西江中下游鳤的遗传多样性与种群动态历史
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摘要
鳤(Ochetobius elongatus)曾经是我国许多河流的重要经济鱼类,然而由于环境污染和人为干扰等原因,鳤的资源量萎缩严重,种群处于极度濒危的境地。目前,常规采样方法获得鳤样本的难度较大,致使相关研究难以开展。本研究通过仔鱼采集和成鱼采集的手段,测定两个线粒体基因和两个核基因,对西江中下游鳤的遗传多样性和种群动态历史进行研究。结果显示,西江中下游鳤的遗传多样性处于较低水平并且出现了衰退的迹象,可能经历了遗传瓶颈效应。此外,种群动态历史分析发现,西江中下游鳤在后更新世期间(0.06和0.13百万年前)经历了种群扩张,刚好处于中更新世(0.78–0.126百万年前)冰期褪去之后,表明更新世气候的波动影响了西江中下游鳤的种群动态。作为鳤可能的重要产卵场,西江中下游部分江段可以考虑建立鳤的自然保护区,用于保育和修复鳤的种质资源。
Ochetobius elongatus used to be an economically important fish species in many rivers of China. However, due to environmental destruction and human disturbance the resources of this fish species have reduced rapidly, and its populations are in a critically endangered condition. At present, it is very difficult to obtain specimens of O. elongatus, which limits research on this species. We obtained specimens of O. elongatus via larva and adult fish collection. Two mitochondrial genes and two nuclear genes were used to explore the genetic diversity and population demography of O. elongatus in middle and lower Xijiang River. Results showed that the genetic diversity of O. elongatus was low and is in recession, suggesting that O. elongatus might have undergone a genetic bottleneck event. Additionally, population demographic analyses revealed that O. elongatus population expanded during the Late Pleistocene(0.06 and 0.13 Million years ago), following the glacial retreat of the Middle Pleistocene glaciations(0.78–0.126 Million years ago). The results also revealed that Pleistocene climatic fluctuations have influenced the population demography of O. elongatus. Due to its potential as an important spawning ground for O. elongatus, sections of middle and lower Xijiang River should be considered as candidates for creating nature reserves to conserve and restore its genetic resources.
Ochetobius elongatus used to be an economically important fish species in many rivers of China. However, due to environmental destruction and human disturbance the resources of this fish species have reduced rapidly, and its populations are in a critically endangered condition. At present, it is very difficult to obtain specimens of O. elongatus, which limits research on this species. We obtained specimens of O. elongatus via larva and adult fish collection. Two mitochondrial genes and two nuclear genes were used to explore the genetic diversity and population demography of O. elongatus in middle and lower Xijiang River. Results showed that the genetic diversity of O. elongatus was low and is in recession, suggesting that O. elongatus might have undergone a genetic bottleneck event. Additionally, population demographic analyses revealed that O. elongatus population expanded during the Late Pleistocene(0.06 and 0.13 Million years ago), following the glacial retreat of the Middle Pleistocene glaciations(0.78–0.126 Million years ago). The results also revealed that Pleistocene climatic fluctuations have influenced the population demography of O. elongatus. Due to its potential as an important spawning ground for O. elongatus, sections of middle and lower Xijiang River should be considered as candidates for creating nature reserves to conserve and restore its genetic resources.
引文
Araujo-Lima CARM,Oliveira EC(1998)Transport of larval fish in the Amazon.Journal of Fish Biology,53,297-306.
Bandelt HJ,Forster P,Rohl A(1999)Median-joining networks for inferring intraspecific phylogenies.Molecular Biology and Evolution,16,37-48.
Chen WJ,Miya M,Saitoh K,Mayden RL(2008)Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes:The order Cypriniformes(Ostariophysi)as a case study.Gene,423,125-134.
Chen YY,Cao WX,Zheng CY(1986)Ichthyofauna of the Zhujiang River with a discussion on zoogeographical divisions for freshwater fishes.Acta Hydrobiologica Sinica,10,228-234.(in Chinese with English abstract)[陈宜瑜,曹文宣,郑慈英(1986)珠江的鱼类区系及其动物地理区划的讨论.水生生物学报,10,228-234.]
Drummond AJ,Rambaut A(2007)BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7,214.
Drummond AJ,Rambaut A,Shapiro B,Pybus OG(2005)Bayesian coalescent inference of past population dynamics from molecular sequences.Molecular Biology and Evolution,22,1185-1192.
Durand JD,Tsigenopoulos CS,Unlu E,Berrebi P(2002)Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA-Evolutionary significance of this region.Molecular Phylogenetics and Evolution,25,91-100.
Edgar RC(2004)MUSCLE:Multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research,32,1792-1797.
Excoffier L,Lischer HEL(2010)Arlequin suite ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10,564-567.
Fu YX(1997)Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection.Genetics,147,915-925.
Gascoyne M,Benjamin GJ,Schwarcz HP,Ford DC(1979)Sea-level lowering during the Illinoian glaciation:Evidence from a Bahama“blue hole”.Science,205,806-808.
Grant WS,Bowen BW(1998)Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation.Journal of Heredity,89,415-426.
Hewitt GM(2004)Genetic consequences of climatic oscillations in the Quaternary.Philosophical Transactions of the Royal Society B-Biological Sciences,359,183-195.
Jiang ZG,Jiang JP,Wang YZ,Zhang E,Zhang YY,Li LL,Xie F,Cai B,Cao L,Zheng GM,Dong L,Zhang ZW,Ding P,Luo ZH,Ding CQ,Ma ZJ,Tang SH,Cao WX,Li CW,Hu HJ,Ma Y,Wu Y,Wang YX,Zhou KY,Liu SY,Chen YY,Li JT,Feng ZJ,Wang Y,Wang B,Li C,Song XL,Cai L,Zang CX,Zeng Y,Meng ZB,Fang HX,Ping XG(2016)Red List of China’s Vertebrates.Biodiversidy Science,24,500-551.[蒋志刚,江建平,王跃招,张鹗,张雁云,李立立,谢锋,蔡波,曹亮,郑光美,董路,张正旺,丁平,罗振华,丁长青,马志军,汤宋华,曹文宣,李春旺,胡慧建,马勇,吴毅,王应祥,周开亚,刘少英,陈跃英,李家堂冯祚建,王燕,王斌,李成,宋雪琳,蔡蕾,臧春鑫,曾岩,孟智斌,方红霞,平晓鸽(2016)中国脊椎动物红色名录.生物多样性,24,500-551.]
Ketmaier V,Bianco PG,Cobollia M,Krivokapic M,Caniglia R,De Matthaeis E(2004)Molecular phylogeny of two lineages of Leuciscinae cyprinids(Telestes and Scardinius)from the peri-Mediterranean area based on cytochrome b data.Molecular Phylogenetics and Evolution,32,1061-1071.
Li J,Li XH,Jia XP,Li YF,He MF,Tan XC,Wang C,Jiang WX(2010)Evolvement and diversity of fish community in Xijiang River.Journal of Fishery Sciences of China,17,298-311.(in Chinese with English abstract)[李捷,李新辉,贾晓平,李跃飞,何美峰,谭细畅,王超,蒋万祥(2010)西江鱼类群落多样性及其演变.中国水产科学,17,298-311.]
Li SF,LüGQ,Bernatchez L(1998)Diversity of mitochondrial DNA in the populations of silver carp,bighead carp,grass carp and black carp in the middle-and lower reaches of the Yangtze River.Acta Zoologica Sinica,44,82-93.(in Chinese with English abstract)[李思发,吕国庆,Bernatchez L(1998)长江中下游鲢鳙草青四大家鱼线粒体DNA多样性分析.动物学报,44,82-93.]
Li YF,Li XH,Tan XC,Li J,Wang C(2012)Occurrence of larval Elopichthys bambusa and its relationship with hydrological conditions in the middle and lower reaches of Pearl River.Journal of Fisheries of China,36(4),15-22.(in Chinese with English abstract)[李跃飞,李新辉,谭细畅,李捷,王超(2012)珠江中下游鳡鱼苗的发生及其与水文环境的关系.水产学报,36,15-22.]
Liang ZS,Mo RL,Chen FC(1985)Species identification and spawning type of common fish species in Xijiang River during early phase.In:The Report of Fishery Research in Pearl River Basin.Compilation Committee of Fishery Resources Survey of Pearl River Basin,Guangzhou.(in Chinese)[梁秩燊,莫瑞林,陈福才(1985)西江常见鱼类早期发育的分类鉴定及其产卵类型.见:珠江水系渔业资源调查研究报告.珠江水系渔业资源调查编委会,广州.]
Librado P,Rozas J(2009)Dna SP v5:A software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25,1451-1452.
Lovejoy NR,Collette BB(2001)Phylogenetic relationships of new world needlefishes(Teleostei:Belonidae)and the biogeography of transitions between marine and freshwater habitats.Copeia,2001,324-338.
Meyer A(1993)Evolution of Mitochondrial DNA in Fishes.Elsevier,The Hague.
Nesler TP,Muth RT,Wasowicz AF(1988)Evidence for baseline flow spikes as spawning cues for Colorado squawfish in the Yampa River,Colorado.In:American Fisheries Society Symposium,pp.68-79.Bethesda,Maryland.
Nylander JAA(2004)MrModeltest v2.Evolutionary Biology Centre,Uppsala University,Uppsala.
Rambaut A,Drummond A(2007)Tracer v1.4.http://beast.bio.ed.ac.uk/Tracer.(accessed on 2018-3-2).
Rogers AR,Harpending H(1992)Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,9,552-569.
Tajima F(1989)The effect of change in population size on DNA polymorphism.Genetics,123,597-601.
Tao W,Zou M,Wang X,Gan X,Mayden RL,He S(2010)Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae(Cypriniformes).PLoS ONE,5,e13508.
Tyus HM,Haines GB(1991)Distribution,habitat use,and growth of age-0 Colorado squawfish in the Green River basin,Colorado and Utah.Transactions of the American Fisheries Society,120,79-89.
Wang X,Li J,He S(2007)Molecular evidence for the monophyly of East Asian groups of Cyprinidae(Teleostei:Cypriniformes)derived from the nuclear recombination activating gene 2 sequences.Molecular Phylogenetics and Evolution,42,157-170.
Wu WJ,Peng M,Wang DP,Shi J,Li YS,Han YQ,Lei JJ,He AY(2015)Comparison of mitochondrial D-Loop and Cyt b sequences of Hypophthalmichthys molitrix.Open Journal of Fisheries Research,2(4),67-73.(in Chinese with English abstract)[吴伟军,彭敏,王大鹏,施军,李育森,韩耀全,雷建军,何安尤(2015)红水河鲢线粒体D-Loop和Cyt b基因序列分析.水产研究,2(4),67-73.]
Xiao W,Zhang Y,Liu H(2001)Molecular systematics of Xenocyprinae(Teleostei:Cyprinidae):Taxonomy,biogeography,and coevolution of a special group restricted in East Asia.Molecular Phylogenetics and Evolution,18,163-173.
Yue PQ(2000)Fauna Sinica,Osteichthyes,Cypriniformes IIScience Press,Beijing.(in Chinese)[乐佩琦(2000)中国动物志.硬骨鱼纲,鲤形目,中卷.科学出版社,北京.]
Zheng CY(1989)The Ichthyography of the Pearl River.Science Press,Beijing.(in Chinese)[郑慈英(1989)珠江鱼类志.科学出版社.北京.]
Zitek A,Schmutz S,Unfer G,Ploner A(2004)Fish drift in a Danube sidearm-system:I.Site-,inter-and intraspecific patterns.Journal of Fish Biology,65,1319-1338.
(1)黎瑞宝(2013)中国海南鲌遗传多样性的比较研究.硕士学位论文,暨南大学,广州.
(1)朱叶(2012)基于线粒体细胞色素b的三江水系草鱼群体遗传多样性分析.硕士学位论文,暨南大学,广州.
(2)付晓艳(2011)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.硕士学位论文,暨南大学,广州.
Bandelt HJ,Forster P,Rohl A(1999)Median-joining networks for inferring intraspecific phylogenies.Molecular Biology and Evolution,16,37-48.
Chen WJ,Miya M,Saitoh K,Mayden RL(2008)Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes:The order Cypriniformes(Ostariophysi)as a case study.Gene,423,125-134.
Chen YY,Cao WX,Zheng CY(1986)Ichthyofauna of the Zhujiang River with a discussion on zoogeographical divisions for freshwater fishes.Acta Hydrobiologica Sinica,10,228-234.(in Chinese with English abstract)[陈宜瑜,曹文宣,郑慈英(1986)珠江的鱼类区系及其动物地理区划的讨论.水生生物学报,10,228-234.]
Drummond AJ,Rambaut A(2007)BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7,214.
Drummond AJ,Rambaut A,Shapiro B,Pybus OG(2005)Bayesian coalescent inference of past population dynamics from molecular sequences.Molecular Biology and Evolution,22,1185-1192.
Durand JD,Tsigenopoulos CS,Unlu E,Berrebi P(2002)Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA-Evolutionary significance of this region.Molecular Phylogenetics and Evolution,25,91-100.
Edgar RC(2004)MUSCLE:Multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research,32,1792-1797.
Excoffier L,Lischer HEL(2010)Arlequin suite ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10,564-567.
Fu YX(1997)Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection.Genetics,147,915-925.
Gascoyne M,Benjamin GJ,Schwarcz HP,Ford DC(1979)Sea-level lowering during the Illinoian glaciation:Evidence from a Bahama“blue hole”.Science,205,806-808.
Grant WS,Bowen BW(1998)Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation.Journal of Heredity,89,415-426.
Hewitt GM(2004)Genetic consequences of climatic oscillations in the Quaternary.Philosophical Transactions of the Royal Society B-Biological Sciences,359,183-195.
Jiang ZG,Jiang JP,Wang YZ,Zhang E,Zhang YY,Li LL,Xie F,Cai B,Cao L,Zheng GM,Dong L,Zhang ZW,Ding P,Luo ZH,Ding CQ,Ma ZJ,Tang SH,Cao WX,Li CW,Hu HJ,Ma Y,Wu Y,Wang YX,Zhou KY,Liu SY,Chen YY,Li JT,Feng ZJ,Wang Y,Wang B,Li C,Song XL,Cai L,Zang CX,Zeng Y,Meng ZB,Fang HX,Ping XG(2016)Red List of China’s Vertebrates.Biodiversidy Science,24,500-551.[蒋志刚,江建平,王跃招,张鹗,张雁云,李立立,谢锋,蔡波,曹亮,郑光美,董路,张正旺,丁平,罗振华,丁长青,马志军,汤宋华,曹文宣,李春旺,胡慧建,马勇,吴毅,王应祥,周开亚,刘少英,陈跃英,李家堂冯祚建,王燕,王斌,李成,宋雪琳,蔡蕾,臧春鑫,曾岩,孟智斌,方红霞,平晓鸽(2016)中国脊椎动物红色名录.生物多样性,24,500-551.]
Ketmaier V,Bianco PG,Cobollia M,Krivokapic M,Caniglia R,De Matthaeis E(2004)Molecular phylogeny of two lineages of Leuciscinae cyprinids(Telestes and Scardinius)from the peri-Mediterranean area based on cytochrome b data.Molecular Phylogenetics and Evolution,32,1061-1071.
Li J,Li XH,Jia XP,Li YF,He MF,Tan XC,Wang C,Jiang WX(2010)Evolvement and diversity of fish community in Xijiang River.Journal of Fishery Sciences of China,17,298-311.(in Chinese with English abstract)[李捷,李新辉,贾晓平,李跃飞,何美峰,谭细畅,王超,蒋万祥(2010)西江鱼类群落多样性及其演变.中国水产科学,17,298-311.]
Li SF,LüGQ,Bernatchez L(1998)Diversity of mitochondrial DNA in the populations of silver carp,bighead carp,grass carp and black carp in the middle-and lower reaches of the Yangtze River.Acta Zoologica Sinica,44,82-93.(in Chinese with English abstract)[李思发,吕国庆,Bernatchez L(1998)长江中下游鲢鳙草青四大家鱼线粒体DNA多样性分析.动物学报,44,82-93.]
Li YF,Li XH,Tan XC,Li J,Wang C(2012)Occurrence of larval Elopichthys bambusa and its relationship with hydrological conditions in the middle and lower reaches of Pearl River.Journal of Fisheries of China,36(4),15-22.(in Chinese with English abstract)[李跃飞,李新辉,谭细畅,李捷,王超(2012)珠江中下游鳡鱼苗的发生及其与水文环境的关系.水产学报,36,15-22.]
Liang ZS,Mo RL,Chen FC(1985)Species identification and spawning type of common fish species in Xijiang River during early phase.In:The Report of Fishery Research in Pearl River Basin.Compilation Committee of Fishery Resources Survey of Pearl River Basin,Guangzhou.(in Chinese)[梁秩燊,莫瑞林,陈福才(1985)西江常见鱼类早期发育的分类鉴定及其产卵类型.见:珠江水系渔业资源调查研究报告.珠江水系渔业资源调查编委会,广州.]
Librado P,Rozas J(2009)Dna SP v5:A software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25,1451-1452.
Lovejoy NR,Collette BB(2001)Phylogenetic relationships of new world needlefishes(Teleostei:Belonidae)and the biogeography of transitions between marine and freshwater habitats.Copeia,2001,324-338.
Meyer A(1993)Evolution of Mitochondrial DNA in Fishes.Elsevier,The Hague.
Nesler TP,Muth RT,Wasowicz AF(1988)Evidence for baseline flow spikes as spawning cues for Colorado squawfish in the Yampa River,Colorado.In:American Fisheries Society Symposium,pp.68-79.Bethesda,Maryland.
Nylander JAA(2004)MrModeltest v2.Evolutionary Biology Centre,Uppsala University,Uppsala.
Rambaut A,Drummond A(2007)Tracer v1.4.http://beast.bio.ed.ac.uk/Tracer.(accessed on 2018-3-2).
Rogers AR,Harpending H(1992)Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,9,552-569.
Tajima F(1989)The effect of change in population size on DNA polymorphism.Genetics,123,597-601.
Tao W,Zou M,Wang X,Gan X,Mayden RL,He S(2010)Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae(Cypriniformes).PLoS ONE,5,e13508.
Tyus HM,Haines GB(1991)Distribution,habitat use,and growth of age-0 Colorado squawfish in the Green River basin,Colorado and Utah.Transactions of the American Fisheries Society,120,79-89.
Wang X,Li J,He S(2007)Molecular evidence for the monophyly of East Asian groups of Cyprinidae(Teleostei:Cypriniformes)derived from the nuclear recombination activating gene 2 sequences.Molecular Phylogenetics and Evolution,42,157-170.
Wu WJ,Peng M,Wang DP,Shi J,Li YS,Han YQ,Lei JJ,He AY(2015)Comparison of mitochondrial D-Loop and Cyt b sequences of Hypophthalmichthys molitrix.Open Journal of Fisheries Research,2(4),67-73.(in Chinese with English abstract)[吴伟军,彭敏,王大鹏,施军,李育森,韩耀全,雷建军,何安尤(2015)红水河鲢线粒体D-Loop和Cyt b基因序列分析.水产研究,2(4),67-73.]
Xiao W,Zhang Y,Liu H(2001)Molecular systematics of Xenocyprinae(Teleostei:Cyprinidae):Taxonomy,biogeography,and coevolution of a special group restricted in East Asia.Molecular Phylogenetics and Evolution,18,163-173.
Yue PQ(2000)Fauna Sinica,Osteichthyes,Cypriniformes IIScience Press,Beijing.(in Chinese)[乐佩琦(2000)中国动物志.硬骨鱼纲,鲤形目,中卷.科学出版社,北京.]
Zheng CY(1989)The Ichthyography of the Pearl River.Science Press,Beijing.(in Chinese)[郑慈英(1989)珠江鱼类志.科学出版社.北京.]
Zitek A,Schmutz S,Unfer G,Ploner A(2004)Fish drift in a Danube sidearm-system:I.Site-,inter-and intraspecific patterns.Journal of Fish Biology,65,1319-1338.
(1)黎瑞宝(2013)中国海南鲌遗传多样性的比较研究.硕士学位论文,暨南大学,广州.
(1)朱叶(2012)基于线粒体细胞色素b的三江水系草鱼群体遗传多样性分析.硕士学位论文,暨南大学,广州.
(2)付晓艳(2011)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.硕士学位论文,暨南大学,广州.