Population genetic structures of Dosidicus gigas in Southeast Pacific Ocean based on mitochondrial NADH dehydrogenase subunit 2 gene
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摘要: 为了解东南太平洋茎柔鱼 (Dosidicus gigas) 大、中、小3种表型群体间的遗传分化和结构，利用线粒体NADH脱氢酶亚基2 (ND2) 基因，对东南太平洋大、中、小3种表型群，共90尾性成熟茎柔鱼样本进行群体遗传学研究。ND2基因序列测序结果显示3个表型群总的单倍型多样性指数 (Hd) 为0.818，核苷酸多样性指数 (Pi) 为0.002 40，表现出较高的单倍型多样性和较低的核苷酸多样性。来源于群体内的变异达到了100.45%，两两群体间的遗传分化系数(Fst)均小于0.05 (P>0.05)，且基因流(Nm)远大于1，说明3种表型的茎柔鱼未出现显著的遗传分化。中性检验呈极显著负值 (Fs=−8.617 73, P<0.01)，核苷酸错配分布曲线均出现明显单峰，推测东南太平洋茎柔鱼在历史上可能经历过快速的群体扩张事件。该研究结果表明分布于东南太平洋不同海域茎柔鱼大、中、小3个表型群之间因生殖行为可能存在广泛的基因交流，应属于同一个种群，在渔业管理上应予以充分考虑。Abstract: To understand the genetic differentiation and structure among the large, medium and small phenotypic groups of Dosidicus gigas in the Southeast Pacific Ocean, we studied a total of 90 samples of matured D. gigas from different phenotypic groups for population genetics by using the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. The average haplotype diversities (Hd) and nucleotide diversities (Pi) of the three groups of D. gigas were 0. 818 and 0.002 40, respectively, showing a high haplotype diversity index but a low nucleotide diversity index. The genetic variation observed within populations reached 100.45%. The value of genetic differentiation index (Fst) was less than 0.05 (P>0.05), but the gene flow (Nm) was far more than 1, indicating no significant genetic divergence among the three phenotypes of D. gigas. The neutrality test was highly significantly negative (Fs=−8.617 73, P<0.01) and the nucleotide mismatch distribution curves all showed significant single peaks, suggesting that D. gigas in the Southeast Pacific Ocean might have historically experienced rapid population expansion events. In conclusion, there may be extensive genetic exchange between different phenotypic groups of D. gigas in Southeast Pacific Ocean due to their reproductive behavior and that they should belong to the same stock, which must be fully considered in fisheries management.
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Key words:
- Dosidicus gigas /
- Population genetic structure /
- Genetic diversity /
- ND2 gene /
- Population expansion
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图 2 基于ND2基因的茎柔鱼群体核苷酸不配对分布
Figure 2. Mismatch distribution graphs of populations based on ND2 gene sequences
图 3 基于ND2基因的茎柔鱼NJ系统进化树
Figure 3. Rooted neighbor-joining tree of populations based on ND2 gene haplotypes
图 4 茎柔鱼ND2基因单倍型的网络图
Figure 4. Median-joining network of ND2 gene haplotypes of D. gigas
表 1 样本采集区域与数量
Table 1. Area and number of samples
样品表型
Phenotype of samples采样区域
Sampling sites采样数目
Number of samples/尾采样时间
Sampling date样品胴长
Mantle length of samples/cm大表型 Large 76°W—81°W, 17°S—20°S 18 2018年10月 100~120 中表型 Middle 79°W—86°W, 3°S—20°S 42 2019年8月 30~60 小表型 Small 95°W—106°W, 1°S—3°S 30 2018年8月 15~25 
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表 2 引物序列
Table 2. Primer sequences
引物
Primer引物序列 (5'—3')
Reference sequence (5'—3')产物长度
Product
length/bpND2-F GCTGCTAACTTTATTTTGAGC 876 ND2-R ATTAGTCTTAGAGAAGTTCC
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表 3 基于ND2序列的茎柔鱼遗传多样性参数
Table 3. Genetic diversity parameters of ND2 gene sequences in D. gigas
项目
Item大表型
Large中表型
Middle小表型
Small全部样本
Total样本数 Number of samples 18 42 30 90 多态性位点数 Number of polymorphism sites 14 18 14 31 单倍型多样性 (Hd) Haplotype diversity 0.797 0.872 0.768 0.818 核苷酸多样性 (Pi) Nucleotide diversity 0.002 25 0.002 85 0.001 86 0.002 40 单倍型数 Number of haplotypes 9 20 13 33
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表 4 基于ND2基因的茎柔鱼群体间遗传分化系数 (对角线下方) 和基因流 (对角线上方)
Table 4. Population pairwise Fst (below diagonal) and gene flow (Nm, above diagonal) of populations based on ND2 gene sequences
遗传分化系数/
基因流
Fst/Nm大表型
Large中表型
Middle小表型
Small大表型 Large Inf Inf 中表型 Middle −0.003 57 (P>0.05) Inf 小表型 Small −0.012 70 (P>0.05) −0.002 14 (P>0.05) 注：Inf. 无限大。 Note: Inf. Infinite.
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表 5 中性检验结果和Raggedness index的计算 (包含P)
Table 5. Results of neutrality tests and Raggedness index including P-values
群体
Population中性检验 Neutrality test 粗糙指数
Raggedness index (P)Tajima's D (P) Fu's Fs (P) 大表型 Large −1.938 06 (P<0.05) −3.754 03 (P<0.05) 0.054 04 (P>0.05) 中表型 Middle −1.303 59 (P>0.05) −13.660 82 (P<0.01) 0.045 89 (P>0.05) 小表型 Small −1.797 99 (P<0.05) −8.438 33 (P<0.01) 0.032 32 (P>0.05) 平均值 Mean −1.679 88 (P<0.05) −8.617 73 (P<0.01) 0.044 08 (P>0.05)
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