.116 | 0.071 | 0.22% | 0.22% | 0.24% | |
红水河 HSH | 0.974 | 0.026 | 0.077 | 0.000 | 0.130 | 0.000 | 0.172 | 0.07% | 0.09% | |
郁江 YJ | 0.974 | 0.126 | 0.083 | 0.047 | 0.026 | 0.041 | 0.120 | 0.091 | 0.09% | |
黔江 QJ | 0.962 | 0.017 | 0.017 | 0.000 | 0.028 | 0.000 | 0.137 | 0.000 | 0.000 |
表3 斑鳠两两种群间遗传分化系数(FST)值(对角线下方)及遗传距离(对角线上方)
Table 3 Pairwise population F-statistics values (FST, below diagonal) and genetic distance (above diagonal) of Hemibagrus guttatus
韩江 HJ | 南盘江 NPJ | 柳江 LJ | 桂江 GJ | 东江 DJ | 贺江 HEJ | 北江 BJ | 红水河 HSH | 郁江 YJ | 黔江 QJ | |
---|---|---|---|---|---|---|---|---|---|---|
韩江 HJ | 1.01% | 1.03% | 1.01% | 1.01% | 1.02% | 1.13% | 1.02% | 1.02% | 1.01% | |
南盘江 NPJ | 0.978 | 0.13% | 0.04% | 0.05% | 0.04% | 0.20% | 0.05% | 0.06% | 0.07% | |
柳江 LJ | 0.913 | 0.111 | 0.14% | 0.13% | 0.14% | 0.29% | 0.15% | 0.14% | 0.15% | |
桂江 GJ | 0.976 | 0.000 | 0.072 | 0.05% | 0.05% | 0.20% | 0.06% | 0.06% | 0.08% | |
东江 DJ | 0.976 | 0.206 | 0.070 | 0.098 | 0.06% | 0.21% | 0.06% | 0.06% | 0.08% | |
贺江 HEJ | 0.976 | 0.000 | 0.055 | 0.000 | 0.086 | 0.21% | 0.06% | 0.07% | 0.08% | |
北江 BJ | 0.970 | 0.150 | 0.185 | 0.010 | 0.116 | 0.071 | 0.22% | 0.22% | 0.24% | |
红水河 HSH | 0.974 | 0.026 | 0.077 | 0.000 | 0.130 | 0.000 | 0.172 | 0.07% | 0.09% | |
郁江 YJ | 0.974 | 0.126 | 0.083 | 0.047 | 0.026 | 0.041 | 0.120 | 0.091 | 0.09% | |
黔江 QJ | 0.962 | 0.017 | 0.017 | 0.000 | 0.028 | 0.000 | 0.137 | 0.000 | 0.000 |
图2 基于0.62%进化速率的总种群(a)、珠江种群(c)和韩江种群(e)的贝叶斯天际线图以及基于0.87%进化速率的总种群(b)、珠江种群(d)和韩江种群(f)贝叶斯天际线图
Fig. 2 Bayesian skyline plots of the overall population (a), the Pearl River population (c) and the Hanjiang River population (e) basedon the evolutionary rate of 0.62%, the overall population (b), the Pearl River population (d) and the Hanjiang River population (f) based on the evolutionary rate of 0.87%
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