Genetic structure and demographic history of Mastacembelus armatus in southern China
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摘要: 为掌握华南地区大刺鳅 (Mastacembelus armatus) 的遗传种质资源现状，并为其管理和保护提供科学依据，采集了华南地区7个独立水系的16个地理群体共计140尾大刺鳅样本，基于Sanger测序获得了2个线粒体基因 (COI和Cytb)，综合多种分析方法对其遗传结构和群体动态史展开研究。结果表明，华南地区大刺鳅群体形成了3个谱系 (I、II和III)，分化时间介于0.596~0.676 Ma (百万年前)。此外，单倍型网状图发现不同谱系群体存在共域分布的现象，并提示海南岛群体与大陆群体之间可能存在两条扩散路线。群体遗传分析发现大刺鳅群体间存在显著的遗传分化 (FST=0.676, P<0.001)，并且符合距离隔离模式 (R=0.463, P=0.001)，暗示空间距离是造成大刺鳅遗传分化的一个重要因素。种群动态历史分析表明大刺鳅群体可能在0.025 Ma经历了种群扩张事件。Abstract: In order to understand the genetic resources of Mastacembelus armatus populations in southern China, and to provide an important scientific basis for their management and protection, we collected 140 individuals from 16 geographical populations from seven independent river systems in southern China and sequenced two mitochondrial genes (COI and Cytb) via PCR amplification and Sanger sequencing, and finally revealed the genetic structure and demographic history of M. armatus populations by phylogenetic analysis, haplotype network, population genetic analysis and Bayesian skyline plot. The results show that M. armatus populations consisted of three lineages (I, II and III) and split between 0.596 and 0.676 million years ago (Ma). Haplotype network shows that there was a common domain distribution among different lineages, and suggests that there might be two diffusion routes between Hainan Island population and mainland population. Population genetic analysis finds significant genetic differentiation (FST=0.676, P<0.001) and isolation by distance pattern (R=0.463, P=0.001) among M. armatus populations, implying that spatial distance was an important factor for genetic differentiation of M. armatus. Demographic analysis shows that M. armatus populations experienced population expansion at 0.025 Ma.
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Key words:
- Mastacembelus armatus /
- Genetic structure /
- Genetic differentiation /
- Demographic history
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图 1 华南地区主要水系大刺鳅的采样示意图
注：采样站位不同颜色代表不同谱系 (见图2)。
Figure 1. Sampling sites of M. armatus in southern China drainages
Note: Different colors represent different lineages (See Fig. 2).
图 2 分子系统树 (a) 和单倍型网络图 (b)
注：数字代表后验概率，黑色实心圆表示未采集到的单倍型，字母简写表示不同的地理群体 (表1)。
Figure 2. Phylogenetic tree (a) and haplotype network (b)
Note: Numbers indicate posterior probability. Black solid circles represent missing haplotype and the abbreviations represent different geographic populations (Table 1).
表 1 群体遗传多样性参数
Table 1. Parameters of genetic diversity
群体
Population水系
River
system样本量
Sample
size经纬度
Coordinate单倍型数/
私有单倍型数
Haplotype/Private
haplotype单倍型多样性
Haplotype
diversity当前核苷酸多样性
Current nucleotide
diversity历史核苷酸多态性
Historical nucleotide
diversity中性检测
Neutrality
test博白 Bobai (BB) 南流江 7 109.967˚E, 22.284˚N 5/4 0.857±0.137 0.000 6±0.000 2 0.000 9±0.000 6 −1.434 昌化 Changhua (CH) 昌化江 2 109.03˚E, 19.151˚N 1/1 从江 Congjiang (CJ) 珠江 14 108˚91˚E, 25.748˚N 4/3 0.495±0.151 0.000 4±0.000 2 0.000 7±0.000 4 −1.222 崇左 Chongzuo (CON) 珠江 5 107.337˚E, 22.398˚N 5/2 1.000±0.126 0.007 2±0.002 3 0.007 3±0.0038 −0.092 潮州 Chaozhou (CZ) 韩江 13 116.652˚E, 23.677˚N 1/0 0 0 0 0.000 大化 Dahua (DH) 珠江 2 107.99˚E, 23.738˚N 2/1 桂平 Guiping (GP) 珠江 9 110.089˚E, 23.392˚N 5/2 0.806±0.002 0.003 6±0.002 1 0.005 4±0.002 4 −1.627 河源 Heyuan (HY) 珠江 14 114.694˚E, 23.522˚N 3/2 0.275±0.148 0.000 2±0.000 1 0.000 5±0.000 4 −1.671 化州 Huazhou (HZ) 鉴江 3 110.632˚E, 21.65˚N 2/1 乐东 Ledong (LD) 昌化江 8 109.175˚E, 18.752˚N 2/2 0.333±0.215 0.000 2±0.000 1 0.000 3±0.000 3 −0.933 连州 Lianzhou (LZ) 珠江 10 112.371˚E, 24.78˚N 7/6 0.911±0.077 0.006 6±0.001 7 0.007 1±0.003 1 −0.386 南丰 Nanfeng (NF) 珠江 13 111.799˚E, 23.741˚N 5/2 0.782±0.079 0.002 7±0.001 6 0.004 7±0.002 0 −1.808 平乐 Pingle (PL) 珠江 6 110˚649'E, 24.627˚N 3/1 0.600±0.215 0.004 7±0.002 7 0.006 1±0.003 1 −1.505 琼海 Qionghai (QH) 万泉河 12 110.451˚E, 19.243˚N 6/6 0.758±0.122 0.000 8±0.000 2 0.001 5±0.000 8 −1.778 阳春 Yangchun (YC) 漠阳江 20 111.777˚E, 22.173˚N 4/2 0.489±0.117 0.006 3±0.001 3 0.0043±0.001 6 1.863 宜州 Yizhou (YZ) 珠江 4 108.628˚E, 24.499˚N 4/2 1.000±0.177 0.007 3±0.003 5 0.008 0±0.004 5 总计 Total 140 42/38 0.895±0.016 0.007 9±0.000 3 0.007 6±0.002 0 0.136 注：加粗数值表示P<0.05，表3同此。 Note: Values in bold indicate P<0.05. The same case in Table 3. 
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表 2 谱系之间的遗传距离 (对角线下) 与分化时间 (对角线上)
Table 2. Genetic distance (Below diagonal) and divergence time (Above diagonal) among different clades
谱系I
Clade I谱系II
Clade II谱系III
Clade III谱系I Clade I 0.596 0.620 谱系II Clade II 1.34% 0.676 谱系III Clade III 1.30% 1.28% 注：分化时间单位为Ma (百万年前)。 Note: The unit of differentiation time is Ma (Million years ago).
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表 3 FST和显著性检验
Table 3. Pairwise FST and significance test
博白 BB 从江 CJ 崇左 CON 潮州 CZ 桂平 GP 河源 HY 乐东 LD 连州 LZ 南丰 NF 平乐 PL 琼海 QH 博白 BB 0.000 从江 CJ 0.963 0.000 崇左 CON 0.665 0.338 0.000 潮州 CZ 0.843 0.982 0.775 0.000 桂平 GP 0.048 0.858 0.455 0.207 0.000 河源 HY 0.756 0.973 0.767 −0.006 0.200 0.000 乐东 LD 0.866 0.974 0.696 0.969 0.451 0.882 0.000 连州 LZ 0.670 0.146 −0.100 0.739 0.529 0.738 0.685 0.000 南丰 NF 0.063 0.874 0.551 0.184 −0.086 0.180 0.484 0.600 0.000 平乐 PL 0.238 0.839 0.324 0.139 −0.087 0.131 0.409 0.432 −0.037 0.000 琼海 QH 0.943 0.950 0.788 0.967 0.842 0.958 0.951 0.742 0.858 0.829 0.000 阳春 YC 0.561 0.247 −0.081 0.615 0.432 0.617 0.601 0.022 0.495 0.347 0.684
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