Genetic structure analysis of Ochetobius elongatus between Yangtze River and Pearl River using multiple loci
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摘要: 为保护极濒危物种鳤 (Ochetobius elongatus) 的遗传多样性，通过野外调查在长江获得了7尾鳤样本，利用Sanger测序技术测定了其2个线粒体基因 [细胞色素b (Cytb) 和酰胺腺嘌呤二核苷酸 (NADH) 脱氧酶亚单位2 (ND2)] 和2个核基因 [肌球蛋白重链6 (myh6) 和重组激活基因2 (RAG2)] 的序列，结合已公开发表的52尾珠江鳤的4个基因序列，采用系统发育分析、单倍型网状图构建、分化时间估算等方法，对珠江和长江鳤的遗传结构和分化历史展开研究。系统发育分析和单倍型网状图表明，珠江和长江鳤群体分别形成了高度分化的遗传谱系，并且在核基因水平上形成了特有的等位基因型，表明这两个水系的鳤群体独立进化且不存在基因交流。分化时间估算表明珠江和长江鳤两谱系在0.38~0.76 Ma (百万年前) 分化，中更新世青藏高原的快速隆升很可能是促进其分化的重要因素。鉴于珠江和长江的鳤群体在线粒体基因和核基因层面上存在严格的地理分化，建议将这两个群体看作不同的演化显著单位 (Evolutionary Significant Unit, ESU) 进行区别管理和保护。Abstract: To protect the genetic diversity of a critically endangered species Ochetobius elongatus, taking seven individuals of O. elongatus collected from the field investigation in the Yangtze River as samples, we sequenced two mitochondrial genes (Cytb and ND2) and two nuclear genes (mhy6 and RAG2) for the seven samples by Sanger sequencing technique. Combining with the published four gene sequences of 52 O. elongatus samples in the Pearl River, we explored the genetic structure of O. elongatus between the Pearl River and the Yangtze River, so as to provide scientific support for its conservation. We applied phylogenetic analyses, haplotype networks and divergence time estimation. Phylogenetic analyses and haplotype networks reveal that O. elongatus populations in the two rivers generated two deep and independent lineages, and formed private alleles at the nuclear gene level. The results suggest that O. elongatus populations in the two rivers evolved independently without agene flow. The rapid lifting of the Qinghai-Xizang Plateau during the middle Pleistocene might be an important factor that triggered the split of O. elongatus populations in the two rivers 0.38~0.76 million years ago (Ma). In view of the strictly geographical division of O. elongatus populations between the two rivers at both mitochondrial and nuclear gene levels, we suggest that these two populations should be regarded as two evolutionary significant units, and targeted strategies should be urgently put forward to manage and protect its resources.
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图 2 单倍型/等位基因中介网状图
注：圆的大小代表单倍型频率，颜色代表所属群体，空心圆代表未检测到的单倍型。
Figure 2. Haplotype/allele median joining network
Note: The size of the circle represents the haplotype frequency; the color represents the group, and the hollow circle represents the undetected haplotype.
图 3 基于不同基因组合的贝叶斯系统发育树
Figure 3. Bayesian phylogenetic trees based on different gene combinations
图 4 基于线粒体基因组合的分化时间结果
Figure 4. Estimation of divergence time based on combination of two mitochondrial genes
表 1 采样信息和GenBank序列号
Table 1. Sampling information and GenBank No.
采样站位
Sampling site样本量
Sample number/尾GenBank序列号 GenBank No. Cytb ND2 myh6 RAG2 公安 Gongan 7 MW657590—MW657596 MW657598—MW657604 MW657606—MW657612 MW657614—MW657620 梧州 Wuzhou 1 MW657432 MW657484 MW657536 MW657588 桂平 Guiping 1 MW657431 MW657483 MW657535 MW657587 肇庆 Zhaoqing 50 MW657381—MW657430 MW657433—MW657482 MW657485—MW657534 MW657537—MW657586 
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表 2 系统发育树构建和分化时间估算的最优模型
Table 2. Optimal model of phylogenetic tree construction and differentiation time estimation
基因组合
Gene combination最优模型
Optimal model不变位点比例
Proportion of invariable siteGamma分布形状参数
Gamma distribution shape parameterCytb+ND2 GTR+I+G 0.474 0.986 myh6+RAG2 K80+I 0.881 — Cytb+ND2+myh6+RAG2 GTR+I+G 0.697 0.857
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表 3 鳤种群的单倍型与遗传多样性指数
Table 3. Haplotypes and genetic diversity indexes of O. elongatus populations
基因组合
Gene combination水系
River system序列数
Sequence number单倍型数
Haplotype number单倍型多样性
Haplotype diversity核苷酸多样性
Nucleotide diversity/%Cytb+ND2 珠江 52 26 0.940±0.017 0.219±0.020 长江 7 3 0.714±0.127 0.187±0.003 合计 59 29 0.950±0.014 0.494±0.080 myh6+RAG2 珠江 104 5 0.546±0.050 0.040±0.006 长江 14 8 0.923±0.044 0.135±0.021 合计 118 13 0.643±0.036 0.071±0.009
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