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 1 主要采样区域
EEZ. 专属经济区；A、B、C. 采样区。
Figure 1. Main sampling sites
EEZ. Exclusive Economic Zone; A, B, C. Sampling sites.
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
圆的面积和单倍型的频率之间成正比。
Figure 4. Median-joining network of ND2 gene haplotypes of D. gigas
Circle sizes are proportional to the frequencies of the respective haplotype.
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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[1] TAIPE A, YAMASHIRO C, MARIATEGUI L, et al. Distribution and concentrations of jumbo flying squid (Dosidicus gigas) off the Peruvian coast between 1991 and 1999[J]. Fish Res, 2001, 54(1): 21-32. doi: 10.1016/S0165-7836(01)00377-0 [2] 陈新军, 刘必林, 王尧耕. 世界头足类[M]. 北京: 海洋出版社, 2009: 312-313. [3] NIGMATULLIN C M, NESIS K N, ARKHIPKIN A I. A review of the biology of the jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae)[J]. Fish Res, 2001, 54(1): 9-19. doi: 10.1016/S0165-7836(01)00371-X [4] FAO. Global Production Statistics 1950-2018[DB/OL]. [2018-10-18]. http://www.fao.org/fishery/statistics/global-production/query/zh. [5] NIGMATULLIN C M, MARKAIDA U. Oocyte development, fecundity and spawning strategy of large sized jumbo squid Dosidicus gigas (Oegopsida: Ommastrephinae)[J]. J Mar Biol Assoc UK, 2009, 89(4): 789-801. doi: 10.1017/S0025315408002853 [6] ARGÜELLES J, TAFUR R. New insights on the biology of the jumbo squid Dosidicus gigas in the Northern Humboldt Current System: size at maturity, somatic and reproductive investment[J]. Fish Res, 2010, 106(2): 185-192. doi: 10.1016/j.fishres.2010.06.005 [7] 陈新军, 陆化杰, 刘必林, 等. 大洋性柔鱼类资源开发现状及可持续利用的科学问题[J]. 上海海洋大学学报, 2012, 21(5): 197-206. [8] 刁乐, 宋炜, 蒋科技, 等. 基于线粒体CO I基因序列的东南太平洋茎柔鱼群体遗传结构分析[J]. 海洋渔业, 2020, 43(3): 266-276. doi: 10.3969/j.issn.1004-2490.2020.03.002 [9] SANCHEZ G, KAWAI K, YAMASHIRO C, et al. Patterns of mitochondrial and microsatellite DNA markers describe historical and contemporary dynamics of the Humboldt squid Dosidicus gigas in the Eastern Pacific Ocean[J]. Rev Fish Biol Fish, 2020, 30(3): 519-533. doi: 10.1007/s11160-020-09609-9 [10] 刘连为, 陈新军, 许强华, 等. 秘鲁外海茎柔鱼大型群与小型群的遗传变异分析[J]. 海洋渔业, 2014, 36(3): 216-223. doi: 10.3969/j.issn.1004-2490.2014.03.004 [11] 萨姆布鲁克 J, 拉塞尔D W. 分子克隆实验指南 (上册)[M]. 4版. 北京: 科学出版社, 2002: 2-42. [12] KUMAR S, STECHER G, TAMURA K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7): 1870-1874. doi: 10.1093/molbev/msw054 [13] ROZAS J, SÁNCHEZ-DELBARRIO J C, LIBRADO P, et al. DnaSP 6: DNA sequence polymorphism analyses of large datasets[J]. Mol Biol Evol, 2017, 34(12): 3299-3302. doi: 10.1093/molbev/msx248 [14] ROGERS A R, HARPENDING H. Population growth makes waves in the distribution of pairwise genetic differences[J]. Mol Biol Evol, 1992, 9(3): 552-569. [15] EXCOFFIER L, LISCHER H E L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3): 564-567. doi: 10.1111/j.1755-0998.2010.02847.x [16] TAJIMA F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595. doi: 10.1093/genetics/123.3.585 [17] FU Y X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection[J]. Genetics, 1997, 147(2): 915-925. doi: 10.1093/genetics/147.2.915 [18] EXCOFFIER L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model[J]. Mol Ecol, 2004, 13(4): 853-864. doi: 10.1046/j.1365-294X.2003.02004.x [19] RAY N, CURRAT M, EXCOFFIER L. Intra-deme molecular diversity in spatially expanding populations[J]. Mol Biol Evol, 2003, 20(1): 76-86. doi: 10.1093/molbev/msg009 [20] MEIKLEJOHN C D, MONTOOTH K L, RAND D M. Positive and negative selection on the mitochondrial genome[J]. Trends Genet, 2007, 23(6): 259-263. doi: 10.1016/j.tig.2007.03.008 [21] 陈唯. 中国沿海短蛸(Octopus ocellatus)谱系地理格局与适应性分化研究[D]. 舟山: 浙江海洋大学, 2018: 38-41. [22] 刘连为, 陈新军, 许强华, 等. 基于线粒体DNA标记的阿根廷滑柔鱼2个产卵群体遗传变异分析[J]. 海洋渔业, 2014, 36(1): 16-23. doi: 10.3969/j.issn.1004-2490.2014.01.003 [23] 刘连为, 许强华, 陈新军. 基于线粒体CO I和Cyt b基因序列的北太平洋柔鱼种群遗传结构研究[J]. 水产学报, 2012, 36(11): 1675-1684. [24] LI Y, LIU C, LIN L, et al. Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution[J]. ZooKeys, 2020, 969: 137-154. doi: 10.3897/zookeys.969.52069 [25] 薛丹, 章群, 郜星晨, 等. 基于线粒体控制区的粤闽三线矶鲈地理群体的遗传变异分析[J]. 海洋渔业, 2014, 36(6): 496-502. doi: 10.3969/j.issn.1004-2490.2014.06.003 [26] 曹洋铭, 王丛丛, 徐豪, 等. 基于线粒体基因标记的中西太平洋鲣群体遗传学分析[J]. 海洋渔业, 2020, 5(9): 542-551. [27] 李敏, 黄梓荣, 许友伟, 等. 基于线粒体cytb序列的花斑蛇鲻种群遗传结构研究[J]. 南方水产科学, 2019, 15(6): 43-50. [28] LIU B L, CAO J, TRUESDELL S B, et al. Reconstructing cephalopod migration with statolith elemental signatures: a case study using Dosidicus gigas[J]. Fish Sci, 2016, 82(3): 425-433. doi: 10.1007/s12562-016-0978-8 [29] TAFUR R, VILLEGAS P, RABÍ M, et al. Dynamics of maturation, seasonality of reproduction and spawning grounds of the jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae) in Peruvian waters[J]. Fish Res, 2001, 54(1): 33-50. doi: 10.1016/S0165-7836(01)00379-4 [30] TAFUR R, KEYL F, ARGELLES J. Reproductive biology of jumbo squid Dosidicus gigas in relation to environmental variability of the northern Humboldt Current System[J]. Mar Ecol Progr Ser, 2010, 400: 127-141. doi: 10.3354/meps08386 [31] ARKHIPKIN A, ARGÜELLES J, SHCHERBICH Z, et al. Ambient temperature influences adult size and life span in jumbo squid (Dosidicus gigas)[J]. Can J Fish Aquat Sci, 2014, 72(3): 1-10. -
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