基于ND2基因的崖沙燕遗传多样性和遗传结构初探
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摘要
利用线粒体DNA中的NADH脱氢酶第二亚基(ND2)对来自齐齐哈尔市50个崖沙燕(Riparia riparia)样本进行扩增和测序,发现了11条新的单倍型序列。结合从GenB ank中下载的104条序列,对崖沙燕3个亚种种群(154只个体)进行序列变异及系统发育分析。结果显示,3个亚种种群中有2个共享单倍型。群体总的单倍型多样性(Hd)为(0. 885±0. 019),群体总的核苷酸多样性(Pi)为(0. 002 92±0. 000 18)。与其近缘物种淡色崖沙燕(Riparia diluta)相比较,崖沙燕种群表现出较低水平的遗传多样性。分子方差分析(AMOVA)显示变异主要来自种群内(72. 82%)。构建的单倍型系统发育树表明,62个单倍型没有形成明显的亚种分化和地理分化。
We amplified partial sequences of NADH dehydrogenase subunit 2( ND2) gene of 50 sand martins( Riparia riparia) from Qiqihar City and obtained sequences of 11 new haplotypes.These sequences together with 104 additional sequences downloaded from GenB ank were used in the analysis of sequence variation and phylogeny of three subspecies of sand martin. The analysis demonstrated that,two shared haplotypes were found in three subspecies populations( 154 individuals). The haplotype diversity( Hd) of the total population was 0. 885 ± 0. 019,and the nucleotide diversity( Pi) was 0. 002 92 ±0. 000 18. Sand martin had a lower level of genetic diversity than did pale martin( Riparia diluta). Molecular variance analysis( AMOVA) showed that variation mainly arose from within populations( 72. 82%). Based on the haplotype phylogenetic tree,62 haplotypes were not distinct subspecies,nor did they differentiate geographically.
We amplified partial sequences of NADH dehydrogenase subunit 2( ND2) gene of 50 sand martins( Riparia riparia) from Qiqihar City and obtained sequences of 11 new haplotypes.These sequences together with 104 additional sequences downloaded from GenB ank were used in the analysis of sequence variation and phylogeny of three subspecies of sand martin. The analysis demonstrated that,two shared haplotypes were found in three subspecies populations( 154 individuals). The haplotype diversity( Hd) of the total population was 0. 885 ± 0. 019,and the nucleotide diversity( Pi) was 0. 002 92 ±0. 000 18. Sand martin had a lower level of genetic diversity than did pale martin( Riparia diluta). Molecular variance analysis( AMOVA) showed that variation mainly arose from within populations( 72. 82%). Based on the haplotype phylogenetic tree,62 haplotypes were not distinct subspecies,nor did they differentiate geographically.
引文
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[25]JONES G.Selection against large size in the sand martin Riparia riparia during a dramatic population crash[J].Ibis,1987,129(Suppl.1):274-280.
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[27]COWLEY E,SIRIWARDENA G M.Long-term variation in survival rates of sand martins Riparia riparia:dependence on breeding and wintering ground weather,age and sex,and their population consequences?[J].Bird Study,2005,52(3):237-251.
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[29]TURNER A,ROSE C.Swallows&martins:an identification guide and handbook[M].Boston:Houghton Mifin Company,1989.
[30]SZPET,LIECHTI F,NAGY K,et al.Discovering the migration and non-breeding areas of sand martins and house martins breeding in the Pannonian Basin(central-eastern Europe)[J].Journal of Avian Biology,2017,48(1):114-122.
[2]洪德元.生物多样性面临的危机[J].中国科学院院刊,1990,5(2):117-120.
[3]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[J].南方水产科学,2017,13(3):43-50.
[4]高玮.中国东北地区鸟类及其生态学研究[M].北京:科学出版社,2006.
[5]郑光美.世界鸟类分类与分布名录[M].北京:科学出版社,2002.
[6]郑光美.中国鸟类分类与分布名录[M].3版.北京:科学出版社,2017.
[7]SCHWEIZER M,LIU Y,OLSSON U,et al.Contrasting patterns of diversification in two sister species of martins(Aves:Hirundinidae):the sand martin Riparia riparia and the pale martin R.diluta[J].Molecular Phylogenetics and Evolution,2018,125:116-126.
[8]PAVLOVA A,ZINK R M,DROVETSKI S V,et al.Pleistocene evolution of closely related sand martins Riparia riparia and R.diluta[J].Molecular Phylogenetics and Evolution,2008,48(1):61-73.
[9]NEAR T J,PESAVENTO J J,CHENG C H.Mitochondrial DNA,morphology,and the phylogenetic relationships of Antarctic icefishes(Notothenioidei:Channichthyidae)[J].Molecular Phylogenetics and Evolution,2003,28(1):87-98.
[10]MARKS B D,HACKETT S J,CAPPARELLA A P.Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the wedgebilled woodcreeper(Aves:Dendrocolaptidae:Glyphorynchus spirurus)[J].Molecular Phylogenetics and Evolution,2002,24(1):153-167.
[11]WANG W J,DAI C Y,ALSTRM P,et al.Past hybridization between two East Asian long-tailed tits(Aegithalos bonvaloti and A.fuliginosus)[J].Frontiers in Zoology,2014,11(1):40.
[12]ALSTRM P,RASMUSSEN P C,ZHAO C,et al.Integrative taxonomy of the plain-backed thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species[J].Avian Research,2016,7(1):1.
[13]CERQUEIRA P V,SANTOS M P D,ALEIXO A.Phylogeography,inter-specific limits and diversification of Turdus ignobilis(Aves:Turdidae)[J].Molecular Phylogenetics ang Evolution,2016,97:177-186.
[14]ZINK R M,PAVLOVA A,ROHWER S,et al.Barn swallows before barns:population histories and intercontinental colonization[J].Proceedings of the Royal Society B:Biological Sciences,2006,273(1591):1245-1251.
[15]TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[16]LIBRADO P,ROZAS J.Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[17]EXCOFFIER L,LISCHER H E L.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567.
[18]NYLANDER J.Mr Modeltest V2.program distributed by the author[DB/OL].(2004-01).https://www.researchgate.net/publication/285805344_Mr Modeltest_V2_Program_Distributed_by_the_Author.
[19]RONQUIST F,HUELSENBECK J P.Mr Bayes 3:bayesian phylogenetic inference under mixed models[J].Bioinformatics,2003,19(12):1572-1574.
[20]NGUYEN L T,SCHMIDT H A,VON HAESELER A,et al.IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J].Molecular Biology and Evolution,2014,32(1):268-274.
[21]SUEOKA N.On the genetic basis of variation and heterogeneity of DNA base composition[J].Proceedings of the National Academy of Sciences of the United States of America,1962,48(4):582-592.
[22]SHAKLEE J B,TAMARU C S,WAPLES R S.Speciation and evolution of marine fishes studied by the electrophoretic analysis of proteins[J].Pacific Science,1982,36(2):141-157.
[23]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[J].Conservation Biology,2007,21(3):697-708.
[24]周慧,李迪强,张于光,等.藏羚羊mt DNA D-loop区遗传多样性研究[J].遗传,2006,28(3):299-305.
[25]JONES G.Selection against large size in the sand martin Riparia riparia during a dramatic population crash[J].Ibis,1987,129(Suppl.1):274-280.
[26]GRYAZNOVA A N,SAVCHENKO A P.Distribution peculiarities of the sand(Riparia riparia Linnaeus 1758)martin and the pale sand(Riparia diluta Sharpe et Wyatt 1893)martin(Passeriformes,Hirundinidae)in the sympatry Zone in southern central Siberia[J].Biology Bulletin,2017,44(8):991-997.
[27]COWLEY E,SIRIWARDENA G M.Long-term variation in survival rates of sand martins Riparia riparia:dependence on breeding and wintering ground weather,age and sex,and their population consequences?[J].Bird Study,2005,52(3):237-251.
[28]THORUP K.Does the migration programme constrain dispersal and range sizes of migratory birds[J].Journal of Biogeography,2006,33(7):1166-1171.
[29]TURNER A,ROSE C.Swallows&martins:an identification guide and handbook[M].Boston:Houghton Mifin Company,1989.
[30]SZPET,LIECHTI F,NAGY K,et al.Discovering the migration and non-breeding areas of sand martins and house martins breeding in the Pannonian Basin(central-eastern Europe)[J].Journal of Avian Biology,2017,48(1):114-122.
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