基于线粒体COⅠ序列的中国前鳞(鱼夋)遗传多样性分析
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摘要
前鳞(鱼夋)(Liza affinis)是分布于西北太平洋的日本南部及中国台湾海域等的经济鱼类。为了解中国前鳞(鱼夋)的遗传背景,该研究分析了采自中国4省82尾样本COⅠ基因5'端712 bp序列,共发现21个单倍型,遗传多样性(H_d=0.4840±0.0700,π=0.0010±0.0002)较低。根据群体所属的地区、海域、海峡进行分组,通过AMOVA分析,得出组间的Fst值皆小于0.05,P值皆大于0.05,组间变异的比例极低(–0.6%～0.46%),表明中国前鳞(鱼夋)群体间无明显分化,其原因可能是:1)频繁的基因交流。前鳞(鱼夋)的洄游范围较大,且受海流影响,导致不同地区的群体间有着密切的基因交流;2)近期种群扩张事件。中国前鳞(鱼夋)整体的Fu’s F_s值为显著性负值(F_S=–20.3900,P=0),核苷酸错配峰图为明显单峰,单倍型网络图呈星状结构,均表明中国前鳞(鱼夋)群体经历过种群扩张,估算扩张大约发生在13.4199～1.4911万年前,可能是冰期和间冰期的交替中海平面的变化所致。此外,洞头群体的遗传多样性(H_d=0.8080±0.1130,π=0.0021±0.0006)明显高于其他地理群体,建议将其作为优先保护的对象。
To assess the genetic background of Liza affinis in the coastal waters of China, the sequence variation in 712 bp of the partial mitochondrial DNA COⅠgene of 84 individuals from 4 provinces was analyzed. In total, 18 polymorphic sites defined 21 haplotypes and low levels of genetic diversity(H_d = 0.8230±0.0400, π=0.0023±0.0002) were detected. Individuals from different sites were intertwined together in the parsimony network, suggesting no geographical clustering. AMOVA analysis of various groupings(sampling sites, seas, division of the Taiwan Strait and Qiongzhou Strait) detected no significant genetic differentiation, as evidenced by pairwise fixation indexes(F_(st) = –0.1940～0.0141, P > 0.05), and the percentage of variation(–0.6%～0.46%) among groups. In the SAMOVA analysis, the Dongtou population was treated as one group, and the others were treated as another group; the percentage of variation among groups was 2.87%, congruent with the results of F_(st) and AMOVA analysis. The pattern of no lineage structure and no obvious genetic differentiation in L. affinis populations in coastal waters of China might have been caused by: 1) Passive transport of larvae and juveniles by marine currents, or active feeding migration and spawning aggregation of adults. 2) Recent population expansion. Significant negative Fu's Fs for all populations(FS = –20.3900, P = 0), and obvious unimodal nucleotide mismatch distribution suggested that L. affinis in coastal waters of China had experienced population expansion and the deduced expansion time was approximately 134.199～14.911 kaBP; i.e., in the late Pleistocene, which might have been caused by the rise and fall of sea-levels with dramatic climatic changes during glacial-interglacial cycles. The Dongtou population should be given priority protection as it has the highest genetic diversity(H_d = 0.8080±0.1130, π = 0.0021±0.0006) among the populations that were studied. Because the study only involved limited L. affinis populations in China, COⅠ might be a more conservative molecular marker than evolutionarily faster control region. Furthermore, maternally inherited mtDNA is independent of nuclear inheritance, and may not completely represent the evolutionary history of a species. Thus, future studies should incorporate more sampling sites across the species range using both nuclear and mtDNA markers together. A better understanding of the genetic background of L. affinis will provide a sound scientific basis for the preservation and sustainable utilization of its germplasm resources.
To assess the genetic background of Liza affinis in the coastal waters of China, the sequence variation in 712 bp of the partial mitochondrial DNA COⅠgene of 84 individuals from 4 provinces was analyzed. In total, 18 polymorphic sites defined 21 haplotypes and low levels of genetic diversity(H_d = 0.8230±0.0400, π=0.0023±0.0002) were detected. Individuals from different sites were intertwined together in the parsimony network, suggesting no geographical clustering. AMOVA analysis of various groupings(sampling sites, seas, division of the Taiwan Strait and Qiongzhou Strait) detected no significant genetic differentiation, as evidenced by pairwise fixation indexes(F_(st) = –0.1940～0.0141, P > 0.05), and the percentage of variation(–0.6%～0.46%) among groups. In the SAMOVA analysis, the Dongtou population was treated as one group, and the others were treated as another group; the percentage of variation among groups was 2.87%, congruent with the results of F_(st) and AMOVA analysis. The pattern of no lineage structure and no obvious genetic differentiation in L. affinis populations in coastal waters of China might have been caused by: 1) Passive transport of larvae and juveniles by marine currents, or active feeding migration and spawning aggregation of adults. 2) Recent population expansion. Significant negative Fu's Fs for all populations(FS = –20.3900, P = 0), and obvious unimodal nucleotide mismatch distribution suggested that L. affinis in coastal waters of China had experienced population expansion and the deduced expansion time was approximately 134.199～14.911 kaBP; i.e., in the late Pleistocene, which might have been caused by the rise and fall of sea-levels with dramatic climatic changes during glacial-interglacial cycles. The Dongtou population should be given priority protection as it has the highest genetic diversity(H_d = 0.8080±0.1130, π = 0.0021±0.0006) among the populations that were studied. Because the study only involved limited L. affinis populations in China, COⅠ might be a more conservative molecular marker than evolutionarily faster control region. Furthermore, maternally inherited mtDNA is independent of nuclear inheritance, and may not completely represent the evolutionary history of a species. Thus, future studies should incorporate more sampling sites across the species range using both nuclear and mtDNA markers together. A better understanding of the genetic background of L. affinis will provide a sound scientific basis for the preservation and sustainable utilization of its germplasm resources.
引文
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Ju HL.Studies on the decrement of fishery resource in the South China Sea.Southeast Asian Studies,2012(6):51-55[鞠海龙.南海渔业资源衰减相关问题研究.东南亚研究,2012(6):51-55]
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Meng W,Gao TX,Song L,et al.almost periodic solution of ordinary differential equations.Periodical of Ocean University of China,2007,37(supp):181-184[孟玮,高天翔,宋林,等.三种鲻科鱼的同工酶分析及鉴别研究.中国海洋大学学报,2007,37(supp):181-184]
Nakajima K,Kitada S,Habara Y,et al.Genetic effects of marine stock enhancement:A case study based on the highly piscivorous Japanese spanish mackerel.Canadian Journal of Fisheries and Aquatic Sciences,2014,71(71):301-314
Ni G,Li QI,Kong L,et al.Comparative phylogeography in marginal seas of the northwestern Pacific.Molecular Ecology,2014,23(3):534-548
Qian GY.Sex and artificial control of fish.Chinese Journal of Zoology,2000,35(1):47-52[钱国英.鱼类的性别及人工控制.动物学杂志,2000,35(1):47-52]
Richardson N,Gordon AK,Muller WJ,et al.A weight-ofevidence approach to determine estuarine fish health using indicators from multiple levels of biological organization.Aquatic Conservation Marine&Freshwater Ecosystems,2011,21(5):423-432
Rogers AR,Harpending H.Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,1992,9(3):52-69
Shi Q,Fan MJ,Zhang Y.Economically important fishes in China.Wuhan:Huazhong University of Science and Technology Press,2015:360-363[石琼,范明君,张勇.中国经济鱼类志.武汉:华中科技大学出版社,2015:360-363]
Stirling CH,Esat TM,Mcculloch MT,et al.High-precision U-series dating of corals from Western Australia and implications for the timing and duration of the last interglacial.Earth&Planetary Science Letters,1995,135(1):115-130
Sun DR,Chen Z.Fish index in the South China Sea(Volume I).Beijing:China Ocean Press,2013,375-377[孙典荣,陈铮.南海鱼类检索(上册).北京:海洋出版社,2013,375-377]
Wang L,Shi X,Su Y,et al.Genetic divergence and historical demography in the endangered large yellow croaker revealed by mtDNA.Biochemical Systematics and Ecology,2013,46(46):137-144
Wang P.Response of Western Pacific marginal seas to glacial cycles:Paleoceanographic and sedimentological features 1.Marine Geology,1999,156(1-4):5-39
Ward RD.Genetics in fisheries management.Hydrobiologia,2000,420(1):191-201
Winograd IJ,Landwehr JM,Ludwig KR,et al.Duration and structure of the past four interglaciations.Quaternary Research,1997,48(2):141-154
Xu D,Lou B,Shi H,et al.Genetic diversity and population structure of Nibea albiflora,in the China Sea revealed by mitochondrial COⅠsequences.Biochemical Systematics and Ecology,2012,45(12):158-165
Xu H,Zhang Y,Xu D,et al.Genetic population structure of miiuy croaker(Miichthys miiuy)in the yellow and east china seas base on mitochondrial COⅠsequences.Biochemical Systematics&Ecology,2014,54(1):240-246
Xu ZT.Molecular identification and phylogeny of larval mugilids in Zhejiang coastal sea.Master′s Thesis of Zhejiang Ocean University,2015,1-68[许则滩.浙江沿岸海域幼鱼期鲻科鱼类的分子鉴定和系统发育研究.浙江海洋学院硕士研究生学位论文,2015,1-68]
Yang XS,Zhang Q,Yu FY,et al.MtDNA ND2 sequence-based genetic analysis of Anabas testudineus from South China and Lancang/Meko,South China Fisheries Science,2017,13(3):43-50[杨喜书,章群,余帆洋,等.华南6水系与澜沧江-湄公河攀鲈线粒体ND2基因的遗传多样性分析.南方水产科学,2017,13(3):43-50]
Bonin A,Nicole F,Pompanon F,et al.Population adaptive index:A new method to help measure intraspecific genetic diversity and prioritize populations for conservation.Conservation Biology,2010,21(3):697-708
Cao Y,Zhang Q,Gong YY,et al.Genetic variation of Scomberomorus niphonius in the coastal waters of China based on mt DNA COⅠsequences.Marine Fisheries,2015,37(6):485-493[曹艳,章群,宫亚运,等.基于线粒体COⅠ序列的中国沿海蓝点马鲛遗传多样性.海洋渔业,2015,37(6):485-493]
Chang CH,Lin HY,Ren Q,et al.DNA barcode identification of fish products in Taiwan:Government-commissioned authentication cases.Food Control,2016,66:38-43
Excoffier L,Lischer H.Arlequin suite Ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,2010,10(3):564-567
Ju HL.Studies on the decrement of fishery resource in the South China Sea.Southeast Asian Studies,2012(6):51-55[鞠海龙.南海渔业资源衰减相关问题研究.东南亚研究,2012(6):51-55]
Kumar S,Stecher G,Tamura K.MEGA7:Molecular evolutionary genetics analysis Version 7.0 for bigger datasets.Molecular Biology and Evolution,2016,33(7):54-58
Kumar S.Molecular clocks:Four decades of evolution.Nature Reviews Genetics,2005,6(8):654-662
Le XL,Zhang Q,Zhao S,et al.A fast and efficient method for isolation of genomic DNA from fish specimens.Biotechnology Bulletin,2010,20(2):202-204[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.生物技术通报,2010,20(2):202-204]
Lesica P,Allendorf FW.When are peripheral populations valuable for conservation?Conservation Biology,1995,9(4):753-760
Li DM,Zhang TQ,Tang SK,et al.Genetic variation in two phenotypical populations of Corbicula fluminea in Hongze Lake.Progress in Fishery Sciences,2017,38(4):111-117[李大命,张彤晴,唐晟凯,等.洪泽湖河蚬(Corbicula fluminea)2种表型群体的遗传变异分析.渔业科学进展,2017,38(4):111-117]
Li S.Population genetics studies on four species of Crassostrea oysters.Master′s Thesis of Ocean University of China,2015,1-103[李双.四种巨蛎属牡蛎群体遗传学研究.中国海洋大学硕士研究生学位论文,2015,1-103]
Librado P,Rozas J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data.Bioinformatics,2009,25(11):1451-1452
Lin HJ,Shao KT,Kuo SR,et al.A trophic model of a sandy barrier lagoon at Chiku in Southwestern Taiwan.Estuarine Coastal and Shelf Science,1999,48(5):575-588
Liu JQ,Wang WY.Quaternary geological dating and time scale.Quaternary Sciences,1997,17(3):193-202[刘嘉麒,王文远.第四纪地质定年与地质年表.第四纪研究,1997,17(3):193-202]
Liu SF,Li XR,Li D,et al.Development of DNAbarcode-microarray for identification of Engraulidae fishes.Progress in Fishery Sciences,2016,37(6):19-25[柳淑芳,李献儒,李达,等.鳀科(Engraulidae)鱼类DNA条形码电子芯片研究.渔业科学进展,2016,37(6):19-25]
Lu ZK.Studies on the reproductive ecology of Mugilidae.Journal of Zhejiang Ocean University,1985,4(1):67-72[陆忠康.关于鲻科鱼类繁殖生态学的研究.浙江海洋学院学报,1985,4(1):67-72]
Meng W,Gao TX,Song L,et al.almost periodic solution of ordinary differential equations.Periodical of Ocean University of China,2007,37(supp):181-184[孟玮,高天翔,宋林,等.三种鲻科鱼的同工酶分析及鉴别研究.中国海洋大学学报,2007,37(supp):181-184]
Nakajima K,Kitada S,Habara Y,et al.Genetic effects of marine stock enhancement:A case study based on the highly piscivorous Japanese spanish mackerel.Canadian Journal of Fisheries and Aquatic Sciences,2014,71(71):301-314
Ni G,Li QI,Kong L,et al.Comparative phylogeography in marginal seas of the northwestern Pacific.Molecular Ecology,2014,23(3):534-548
Qian GY.Sex and artificial control of fish.Chinese Journal of Zoology,2000,35(1):47-52[钱国英.鱼类的性别及人工控制.动物学杂志,2000,35(1):47-52]
Richardson N,Gordon AK,Muller WJ,et al.A weight-ofevidence approach to determine estuarine fish health using indicators from multiple levels of biological organization.Aquatic Conservation Marine&Freshwater Ecosystems,2011,21(5):423-432
Rogers AR,Harpending H.Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,1992,9(3):52-69
Shi Q,Fan MJ,Zhang Y.Economically important fishes in China.Wuhan:Huazhong University of Science and Technology Press,2015:360-363[石琼,范明君,张勇.中国经济鱼类志.武汉:华中科技大学出版社,2015:360-363]
Stirling CH,Esat TM,Mcculloch MT,et al.High-precision U-series dating of corals from Western Australia and implications for the timing and duration of the last interglacial.Earth&Planetary Science Letters,1995,135(1):115-130
Sun DR,Chen Z.Fish index in the South China Sea(Volume I).Beijing:China Ocean Press,2013,375-377[孙典荣,陈铮.南海鱼类检索(上册).北京:海洋出版社,2013,375-377]
Wang L,Shi X,Su Y,et al.Genetic divergence and historical demography in the endangered large yellow croaker revealed by mtDNA.Biochemical Systematics and Ecology,2013,46(46):137-144
Wang P.Response of Western Pacific marginal seas to glacial cycles:Paleoceanographic and sedimentological features 1.Marine Geology,1999,156(1-4):5-39
Ward RD.Genetics in fisheries management.Hydrobiologia,2000,420(1):191-201
Winograd IJ,Landwehr JM,Ludwig KR,et al.Duration and structure of the past four interglaciations.Quaternary Research,1997,48(2):141-154
Xu D,Lou B,Shi H,et al.Genetic diversity and population structure of Nibea albiflora,in the China Sea revealed by mitochondrial COⅠsequences.Biochemical Systematics and Ecology,2012,45(12):158-165
Xu H,Zhang Y,Xu D,et al.Genetic population structure of miiuy croaker(Miichthys miiuy)in the yellow and east china seas base on mitochondrial COⅠsequences.Biochemical Systematics&Ecology,2014,54(1):240-246
Xu ZT.Molecular identification and phylogeny of larval mugilids in Zhejiang coastal sea.Master′s Thesis of Zhejiang Ocean University,2015,1-68[许则滩.浙江沿岸海域幼鱼期鲻科鱼类的分子鉴定和系统发育研究.浙江海洋学院硕士研究生学位论文,2015,1-68]
Yang XS,Zhang Q,Yu FY,et al.MtDNA ND2 sequence-based genetic analysis of Anabas testudineus from South China and Lancang/Meko,South China Fisheries Science,2017,13(3):43-50[杨喜书,章群,余帆洋,等.华南6水系与澜沧江-湄公河攀鲈线粒体ND2基因的遗传多样性分析.南方水产科学,2017,13(3):43-50]