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多基因解析长江与珠江鳤的遗传结构

陈蔚涛 段辛斌 高雷 李新辉 杨计平 汪登强

陈蔚涛, 段辛斌, 高雷, 李新辉, 杨计平, 汪登强. 多基因解析长江与珠江鳤的遗传结构[J]. 南方水产科学. doi: 10.12131/20220007
引用本文: 陈蔚涛, 段辛斌, 高雷, 李新辉, 杨计平, 汪登强. 多基因解析长江与珠江鳤的遗传结构[J]. 南方水产科学. doi: 10.12131/20220007
CHEN Weitao, DUAN Xinbin, GAO Lei, LI Xinhui, YANG Jiping, WANG Dengqiang. Genetic structure analysis of Ochetobius elongatus between Yangtze River and Pearl River using multiple loci[J]. South China Fisheries Science. doi: 10.12131/20220007
Citation: CHEN Weitao, DUAN Xinbin, GAO Lei, LI Xinhui, YANG Jiping, WANG Dengqiang. Genetic structure analysis of Ochetobius elongatus between Yangtze River and Pearl River using multiple loci[J]. South China Fisheries Science. doi: 10.12131/20220007

多基因解析长江与珠江鳤的遗传结构

doi: 10.12131/20220007
基金项目: 国家重点研发计划项目 (2018YFD0900903);珠江渔业资源调查与评估创新团队项目 (2020TD10, 2020ZJTD-04)
详细信息
    作者简介:

    陈蔚涛 (1988—),男,博士,助理研究员,从事鱼类分子生态学研究。E-mail: ncuskchenweitao@163.com

    通讯作者:

    汪登强 (1973—),男,研究员,博士,从事渔业生态研究。E-mail: wdq@yfi.ac.cn

  • 中图分类号: S 932.4

Genetic structure analysis of Ochetobius elongatus between Yangtze River and Pearl River using multiple loci

  • 摘要: 通过野外调查在长江获得了7尾极濒危物种鳤 (Ochetobius elongatus) 的样本,利用Sanger测序技术测定了其2个线粒体基因 [细胞色素b (Cytb) 和酰胺腺嘌呤二核苷酸 (NADH) 脱氧酶亚单位2 (ND2)] 和2个核基因 [肌球蛋白重链6 (myh6) 和重组激活基因2 (RAG2)] 的序列,结合已公开发表的52尾珠江鳤的4个基因序列,采用系统发育分析、单倍型网状图构建、分化时间估算等方法,对珠江和长江鳤的遗传结构和分化历史展开研究。系统发育分析和单倍型网状图表明,珠江和长江鳤群体分别形成了高度分化的遗传谱系,并且在核基因水平上形成了特有的等位基因型,表明两个水系鳤群体是独立进化且不存在基因交流。分化时间估算表明珠江和长江鳤两谱系在0.38~0.76个百万年前分化,中更新世青藏高原快速隆升很可能是促进其分化的重要因素。鉴于珠江和长江的鳤群体在线粒体基因和核基因层面上存在严格的地理分化,建议将这两个群体看作不同的演化显著单位 (Evolutionary Significant Unit, ESU) 进行区别管理和保护。
  • 图  1  采样示意图

    Figure  1.  Map of sampling sites

    图  2  单倍型/等位基因中介网状图

    Figure  2.  Haplotype/allele median joining network

    图  3  基于不同基因组合的贝叶斯系统发育树

    Figure  3.  Bayesian phylogenetic trees based on different gene combinations

    图  4  基于线粒体基因组合的分化时间结果

    Figure  4.  Estimation of divergence time based on combination of two mitochondrial genes

    表  1  采样信息以及GenBank序列号

    Table  1.   Sampling information and GenBank No.

    采样站位
    Sampling site
    样本量
    Sample number
    GenBank序列号
    GenBank No.
    CytbND2myh6RAG2
    公安 Gongan7MW657590-596MW657598-604MW657606-612MW657614-620
    梧州 Wuzhou1MW657432MW657484MW657536MW657588
    桂平 Guiping1MW657431MW657483MW657535MW657587
    肇庆 Zhaoqing50MW657381-430MW657433-482MW657485-534MW657537-586
    下载: 导出CSV

    表  2  系统发育树构建和分化时间估算的最优模型

    Table  2.   Optimal model of phylogenetic tree construction and differentiation time estimation

    基因组合
    Gene combination
    最优模型
    Optimal model
    不变位点比例
    Proportion of invariable site
    Gamma分布形状参数
    Gamma distribution shape parameter
    Cytb+ND2GTR+I+G0.4740.986
    myh6+RAG2K80+I0.881
    Cytb+ND2+myh6+RAG2GTR+I+G0.6970.857
    下载: 导出CSV

    表  3  鳤种群的单倍型与遗传多样性指数

    Table  3.   Haplotypes and genetic diversity indexes of O. elongatus populations

    基因组合
    Gene combination
    水系
    River system
    序列数
    Sequence number
    单倍型数
    Haplotype number
    单倍型多样性
    Haplotype diversity
    核苷酸多样性
    Nucleotide diversity/%
    Cytb+ND2珠江52260.940±0.0170.219±0.020
    长江730.714±0.1270.187±0.003
    合计59290.950±0.0140.494±0.080
    myh6+RAG2珠江10450.546±0.0500.040±0.006
    长江1480.923±0.0440.135±0.021
    合计118130.643±0.0360.071±0.009
    下载: 导出CSV
  • [1] 乐佩琦. 中国动物志. 硬骨鱼纲. 鲤形目. 中卷[M]. 北京: 科学出版社, 2000: 1-531.
    [2] 周解, 张春光. 广西淡水鱼类志[M]. 南宁: 广西人民出版社, 2006: 1-535.
    [3] 郑慈英. 珠江鱼类志[M]. 北京: 科学出版社, 1989: 1-438.
    [4] 李捷, 李新辉, 贾晓平, 等. 西江鱼类群落多样性及其演变[J]. 中国水产科学, 2010, 17(2): 298-311.
    [5] 范凤娟, 章群. 汩罗江与柳江鳤鱼线粒体细胞色素b基因的遗传变异初探[J]. 生态科学, 2009, 28(5): 457-459. doi: 10.3969/j.issn.1008-8873.2009.05.015
    [6] 蒋志刚, 江建平, 王跃招, 等. 中国脊椎动物红色名录[J]. 生物多样性, 2016, 24(5): 500-551. doi: 10.17520/biods.2016076
    [7] WANG X, LI J, HE S. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences[J]. Mol phylogenet Evol, 2007, 42(1): 157-170. doi: 10.1016/j.ympev.2006.06.014
    [8] TAO W, ZOU M, WANG X, et al. Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes)[J]. PLoS One, 2010, 5(10): e13508. doi: 10.1371/journal.pone.0013508
    [9] 杨计平, 李策, 陈蔚涛, 等. 西江中下游鳤的遗传多样性与种群动态历史[J]. 生物多样性, 2018, 26(12): 1289-1295. doi: 10.17520/biods.2018121
    [10] XING Y, ZHANG C, FAN E, et al. Freshwater fishes of China: species richness, endemism, threatened species and conservation[J]. Divers Distrib, 2016, 22(3): 358-370. doi: 10.1111/ddi.12399
    [11] YANG L, MAYDEN R L, HE S. Population genetic structure and geographical differentiation of the Chinese catfish Hemibagrus macropterus (Siluriformes, Bagridae): evidence for altered drainage patterns[J]. Mol phylogenet Evol, 2009, 51(2): 405-411. doi: 10.1016/j.ympev.2009.01.004
    [12] PERDICES A, CUNHA C, COELHO M M. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (=Yangtze) drainage inferred from cytochrome b sequences[J]. Mol phylogenet Evol, 2004, 31(1): 192-203. doi: 10.1016/j.ympev.2003.07.001
    [13] PERDICES A, SAYANDA D, COELHO M M. Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages[J]. Mol Phylogenet Evol, 2005, 37(3): 920-927. doi: 10.1016/j.ympev.2005.04.020
    [14] EDGAR R C. MUSCLE: multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Res, 2004, 32(5): 1792-1797. doi: 10.1093/nar/gkh340
    [15] ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Mol Biol Evol, 2017, 34(12): 3299-3302. doi: 10.1093/molbev/msx248
    [16] BANDELT H J, FORSTER P, ROHL A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol, 1999, 16(1): 37-48. doi: 10.1093/oxfordjournals.molbev.a026036
    [17] RONQUIST F, TESLENKO M, van der MARK P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[J]. Syst Biol, 2012, 61(3): 539-542. doi: 10.1093/sysbio/sys029
    [18] NYLANDER J. MrModeltest v2. Program distributed by the author (ed. Nylander JAA)[M]. Uppsala: Evolutionary Biology Centre, Uppsala University, 2004: 1-2.
    [19] KIMURA M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. J Mol Evol, 1980, 16(2): 111-120. doi: 10.1007/BF01731581
    [20] 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
    [21] DRUMMOND A J, RAMBAUT A. BEAST: Bayesian evolutionary analysis by sampling trees[J]. BMC Evol Biol, 2007, 7: 214. doi: 10.1186/1471-2148-7-214
    [22] DURAND J D, TSIGENOPOULOS C S, UNLU E, et al. Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA: evolutionary significance of this region[J]. Mol Phylogenet Evol, 2002, 25(1): 218-218. doi: 10.1016/S1055-7903(02)00343-3
    [23] KETMAIER V, BIANCO P G, COBOLLIA M et al. Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data[J]. Mol Phylogenet Evol, 2004, 32(3): 1061-1071. doi: 10.1016/j.ympev.2004.04.008
    [24] MEYER A. Evolution of mitochondrial DNA in fishes[M]. The Hague: Elsevier, 1993: 1-38.
    [25] RAMBAUT A, DRUMMOND A J. Tracer v1. 4[DB/OL]. http://beast.bio.ed.ac.uk/Tracer, 2007.
    [26] CHEN W, ZHONG Z, DAI W, et al. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China[J]. BMC Evol Biol, 2017, 17(1): 216. doi: 10.1186/s12862-017-1058-0
    [27] LI G Y, WANG X Z, ZHAO Y H, et al. Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations[J]. Zool Stud, 2009, 48(4): 569-583.
    [28] 朱叶. 基于线粒体细胞色素b的3江水系草鱼群体遗传多样性分析[D]. 广州: 暨南大学, 2012: 1-54.
    [29] 付晓艳. 长江和珠江水系青鱼线粒体细胞色素b基因遗传多样性分析[D]. 广州: 暨南大学, 2011: 1-42.
    [30] LI C, WANG J, CHEN J, et al. Native bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix populations in the Pearl River are threatened by Yangtze River introductions as revealed by mitochondrial DNA[J]. J Fish Biol, 2020, 96(3): 651-662. doi: 10.1111/jfb.14253
    [31] 任美锷, 包浩生, 韩同春, 等. 云南西北部金沙江河谷地貌与河流袭夺问题[J]. 地理学报, 1959, 26(2): 135-155. doi: 10.11821/xb195902003
    [32] YAP S Y. On the Distributional patterns of southeast-east Asian freshwater fish and their history[J]. J Biogeogr, 2002, 29(9): 1187-1199. doi: 10.1046/j.1365-2699.2002.00771.x
    [33] 张荣祖. 中国动物地理[M]. 北京: 科学出版社, 1999: 1-502.
    [34] DUFRESNES C, NICIEZA A G, LITVINCHUK S N, et al. Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs[J]. Mol Ecol, 2020, 29(5): 986-1000. doi: 10.1111/mec.15368
    [35] RINCÓN-SANDOVAL M, BETANCUR R R, OCAMPO J A M. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers[J]. Mol Ecol, 2019, 28(5): 1096-1115. doi: 10.1111/mec.15036
    [36] 李吉均, 方小敏. 青藏高原隆起与环境变化研究[J]. 科学通报, 1998, 43(15): 1568-1574.
    [37] 李吉均, 方小敏, 潘保田, 等. 新生代晚期青藏高原强烈隆起及其对周边环境的影响[J]. 第四纪研究, 2001, 21(5): 381-391. doi: 10.3321/j.issn:1001-7410.2001.05.001
    [38] HE D K, CHEN Y F. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences[J]. J Biogeogr, 2006, 33(8): 1448-1460. doi: 10.1111/j.1365-2699.2006.01510.x
    [39] YANG J, YANG J X, CHEN X Y. A re-examination of the molecular phylogeny and biogeography of the genus Schizothorax (Teleostei: Cyprinidae) through enhanced sampling, with emphasis on the species in the Yunnan-Guizhou Plateau, China[J]. J Zool Syst Evol Res, 2012, 50(3): 184-191. doi: 10.1111/j.1439-0469.2012.00661.x
    [40] 曹文宣, 陈宜瑜, 武云飞, 等. 裂腹鱼类的起源和演化及其与青藏高原隆起的关系[M]. 北京: 科学出版社; 1981: 118-130.
    [41] 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): 41-48. doi: 10.12131/20190123
    [42] 徐豪, 梁绪虹, 王丛丛, 等. 基于线粒体NADH脱氢酶亚基2标记的东南太平洋不同表型间茎柔鱼群体遗传学分析[J]. 南方水产科学, 2022, 18(1): 153-159. doi: 10.12131/20210119
    [43] RYDER O A. Species conservation and systematics: the dilemma of subspecies[J]. Trends Ecol Evol, 1986, 1: 9-10. doi: 10.1016/0169-5347(86)90059-5
    [44] MORITZ C. Defining 'Evolutionarily Significant Units' for conservation[J]. Trends Ecol Evol, 1994, 9(10): 373-375. doi: 10.1016/0169-5347(94)90057-4
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  • 收稿日期:  2022-01-10
  • 修回日期:  2022-02-20
  • 录用日期:  2022-03-28
  • 网络出版日期:  2022-04-15

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