Volume 12 Issue 5
Oct.  2016
Turn off MathJax
Article Contents
Abstract
References
CAO Yan, ZHANG Qun, GONG Yayun, LÜ Jinlei, YANG Xishu. Genetic variation of mtDNA COI sequence of Scomberomorus commerson populations in the South China Sea[J]. South China Fisheries Science, 2016, 12(5): 53-60. DOI: 10.3969/j.issn.2095-0780.2016.05.007
Citation: CAO Yan, ZHANG Qun, GONG Yayun, LÜ Jinlei, YANG Xishu. Genetic variation of mtDNA COI sequence of Scomberomorus commerson populations in the South China Sea[J]. South China Fisheries Science, 2016, 12(5): 53-60. DOI: 10.3969/j.issn.2095-0780.2016.05.007
shu

Genetic variation of mtDNA COI sequence of Scomberomorus commerson populations in the South China Sea

  • Department of Ecology, Jinan University, Guangzhou 510632, China

More Information
  • Received Date: October 15, 2015
  • Revised Date: November 30, 2015
    Graphical Abstract
    • Abstract

  • We analyzed 711 bp segment of the mtDNA cytochrome oxidase subunit Ⅰ of 62 individuals of Scomberomorus commerson collected from Raoping, Yangjiang in Guangdong Province and Dongxing in Guangxi Province, among which 26 mutations and 18 haplotypes were detected. Generally, the haplotype diversity (Hd=0.808±0.040) level was relatively high, while the nucleotide diversity was much poorer (π=0.004 0±0.000 6). Three shallow clades appeared in the Kimura 2-parameter based on neighbor-joining tree and parsimony network; pairwise fixation index Fst value ranged from 0.811 to 0.833 (P<0.001); gene flow ranged from 0.1 to 0.117. Analysis of molecular variance shows that the genetic variation among three clades was 82.61%, suggesting significantly high genetic differentiation. The deduced divergence time was about 890~226.7 ka BP (i.e., during the middle Pleistocene period), and the Glacial interglacial cycles in Pleistocene might be the reason of genetic differentiation. However, individuals from various locations were intertwined together in all clades; pairwise Fst (-0.027~0.066) and gene flow among sampling sites revealed no significant differentiation. AMOVA analysis shows that the percentage of population variation was 96.34%, suggesting a relatively high level of gene flow among sampling sites in the South China Sea. In Clade A, the significant negative values of neutral test and the unimodal mismatch distribution suggest a recent population expansion occurred in this clade about 890 000~226 700 years ago, due to the effects of changed living space and marine currents during Pleistocene glaciations.

    • FullText(HTML)
    • References (34)
  • [1]
    COLLETTE B B, RUSSO J L. Morphology, systematics and biology of the Spanish mackerel (Scomberomorus, Scombridae)[J]. Fish Bull, 1984, 82(4): 545-692.
    [2]
    陈再超, 刘继兴. 南海经济鱼类[M]. 广州: 广东科技出版社, 1982: 216-221.
    [3]
    FAUVELOT C, BORSA P. Patterns of genetic isolation in a widely distributed pelagic fish, the narrow-barred Spanish mackerel (Scomberomorus commerson)[J]. Biol J Linnean Soc, 2011, 104(4): 886-902. doi: 10.1111/j.1095-8312.2011.01754.x
    [4]
    LI W, CHEN X, XU Q, et al. Genetic population structure of Thunnus albacares in the Central Pacific Ocean based on mtDNA COI gene sequences[J]. Biochem Genet, 2015, 53(1/2/3): 8-22. doi: 10.1007/s10528-015-9666-0
    [5]
    KUMAR G, KUNAL S P. Historic demography and phylogenetic relationship of Euthynnus species based on COI sequence analyses[J]. Int J Bioinform Res Appl, 2013, 9(5): 547-555. doi: 10.1504/IJBRA.2013.056088
    [6]
    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
    [7]
    HOOLIHAN J P, ANANDH P, van HERWERDEN L. Mitochond-rial DNA analyses of narrow-barred Spanish mackerel (Scomberomorus commerson) suggest a single genetic stock in the ROPME sea area (Arabian Gulf, Gulf of Oman, and Arabian Sea)[J]. ICES J Mar Sci, 2006, 63(6): 1066-1074. doi: 10.1016/j.icesjms.2006.03.012
    [8]
    SULAIMAN Z H, OVENDEN J R. Population genetic evidence for the East-West division of the narrow-barred Spanish mackerel (Scomberomorus commerson, Perciformes: Teleostei) along Wallace's Line[J]. Biodivers Conserv, 2010, 19(2): 563-574. doi: 10.1007/s10531-009-9699-y
    [9]
    van HERWERDEN L, MCILWAIN J, AL-OUFI H, et al. Development and application of microsatellite markers for Scomberomorus commerson (Perciformes; Teleostei) to a population genetic study of Arabian Peninsula stocks[J]. Fish Res, 2006, 79(3): 258-266. doi: 10.1016/j.fishres.2006.04.004
    [10]
    杨炳忠, 杨吝, 谭永光, 等. 马鲛体型特征与网目尺寸关系的初步探讨[J]. 南方水产科学, 2013, 9(5): 120-125. doi: 10.3969/j.issn.2095-0780.2013.05.018
    [11]
    MULVEY M, LIU H P, KANDL K. Application of molecular genetic markers to conservation of freshwater bivalves[J]. J Shellfish Res, 1998, 17(5): 1395-1405.
    [12]
    TAKESHIMA H, IGUCHI K, NISHIDA M. Unexpected ceiling of genetic differentiation in the control region of the mitochondrial DNA between different subspecies of the Ayu Plecoglossus altivelis[J]. Zool Sci, 2005, 22(4): 401-410. doi: 10.2108/zsj.22.401
    [13]
    HEBERT P N, CYWINSKA A, BALL S L, et al. Biological identifications through DNA barcodes[J]. Proc Royal Soc London Biol Sci, 2003, 270(1512): 313-321. doi: 10.1098/rspb.2002.2218
    [14]
    WARD R D, ZEMLAK T S, INNES B H, et al. DNA barcoding Australia's fish species[J]. Philos Trans R Soc Lond B Biol Sci, 2005, 360(1462): 1847-1857. doi: 10.1098/rstb.2005.1716
    [15]
    WANG L, SHI X F, SU Y Q, et al. Genetic divergence and historical demography in the endangered large yellow croaker revealed by mtDNA[J]. Biochem Syst Ecol, 2013, 46: 137-144. doi: 10.1016/j.bse.2012.09.021
    [16]
    BENTLEY B P, HARVEY E S, NEWMAN S J, et al. Local genetic patchiness but no regional differences between Indo-West Pacific populations of the dogtooth tuna Gymnosarda unicolor[J]. Mar Ecol Prog Ser, 2014, 506: 267-277. doi: 10.3354/meps10819
    [17]
    SUN P, YIN F, SHI Z, et al. Genetic structure of Silver pomfret (Pampus argenteus (Euphrasen, 1788)) in the Arabian Sea, Bay of Bengal, and South China Sea as indicated by mitochondrial COI gene sequences[J]. J Appl Ichthyol, 2013, 29(4): 733-737. doi: 10.1111/jai.12130
    [18]
    乐小亮, 章群, 赵爽, 等. 一种高效快速的鱼类标本基因组DNA提取方法[J]. 生物技术通报, 2010(2): 202-204. https://biotech.aiijournal.com/CN/abstract/abstract5369.shtml
    [19]
    TAMURA K, STECHER G, PETERSON D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729. doi: 10.1093/molbev/mst197
    [20]
    BANDELT H J, FORSTER P, RÖHL A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol, 1999, 16(1): 37-48. doi: 10.1093/oxfordjournals.molbev.a026036
    [21]
    LIBRADO P, ROZAS J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452. doi: 10.1093/bioinformatics/btp187
    [22]
    RAMOS-ONSINS S E, ROZAS J. Statistical properties of new neutrality tests against population growth[J]. Mol Biol Evol, 2002, 19(12): 2092-2100. doi: 10.1093/oxfordjournals.molbev.a004034
    [23]
    EXCOFFIER L, LAVAL G, SCHNEIDER S. Arlequin (version 3.0): an integrated software package for population genetics data analysis[J]. Evol Bioinform Online, 2005, 1: 47-50. https://pubmed.ncbi.nlm.nih.gov/19325852/
    [24]
    KARTAVTSEV Y P, SHARINA S N, GOTO T A, et al. Sequence diversity at Cytochrome Oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights[J]. Genes Genom, 2009, 31(2): 183-197. doi: 10.1007/BF03191151
    [25]
    GRANDCOURT E M, ABDESSALAAM T, FRANCIS F, et al. Preliminary assessment of the biology and fishery for the narrow-barred Spanish mackerel, Scomberomorus commerson (Lacépède, 1800), in the southern Arabian Gulf[J]. Fish Res, 2005, 76(2): 277-290. doi: 10.1016/j.fishres.2005.07.001
    [26]
    茅晟懿, 朱小畏, 吴能友, 等. 南海北部末次冰盛期晚期以来冰融水与气候事件记录: 长链脂肪醇陆源输入指示[J]. 热带海洋学报, 2015, 34(2): 52-65. doi: 10.11978/j.issn.1009-5470.2015.02.007
    [27]
    GRANT W S, BOWEN B W. Shallow population histories in deep evolutionary linages of marine fishes: insights from sardines and anchovies and lessons for conservation[J]. J Heredity, 1998, 89(5): 415-426.
    [28]
    高天翔, 毕潇潇, 赵林林, 等. 基于线粒体Cytb基因全序列的松江鲈群体遗传结构分析[J]. 水生生物学报, 2013, 37(2): 199-207. doi: 10.7541/2013.5
    [29]
    邓春兴. 基于COI基因序列的中国东南沿海四指马鲅属鱼类的遗传多样性分析[D]. 广州: 暨南大学, 2014: 27-28.https://www.zhangqiaokeyan.com/academic-degree-domestic_mphd_thesis/020311700237.html
    [30]
    NI G, LI Q, KONG L, et al. Comparative phylogeography in marginal seas of the northwestern Pacific[J]. Mol Ecol, 2014, 23(3): 534-548. doi: 10.1111/mec.12620
    [31]
    HEWITT G. The genetic legacy of the Quaternary ice ages[J]. Nature, 2000, 405(6789): 907-913. https://www.nature.com/articles/35016000
    [32]
    薛丹, 章群, 郜星晨, 等. 基于线粒体控制区序列的南海北部近岸的遗传多样性[J]. 中国水产科学, 2015, 22(4): 749-756.
    [33]
    毕潇潇. 松江鲈(Trachidermus fasciatus)种群的形态学与遗传学研究[D]. 青岛: 中国海洋大学, 2013: 98.https://www.xueweilunwen.com/doc/560659
    [34]
    AVISE J C. Phylogeography: the history and formation of species[M]. London: London Harvard University Press, 2000: 9-32.
    • Related Articles

  • Cited by

    Periodical cited type(8)

    1. 鲁超，刘炜，马祖友，樊立静，兰旺荣，温冬，程宏，陈拥，李允，郇凤. 近岸沉积物油类紫外分光光度法检测中硫单质干扰清除研究. 环境污染与防治. 2025(02): 108-113+156 .
    2. 王赛男，许赞，刘亮，孙茜，赵文奎，王震. 一种便携式荧光测油仪在海上溢油应急监测中的适用性研究. 中国环境监测. 2023(03): 190-196 .
    3. 张婉萍，樊敏，陶伟，谌书，彭晓鹃，董燕红. 基于正定矩阵因子模型的大亚湾海域污染特征解析研究. 海洋环境科学. 2022(06): 872-880 .
    4. 刘荣林，孔小丽，王志远，孙妮，于红兵. 琼州海峡东部石油类污染特征研究. 环境科学与技术. 2021(S2): 210-215 .
    5. 刘芳，柯盛，周立喜，陈成琼，陈耀. 广东雷州珍稀海洋生物国家级自然保护区水体和沉积物中石油类含量与分布特征. 海洋开发与管理. 2020(01): 69-74 .
    6. 杨文超，黄道建，陈继鑫，陈晓燕，王宇珊，孙丽梅. 大亚湾2010—2018年表层沉积物中重金属含量时空分布及生态风险评价. 南方水产科学. 2020(04): 39-46 . 本站查看
    7. 杨文超，黄道建，陈继鑫，陈晓燕，王宇珊，孙丽梅. 大亚湾海域2009—2018年重金属时空分布及污染评价. 华南师范大学学报(自然科学版). 2020(05): 65-75 .
    8. 杨文超，黄道建，陈继鑫，陈晓燕，刘旺，王宇珊. 大亚湾石化区第2条排污管线排污口海域生态环境质量研究. 海洋学研究. 2019(04): 85-91 .

    Other cited types(5)

Catalog

    Get Citation
    PDF
    XML
    Article views PDF downloads Cited by(13)
    Related

    Supported by: Beijing Renhe Information Technology Co., Ltd.  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return