Volume 12 Issue 5
Oct.  2016
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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

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  • Received Date: October 15, 2015
  • Revised Date: November 30, 2015
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    • 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.

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  • [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.
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