基于线粒体基因序列探讨广义花臭蛙种群遗传结构
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摘要
花臭蛙(Odorrana schmackeri),隶属于蛙科(Raninae)臭蛙属(Odorrana) ,主要分布于我国亚热带和热带地区,分布区遍布西北、西南、华东、华中、华南。迄今对花臭蛙不同地理种群的遗传分化和遗传结构的研究还未见报道,种群遗传学是花臭蛙资源利用与保护的基础,本文利用线粒体基因作为分子标记对花臭蛙12个地理种群的遗传结构进行了研究。
本论文采用PCR和直接测序法,分析花臭蛙12个种群(南召种群、栾川种群、兰草谷种群、高家堰种群、五峰种群、碧口种群、青木川种群、雷公山种群、江口种群、武夷山种群、黄山种群、天目山种群)的遗传变异。通过测定118个样品的线粒体12SrDNA序列片段(774bp)、16SrDNA序列片段(1056bp),研究了花臭蛙12SrDNA、16SrDNA序列的遗传多样性及种群的遗传结构。
对12SrDNA与16SrDNA的联合序列分析结果表明,在118个花臭蛙个体中,共检测到295个变异位点,获得25种单倍型,其中H1、H2、H3为一些地方种群的共享单倍型。整个种群的核苷酸多样性为0.837±0.023,单倍型多样性为0.05122±.00099。这样高的单倍型多样性和核苷酸多样性与花臭蛙作为东洋界的广布种、种群大是相应的。南召种群、兰草谷种群和高家堰种群的核苷酸多样性、单倍型多样性均较高,且三种群的单倍型都分别聚在两个进化支上,说明他们是异域起源并发生了二次接触,推测他们至少包括两个遗传上显著不同的源种群。青木川种群、武夷山种群、雷公山种群、黄山种群和江口种群的的单倍型多样性较高,而核苷酸多样性较低,说明他们由一个较小的有效种群迅速增长而来。栾川种群、碧口种群和五峰种群的单倍型多样性和核苷酸多样性均低,暗示这些种群可能在历史上经历过严重的瓶颈效应。天目山种群的h值较低,π值较高,说明天目山种群经历了短暂的瓶颈效应,丧失了一定的单倍型多样性。
比较两两种群间的固定系数(Fst)及基因交流值(Nm)表明,雷公山种群、江口种群、武夷山种群相互间的遗传分化程度较低,他们与其他种群间的遗传分化程度较高。黄山种群与天目山种群间,碧口种群与青木川种群间的基因交流非常频繁。高家堰种群与碧口种群、青木川种群、南召种群、栾川种群、兰草谷种群、五峰种群间有共享单倍型H1、H3,且高家堰种群与他们之间的遗传分化程度较低。
单倍型的地理分布特点和AMOVA分析结果表明花臭蛙的不同地理种群之间及种群内都存在极其显著的分化,通过不同方法构建的系统发育树也证明了这一点。这种遗传分化最可能的原因是受第四纪冰川的影响。
Odorrana schmackeri belongs to Odorrana of Raninae. It mainly distributes in subtropical and tropical regions of China,including Northern west China, Southern west China, Eastern China,Center China and Southern China. So far no research has investigated the genetic differentiation and structure of Odorrana schmackeri.For better protection and utilization of Odorrana schmackeri,the knowledge of its population genetics is essential.This paper studied on genetic structure of 12 populations in Odorrana schmackeri with mitochondrial gene sequences.
In this paper, Polymerase chain reaction(PCR)and dideoxy direct sequencing methods were used to analyze the genetic variation of Odorrana schmackeri from 12 different populations:NZ population,LC population,GJY population,LCG population,WF population,BK population,QMC population,WYS population,JK population,HS population and TMS population. A total of 1830 base pairs of the mitochondrial 12SrRNA (774bp) and 16SrRNA (1056bp) genes were sequenced in 118 samples to analysis the genetic structure and genetic diversity of Odorrana schmackeri.
By comparing sequences of the mtDNA 12SrRNA and 16SrRNA in 118 individuals from twelve populations.we found 295 variable sites, twenty-five haplotypes were defined. Among the twenty-five haplotypes,H1,H2 and H3 were shared haplotypes.The overall species diversity(h)and nucleotide diversity(π) were 0.05122±.00099 and 0.837±0.023. This is corresponding to huge population size and extensive distribution of Odorrana schmackeri throughout Oriental Regions.The nucleotide diversity(π) and haplotype diversity(h) of NZ population,LCG population,GJY population were high.The haplotypes of these populations were clustered into both B clad and C clad,which may come from different ancestral populations and have secondary contact. QMC population、WYS population、LGS population、HS population and JK population had higher haplotype diversity(h) and lower nucleotide diversity(π) ,these populations may grow up from a small size population. LC population, BK population ,WF population and TMS population had lower haplotype diversity(h) ,which may result from bottleneck effect.
The value of Fst and Dxy suggested that the level of genetic differentiation among LGS population、JK population、WYS population was low,but the three populations showed higher genetic differentiation level compared with the other populations.Frequent gene glow happened between HS population and TMS population,also between BK population and QMC population.There was no abvious differention between GJY population and BK population, QMC population, NZ population, LC population, LCG population, WF population.
The geographical distribution of haplotypes and analysis of molecular variance (AMOVA) suggested that there was marked genetic differentiation within populations and among groups. The most possible cause might be referred to the effect of Quaternary glaciation.
本论文采用PCR和直接测序法,分析花臭蛙12个种群(南召种群、栾川种群、兰草谷种群、高家堰种群、五峰种群、碧口种群、青木川种群、雷公山种群、江口种群、武夷山种群、黄山种群、天目山种群)的遗传变异。通过测定118个样品的线粒体12SrDNA序列片段(774bp)、16SrDNA序列片段(1056bp),研究了花臭蛙12SrDNA、16SrDNA序列的遗传多样性及种群的遗传结构。
对12SrDNA与16SrDNA的联合序列分析结果表明,在118个花臭蛙个体中,共检测到295个变异位点,获得25种单倍型,其中H1、H2、H3为一些地方种群的共享单倍型。整个种群的核苷酸多样性为0.837±0.023,单倍型多样性为0.05122±.00099。这样高的单倍型多样性和核苷酸多样性与花臭蛙作为东洋界的广布种、种群大是相应的。南召种群、兰草谷种群和高家堰种群的核苷酸多样性、单倍型多样性均较高,且三种群的单倍型都分别聚在两个进化支上,说明他们是异域起源并发生了二次接触,推测他们至少包括两个遗传上显著不同的源种群。青木川种群、武夷山种群、雷公山种群、黄山种群和江口种群的的单倍型多样性较高,而核苷酸多样性较低,说明他们由一个较小的有效种群迅速增长而来。栾川种群、碧口种群和五峰种群的单倍型多样性和核苷酸多样性均低,暗示这些种群可能在历史上经历过严重的瓶颈效应。天目山种群的h值较低,π值较高,说明天目山种群经历了短暂的瓶颈效应,丧失了一定的单倍型多样性。
比较两两种群间的固定系数(Fst)及基因交流值(Nm)表明,雷公山种群、江口种群、武夷山种群相互间的遗传分化程度较低,他们与其他种群间的遗传分化程度较高。黄山种群与天目山种群间,碧口种群与青木川种群间的基因交流非常频繁。高家堰种群与碧口种群、青木川种群、南召种群、栾川种群、兰草谷种群、五峰种群间有共享单倍型H1、H3,且高家堰种群与他们之间的遗传分化程度较低。
单倍型的地理分布特点和AMOVA分析结果表明花臭蛙的不同地理种群之间及种群内都存在极其显著的分化,通过不同方法构建的系统发育树也证明了这一点。这种遗传分化最可能的原因是受第四纪冰川的影响。
Odorrana schmackeri belongs to Odorrana of Raninae. It mainly distributes in subtropical and tropical regions of China,including Northern west China, Southern west China, Eastern China,Center China and Southern China. So far no research has investigated the genetic differentiation and structure of Odorrana schmackeri.For better protection and utilization of Odorrana schmackeri,the knowledge of its population genetics is essential.This paper studied on genetic structure of 12 populations in Odorrana schmackeri with mitochondrial gene sequences.
In this paper, Polymerase chain reaction(PCR)and dideoxy direct sequencing methods were used to analyze the genetic variation of Odorrana schmackeri from 12 different populations:NZ population,LC population,GJY population,LCG population,WF population,BK population,QMC population,WYS population,JK population,HS population and TMS population. A total of 1830 base pairs of the mitochondrial 12SrRNA (774bp) and 16SrRNA (1056bp) genes were sequenced in 118 samples to analysis the genetic structure and genetic diversity of Odorrana schmackeri.
By comparing sequences of the mtDNA 12SrRNA and 16SrRNA in 118 individuals from twelve populations.we found 295 variable sites, twenty-five haplotypes were defined. Among the twenty-five haplotypes,H1,H2 and H3 were shared haplotypes.The overall species diversity(h)and nucleotide diversity(π) were 0.05122±.00099 and 0.837±0.023. This is corresponding to huge population size and extensive distribution of Odorrana schmackeri throughout Oriental Regions.The nucleotide diversity(π) and haplotype diversity(h) of NZ population,LCG population,GJY population were high.The haplotypes of these populations were clustered into both B clad and C clad,which may come from different ancestral populations and have secondary contact. QMC population、WYS population、LGS population、HS population and JK population had higher haplotype diversity(h) and lower nucleotide diversity(π) ,these populations may grow up from a small size population. LC population, BK population ,WF population and TMS population had lower haplotype diversity(h) ,which may result from bottleneck effect.
The value of Fst and Dxy suggested that the level of genetic differentiation among LGS population、JK population、WYS population was low,but the three populations showed higher genetic differentiation level compared with the other populations.Frequent gene glow happened between HS population and TMS population,also between BK population and QMC population.There was no abvious differention between GJY population and BK population, QMC population, NZ population, LC population, LCG population, WF population.
The geographical distribution of haplotypes and analysis of molecular variance (AMOVA) suggested that there was marked genetic differentiation within populations and among groups. The most possible cause might be referred to the effect of Quaternary glaciation.
引文
[1]费梁,叶昌媛,黄永昭.中国两栖动物检索[M].重庆:科学技术文献出版社重庆分社, 1990, 1-364.
[2]费梁,胡淑琴,叶昌媛,等.中国动物志.两栖纲(下卷)[M].北京:科学出版社, 2009, 1283-1289.
[3]张荣祖.中国动物地理[M].北京:科学技术出版社, 1999.
[4]叶昌媛,费梁.我国臭蛙属(两栖纲:蛙科)的系统发育[J].动物学报, 2001, 47 (5) :528-534.
[5]徐宁,魏刚,李德俊.花臭蛙核型、C-带、银带的研究[J].遗传, 1990, 12(3):22-24.
[6]周建武,李珑,柯李晶,等.花臭蛙皮肤分泌物中抗菌肽Odorranin的分离纯化与表征[J].中国兽药杂志, 2007, 41(12):20-23.
[7]费梁,叶昌嫒,谢锋,等.中国四川省蛙科一新种—南江臭蛙(两栖纲,无尾目)[J].动物学研究, 2007, 28 ( 5) : 551-555.
[8]陈晓虹,周开亚,郑光美.中国臭蛙属一新种[J].动物分类学报, 2010, 35(1):206-211.
[9] Evans , B . J . , Mo rales , J . C,Picker , M. D . , et al. Comparative molecular phylogeography of two Xenopus species , X . gilli and X . laevis ,in the south - western Cape Province , South Africa [J]. Molecular Ecology, 1997,6; 333-343.
[10] Slade RW, Moritz C.,Phylogeography of Bufo marinus from its natural and introduced ranges[J].Proceedings of the Royal Society of London Series B - Biological Sciences . 1998,265 : 769-777.
[11] Symula R , Schulte R , Summers K .Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobares[J]. Molecular Phylogenetics and Evolution,2003,26:452- 475.
[12] Austin JD , Lougheed SC , Boag PT . Discordant temporal and geographic patterns in maternal lineages of eastern North American frogs , Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae ) [J]. Molecular Phylogenetics and Evolution . 2004,32(3):799-816.
[13] Garner TW, Pearman PB , Angelone S .Genetic diversity across a vertebrate species ' range :a test of the central - peripheral hypothesis[J] .Molecular Ecology ,2004, 13 : 1047-1053.
[14] Hoffman EA , Blouin MS. Evolutionary history of the northern leopard frog .reconstruction of phylogeny , phylogeography , and historical changes in population demography from mitochondrial DNA[J]. Evolution Int J Org Evolution. , 2004,58 : 145-159 .
[15] Jennifer L. Roberts, Jason L. Brown , Rudolf von May , et al. Wilfredo Arizabal ,Rainer Schulte, Kyle Summers.Genetic divergence and speciation in lowland and montane peruvian poison frogs[J]. Molecular Phylogenetics and Evolution ,2006,41 :149-164.
[16] HUANG Zu Hao,LIU Nai Fa, LONG Jin. Population genetic structure, haplotype distribution and genetic diversity of the rusty-necklaced partridge Alectoris magna lanzhouensis based on mtDNA control region sequences[J]. Acta Zoologica Sinica,2006, 52 (4) :738-745 .
[17]黄勤华,刘若余,吴芸等.贵州麻羊mt DNA Cytb基因遗传多样性分析[J].山地农业生物学报, 2008, 27 (5): 417-420.
[18]鲍毅新,程宏毅,周襄武等.黑麂( Muntiacus crinifrons ) 3个种群的遗传多样性[J].生态学报, 2008, 28(8): 4030-4036.
[19]祁得林,晁燕,郭松长等.黄河裸裂尻鱼五种群mtDNA控制区的遗传结构[J].动物学报, 2008, 54 (6) : 972-980.
[20]张保卫,张晨岭,陈建琴等.基于微卫星标记的中国大陆地区野猪种群结构分析与亚种分化[J].动物学报, 2008, 54 (5) : 753-761.
[21]刘文娟,刘迺发.基于线粒体Cytb基因的雉鸡甘肃亚种的种群遗传结构[J].动物学报, 2008, 54 (2) : 225 -232.
[22]陶峰勇,王小明,郑合勋,等.中国大鲵四种群的遗传结构和地理分化[J].动物学研究, 2005, 26(2): 162 -167.
[23]蔡垚.应用微卫星标记进行江豚种群遗传结构和亲缘关系判别的研究[D].南京:南京师范大学, 2004.
[24] Jiawu Xu, Tin-Yam Chan, Ling Ming Tsang, et al. Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia:Pleistocene isolation,population expansion and secondary contact[J]. MolecularPhylogenetics and Evolution, 2009, 52, 45-56.
[25]杨玉慧,张德兴,李义明,等.中国黑斑蛙种群的线粒体DNA多样性和生物地理演化过程的初探[J].动物学报, 2004, 50(2): 193 -201.
[26]张雄飞,周开亚,常青.中国大陆黑斑侧褶蛙基于mtDNA控制区序列的种群遗传结构[J].遗传学报, 2004, 31(11): 1232-1240.
[27]刘忠权.中国泽蛙线粒体基因组结构及种群系统地理学研究[D].南京:南京师范大学, 2003.
[28] Hua Zhang, Jie Yan, Guoqiang Zhang, et al. Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata):Evidence for Independent Refugia Expansion and Secondary Contact[J]. BMC Evolutionary Biology, 2008, 8:21.
[29] Mingwang Zhang, Dingqi Rao, Junxing Yang, et al. Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China[J]. Molecular Phylogenetics and Evolution, 2010, 54, 47-58.
[30] Nei M.Molecular Evolutionary Genetics[M]. New York: Columbia University Press, 1987.
[31] Lynch M., CreaseT.J. The analysis of population survey data on DNA sequence variation[J]. Mol.Biol.Evol, 1990, 7: 377-394.
[32] Husband BC, Barrett SCH. Estimates of gene flow in Eichhornia paniculata (Pontederi aceae):Effects of range substructure[J]. Heredity, 1995, 75: 549-560.
[33]李忠超,王小兰.保护生物学中若干术语的理解和辨析(2)*[J]生物学通报, 2005, 40(11): 3-5.
[34] Avise J C, Arnold J, Ball R M, et a1.Intraspecific phylogeography: the mitoc hondrial DNA bridge between population genetics and systematics[J]. Annual Review of Ecology and Systematics, 1987, 18: 489-522.
[35] Templeton A R. Nested clade analysis of phylogeographic data: testing hypotheses about gene flow and population history [J]. Molecular Ecology, 1998, 7: 381-397.
[36]钱迎倩,马克平.生物多样性研究的原理与方法[M].北京:中国科学技术出版社, 1994, 13-361.
[37] Moritz,C. ,D.M.Hillis. Molecular systematics :context and controversies[C]. In Hillis,D.M.andC.Moritz (eds.).Molecular systematics. Sunderland :Sinauer,1990,1-11.
[38] Grant ,V. The Evolutionary Process:A Critical Study of Evolutionary Theory .(2nd ed.)[M]. New York :Columbia University Press,1991.
[39] Ayala FJ,JW Valentine(胡凯译).现代综合进化论[M].成都:四川教育出版社, 1990, 114-136.
[40] Nass MMK,Nass S. Fibrous structures within the atrix of developing chick embryo mitochondria[J]. Exptl.Cell Res, 1962, 26: 424-427.
[41] Nass MMK, Nass S. Intramitochondrial fibers With DNA characteristics.I. Fixation and electron staining reactions[J] .J.Cell Bio.l, 1963, 19: 593-611.
[42] Nass MMK, Nass S. Intramitochondrial fibers With DNA characteristics.II. Enzymatic and other hydrolytic treatments[J]. J.Cell Bi0l., 1963, 19: 613-629.
[43]张亚平.从DNA序列到物种树[J].动物学研究, 1996, 17: 247-252.
[44] Sumida M, Kanamori Y, Kaneda H, et al. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata[J]. Genes Genet Syst, 2001, 76(5): 311-325.
[45] Liu,Z.Q., Wang,Y.Q., Su,B. The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate[J]. Gene, 2005, 346: 145-151.
[46] Su,X., Wu,X.B., Yan,P., et al. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus[J]. Gene, 2007, 394 (1-2):25-34.
[47] Kurabayashi,A., Igawa,T., Sumida,M. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings[J]. Gene,2008, 407 (1-2):116-129.
[48] Zhang,J.F., Nie,L.W., Wang,Y., et al. The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA[J]. Gene ,2009,442 (1-2):119-127.
[49]张际峰,聂刘旺,王洋,等.大头蛙和脆皮大头蛙线粒体3个基因的测定及两栖类亲缘关系研究[J].水生生物学报, 2007, 31(6): 822-828.
[50] Wong,J.F., Ma,D.P., Wilson,R.K., etal. DNA sequence of the Xenopus laevis mitochondrial heavy and light strand replication origins and flanking tRNA genes[J].J.Biol. Chem. ,1985, 260 (17): 9759-9774.
[51] Igawa,T., Kurabayashi,A., Usuki,C., etal. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings[J]. Gene,2008, 407 (1-2):116-129.
[52] Arnason,U., Gullberg,A., Janke,A., etal. Mitogenomic analyses of deep gnathostome divergences: a fish is a fish[J].Gene,2004,333:61-70.
[53] Zhang,P., Chen,Y.Q., Liu,Y.F., etal. The complete mitochondrial genome of the Chinese giant salamander,Andrias davidianus (Amphibia: Caudata)[J]. Gene,2003,311:93-98.
[54] Zhang,P., Chen,Y.Q., Zhou,H., et al. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny[J]. Mol. Phylogenet. Evol. ,2003,28 (3):620-626.
[55] Chang Y,Huang F., Lo T. The complete nucleotide sequence and gene organization of carp(Cyprinus carpio)mitochondrial genome[J].J.Mol.Evol.,1994,38:138-155.
[56] Stanley HF,Casey S,Carnaham JM, et al. Worldlwide patterns of mitochondrial DNA differentiation in the harbor seal hocavitulina[J].Mol Bio.Evol.,1996,13:368-382.
[57] Bonatto SL,Salzano FM. A simple and early migration for control region sequences in a marine mammal:implications for conservation and biogeography of Steller seallions Eumelopias jubatus[J].Mammal,1997,77:95-108.
[58] Vila C,Savolainen I,Maldonado JE, et al. Mutiple and ancient origins of the domestic dog[J]. Science,1997,276:1687-1689.
[59]苟德明,王智新.动物线粒体DNA特性及多态性研究[J].遗传育种, 1996, 22 (4): 7-10.
[60] Brown W. M. , Prager E . M.,Wang A . et al.Mitochondrial DNA sequences of primates:tempo and mode of evolution [J]. J.Mo l . Evol., 1982, 18: 225-239.
[61] Brown W.M..Evolution of animal mitochondrial DNA[C].In:Nei M.,Koehn R.K.eds . Evolution of Genes and Proteins.Sunderland:Sinauer,1983,62-68.
[62] Brennicke A .,Clayton D.A .Nucleotide assignment of alkili-sensitive sites in mouse mitochondrial DNA[J].Proc.Natl.Acad.Sci.,1981,83:4350-4353.
[63] Clayton DA.Transcription of the mammalian mitochondrial genome[J].Annu.Rev.Btochem,1984,53: 573 -594.
[64] Avise J .C .Mitochondrial DNA and evolutionary genetics of higher animals [J].Philos .Trans.R.Soc. London.B,1986,312:328-334.
[65] Wilson A.C . ,RL . Cann ,S. M.Carr,M.Geoge, U.B . Gyliensten, K.M. Helimbychowski,R.CxHiguchi ,S. R . Palumbi ,E.M. Prager,R.D Sage, and M.Stoneking .Mitochondrial DNA and two perspectives on evolutionary genetics [J] .Biol .J.Linnaean Sot.,1985,26:375-400.
[66] Ingman M,Kaessmann H,Paabo S,et al.Mitochondrial genome variation and the origin of modern humans [J].Nature,2000,408:708-713.
[67] Avise J. C., Lansman R. A..Polymerase of mitochondrial DNA in populations of high animals[C].In:Nei M.and Koehn R K.Ecolution of genes and protoins.Stander.,1983,65-138.
[68] Denao M.Ethnic variation in Hap I endonuclease cleavage patterns of human mitochondrial DNA[J]. Proc.Natl.Acad.Sci.,1981,78:5768-5772.
[69] Taberlet,P.,Bouvet,J. Mitochondrial DNA polymorphism,phylogeography ,and conservation genetics the brow bear(Ursus arctos) in Europe[J]. Proc. R . Soc. Lond. B , 1994,255:195-200.
[70] Wooding , S., Ward , R.. Phylogeography and pleistocene evolution in the North American Black bear[J]. Mol . Biol .Evol.,1997,14(11):1096-1105.
[71] Fermando , P. , Pfrender ,M. E. , Encalada ,S. E.et al.Mitochondrial DNA variation , phylogeography and population structure of the Asian elephant[J].Heredity,2000,3:362-372.
[72] Sumida M, Kaneda H, Kato Y, et al.. Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs[J].Genes Genet Syst,2000,75(2):79-92.
[73] Zhang XF, Zhou KY, Chang Q.Population genetic structure of Pelophylax nigromaculata in Chinese mainland, based on mtDNA control region sequences[J].Acta Genetica Sinica,2004,31(11):1232-1240.
[74] Talbot , S. L., Shields ,G. F. Phylogeography of brown bears (ursus actors) of Alaska and Paraphyly within the Ursida[J].Molecular Phylogenetics and Evolution,1996,5(3):477-494.
[75] Santucci , F.,Emerson ,B. C., Hewitt,G. M.Mitochondrial DNA phylogeography of European hedgehogs[J].Molecular Ecology,1998,7:1163-1172.
[76] Gubitz , T. , Thorpe ,R. S., Malhotra ,A..Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii:testing historical and adaptive hypotheses[J]. Molecular Ecology,2000,9:1213-1221.
[77] H. Hurston , L. Voith , J. Bonanno, et al. Effects of fragmentation on genetic diversity in island populations of the Aegean wall lizard Podarcis erhardii (Lacertidae, Reptilia)[J].MolecularPhylogenetics and Evolution,2009,52:395-405.
[78] Hua Zhang, Jie Yan, Guoqiang Zhang, et al. Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact[J].BMC Evolutionary Biology,2008,8:21.
[79] Mark P. Miller, Suan M. Haig, R. Steven Wagner. Phylogeography and Spatial Genetic Structure of the Southern Torrent Salamander: Implications for Conservation and Management[J].Journal of Heredity, 2006,97(6):561-570.
[80] Yuchi Zheng , Jinzhong Fu , Shuqiang Li. Toward understanding the distribution of Laurasian frogs:A test of Savage’s biogeographical hypothesis using the genus Bombina[J].Molecular Phylogenetics and Evolution.,2009,52:70-83.
[81] Redenbach , Z., Taylor ,E. B. Zoogeographical implications of variation in mitochondrial DNA of Arctic grayling ( Thymallus arcticus) [J].Molecular Ecology,1999,8:23-35.
[82] J. Robert Macey, Jared L, Strasburg, et al. Molecular Phylogenetics of Western North American Frogs of the Rana boylii Species Group[J].Molecular Phylogenetics and Evolution,2001,19:131-143.
[83] Brown , R. P. , Pestano ,J . Phylogeography of skinks (Chalcides) in the Canary Islands inferred f rom mitochondrial DNA sequences[J].Molecular Ecology,1998,7:1183-1191.
[84] Sharon B. Emerson,Robert F. Inger, Djoko Iskandar. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution,2000,16:131-142.
[85] Franky Bossuyt, Rafe M. Bruwn, David M. Hillis,et al. Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-Scale Endemism in the Family Ranidae[J]. Syst. Biol,2006, 55(4): 579-594.
[86] Ben J. Evans, Darcy B. Kelley,Richard C. Tinsley,et al. A mitochondrial DNA phylogeny of African clawed frogs:phylogeography and implications for polyploid evolution[J]. Molecular Phylogenetics and Evolution, 2004, 33: 197-213.
[87] Johnson,W.E.,Slattery,J.P.,Eizirik ,E.et al..Disparate phylogeographic patterns of molecular genetic variation in four closely related South American small cat species[J]. Molecular Ecology, 1999, 8: 879-894.
[88] Javier,J.B, Alvarez,Y., Tabares.E, et al. Phylogeography of African Fruitbats (Megachiroptera)[J]. Molecular Phylogenetics and Evolution, 1999, 3: 596-604.
[89] Sharon B. Emerson, Robert F. Inger, Djoko Iskandar. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution, 2000,16(1): 131-142.
[90] Ben J. Evans, Darcy B. Kelley, Richard C. Tinsley, et al. A mitochondrial DNA phylogeny of African clawed frogs:phylogeography and implications for polyploid evolution[J]. Molecular Phylogenetics and Evolution, 2004, 33: 197-213.
[91] Elizabeth K. Timpe , Sean P. Grahamb, Ronald M. Bonett. Phylogeography of the Brownback Salamander reveals patterns of local endemism in Southern Appalachian springs[J]. Molecular Phylogenetics and Evolution, 2009, 52: 368-376.
[92] Trevino,S.E., Dizon ,A. E. Phylogeography,intraspecificst ructure and sex-biased dispersal of Dall’s porpoise,Phocoenoides dalli,revealed by mitochondria and microsatellite DNA analyses[J]. Molecular Ecology, 2000, 9: 1049-1060.
[93] Hillis D.M., Moritz M., Mable K . M. Molecular systematic[M]. Sunderland:Sinauer Aaaociates, 1996.
[94]郑冬,刘学东,马建章. 12S rRNA基因及其二级结构在系统学研究中的应用[J].东北林业大学学报, 2003, 31(3): 59 -61.
[95] Hixson J . E ., Brown W. M. A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans:sequence ,structure , evolution and phylogenetic implications[J]. Mol.Biol.Evol.,1986, 3: 1-18.
[96] Springer M. S ., Emmamuel D. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules[J]. J.Mol.Evol.,1996,43:357-373.
[97] Jiang J P , Zhou KY. Evolutionary relationships among Chinese ranid frogs inferred from mitochondrial sequence 12 S rRNA gene[J]. Acta Zool.Sin., 2001, 47 (1): 38-44.
[98] Jiang J P , Zhou KY. Phylogenetic relationships of Chinese brown frogs inferred from mitochondrial DNA sequences of 12 S ribosomal RNA gene [J]. Zool.Res., 2001, 22(1): 27 - 32.
[99] Jiang J P , Yuan FR , Xie F ,et al . Phylogenetic relation of some species and genera in Megophryids inferred from partial sequences of mitochondrial 12 S and 16 S rRNA genes [J]. Zool .Res., 2003, 24(4): 241-248.
[100] Miguel Vences, Joachim Kosuch, Stefan Lotters, et al. Phylogeny and Classification of Poison Frogs(Amphibia:Dendrobatidae), Based on Mitochondrial 16S and 12S Ribosomal RNA Gene Sequences[J]. Molecular Phylogenetics and Evolution, 2000,15(1): 34-40.
[101] Sharon B. Emerson, Robert F, Inger, et al. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution,2000,16:131–142.
[102] Abeda Dawood, Alan Channing, James P. Bogart. A Molecular Phylogeny of the Frog Genus Tomopterna in Southern Africa:Examining Species Boundaries with Mitochondrial 12S rRNA Sequence Data[J]. Molecular Phylogenetics and Evolution, 2002,22: 407–413.
[103] Mark Clough, Kyle Summers. Phylogenetic systematics and biogeography of the poison frogs:evidence from mitochondrial DNA sequences[J].Biological Journal of the Linnean Society,2000,70:515–540.
[104] Hennig,W. Phylogenetic systematics[M]. University of lllinois Press,Urbana,1966.
[105] Eck,R.V, M.O. Dayhoff .1966. Atlas of Protein sequence and structure[M]. National Biomedical Research Roundation,Silver Springs,MD.1966.
[106] Fitch,W.M. Towards defining the course of evolution:Minimum change for a specific tree topology [J]. Syst Zool.,1971,20:406-416.
[107] Hartigan,J.A. Minimum evolution fits in man[J].Proc.R. Soc .Lond B.,1973,164:298-310.
[108] Miyamoto,M M., J.Cracraft. Phylogenetic inference,DNA sequence analysis,and the future of molecular systematics[C].In Phylogenetice analysis of DNA squenees(M.M.Miyamota and J. Carcartf,eds.),pp.3-17.Oxford University Press,New York.
[109] Sourdis,J, M.Nei. Relative efficiencies of the maximum parsimony anddistance-matrix methods in obtanining the correct phylogenetic tree[J].Mol. Biol.Evol., 1988,5:298-311.
[110] Nei,M. Relative efficiencies of different tree making methods for molecular data[C].In Recent advances in phylogenetic studies of DNA sequences(M.M.Miyamoto and J.L.Cracraft,eds.),pp.133-147.Oxford University Press,Oxford,U.K.,1991.
[111] Felsenstein,J. Evolutionary trees from DNA sequences:A maximum likelihood approach[J].J.Mol.Evol.,1981,17:368-376.
[112] Kishinodg,H,T.Miyata, M.Hasegawa. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts[J].J.Mol.Evol.,1990,31:151-160.
[113] Posada D, Crandall KA.1998.Modeltest:testing the model of DNA substitution[J].Bioinformatics,2000,14:817-818.
[114] Huelsenbeck J.P., Crandall K.A. .Phylogeny estimation and hypothesis testing using maximum likelihood[J].Annu.Rev.Ecol.Syst.,1997,28:437-466.
[115] Nei M.and Kumer. Molecular Evolution and Phylogenetics[M].Oxford:Oxford Univ.Press,2000.
[116]郝柏林,张淑誉.生物信息学手册[M].上海:上海科学技术出版社,2000,36-37.
[117] Posada D,Buckley TR..Model selection and model averaging in phylogenetics : advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests [J].Systems Biology ,2004,53 :793-808.
[118] Kim R.C., Stansfield W.D. A dictionary og genetics[M].NewYork: Oxofrd Universtiy Press,1997.
[119] Sambrook J, Fritscher EF, Maniatis T. .Molecular Cloning:a Laboratory Manual[M].New York:Cold Spring Harbor Laboratory Press,1989.
[120] Kocher TD, Thomas WK, Edwards SV, et al. Dynamics of mitochondrial DNA evolution in animals: amplifications and sequencing with conserved primers[J]. Proc Natl Acad Sci USA.1989,86:6196-6200.
[121] Palumbi, S., Martin, A., Romano, S.,et al.“The Simple Fool’s Guide to PCR, Version 2.”[M].Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI,1991.
[122] Jeanmougin F ,Thompson J D , Gouy M, et al. Multiple sequence alignment with Clustal X [J]. Trends Biochem Sci ,1998,23 : 403-405.
[123] Kumar S, Tamura K , Nei M .2004 .MEGA3:Integrated Software for Molecular Evolutionary Analysis and Sequence Alignment [J].Bioinformatics,5:150-163.
[124] Rozas, J., Sánchez-Delbarrio, J.C., Messeguer, X., et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics,2003,19, 2496-2497.
[125] Fu, Y. X. ,W. H. Li. Statistical tests of neutrality of mutations[J].Genetics,1993,133: 693-709.
[126] Kimura M.A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences[J].Jounal of Molecular Evolution ,1980,16:111-120.
[127] Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distanceamong DNA restriction data[J]. Genetics ,1992,131:479-491.
[128] Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies[J]. Molecular Biology and Evolution, 1999,16, 37-48.
[129] Crandall KA, Templeton AR. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny construction. Genetics,1993, 134, 959-969.
[130] Posada D,Crandall KA. .MODELTEST:Testing the model of DNA substitution [J].Bioinformatics,1998,14:817-818.
[131] Huelsenbeck JP, Ronquist F. MrBAYES:Bayesian inference of phylogeny[J].Bioinformatics,2001,17:754-755.
[132] Swofford DL.PAUP4.0b10.Phylogenetic analysis using parsimony (and other methods). Version 4[M]. Sunderland,2002, MA: Sinauer Associates.
[133] Felsenstein , J. Confidence limits on phylogenies : an approach using the bootstrap [J]. Evolution , 1985,39:783-791.
[134] Fu YX. Statistical tests of neutrality of mutations against population growth,and background selection[J].Genetics,1997,147:915-925.
[135] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics,1989,123, 585-595.
[136] Harpending, H.C., Batzer, M.A., Gurven, M.,et al.Genetic traces of ancient demography[J]. Proc. Natl. Acad. Sci. 1998, 95, 1961-1967.
[137] Avise JC. Phylogeography :the History and Formation of Species[M]. Cambridge,Massachusetts London, England: Harvard University,2000.
[138] Hewitt,G.M. Some genetic consequences of iceages,and their role in divergence and speciation[J].Biol.JLinn.Soc.,1996,58:247-276.
[139] Slatkin M. Gene flow and the geographic structure of natural populations[J]. Sci.,1987,236:787-792.
[140] Babik W, Szymura JM, Rafinski J. Nuclear markers,mitochondrial DNA and male secondary sexual traits variation in a newt hybrid zone(Triturus vulgaris×T.montandoni)[J]. Mol.Eco., 2003, 12, 1913-1930.
[141]司徒尚纪.珠江传[M].河北:河北大学出版社. 2001 24-25.
[142] Neigel J E.Is FST obsolete ? [J] Conserv Genet , 2002, 3 :167-173.
[143]江兴亮.试论新构造运动在风景地貌形成中的作用及其旅游开发———以黄山为例[J].安徽师大学报(自然科学版), 1998, 12(4): 358-360.
[144] Babik W, Rafinski J. Relationship between morphometric and genetic variation in pure and hybrid populations of the smooth and Montandon’s newt(Triturus vulgaris×T.montandoni) [J].J.Zool.,2004,262,135-143.
[145] DeChaine, E.G., Martin, A.P. Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA[J]. Evolution,2004,58, 113-127.
[146] Yuan, S.L., Lin, L.K., Oshida, T..Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal [J]. Mol. Ecol. ,2006,15, 2119-2130.
[2]费梁,胡淑琴,叶昌媛,等.中国动物志.两栖纲(下卷)[M].北京:科学出版社, 2009, 1283-1289.
[3]张荣祖.中国动物地理[M].北京:科学技术出版社, 1999.
[4]叶昌媛,费梁.我国臭蛙属(两栖纲:蛙科)的系统发育[J].动物学报, 2001, 47 (5) :528-534.
[5]徐宁,魏刚,李德俊.花臭蛙核型、C-带、银带的研究[J].遗传, 1990, 12(3):22-24.
[6]周建武,李珑,柯李晶,等.花臭蛙皮肤分泌物中抗菌肽Odorranin的分离纯化与表征[J].中国兽药杂志, 2007, 41(12):20-23.
[7]费梁,叶昌嫒,谢锋,等.中国四川省蛙科一新种—南江臭蛙(两栖纲,无尾目)[J].动物学研究, 2007, 28 ( 5) : 551-555.
[8]陈晓虹,周开亚,郑光美.中国臭蛙属一新种[J].动物分类学报, 2010, 35(1):206-211.
[9] Evans , B . J . , Mo rales , J . C,Picker , M. D . , et al. Comparative molecular phylogeography of two Xenopus species , X . gilli and X . laevis ,in the south - western Cape Province , South Africa [J]. Molecular Ecology, 1997,6; 333-343.
[10] Slade RW, Moritz C.,Phylogeography of Bufo marinus from its natural and introduced ranges[J].Proceedings of the Royal Society of London Series B - Biological Sciences . 1998,265 : 769-777.
[11] Symula R , Schulte R , Summers K .Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobares[J]. Molecular Phylogenetics and Evolution,2003,26:452- 475.
[12] Austin JD , Lougheed SC , Boag PT . Discordant temporal and geographic patterns in maternal lineages of eastern North American frogs , Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae ) [J]. Molecular Phylogenetics and Evolution . 2004,32(3):799-816.
[13] Garner TW, Pearman PB , Angelone S .Genetic diversity across a vertebrate species ' range :a test of the central - peripheral hypothesis[J] .Molecular Ecology ,2004, 13 : 1047-1053.
[14] Hoffman EA , Blouin MS. Evolutionary history of the northern leopard frog .reconstruction of phylogeny , phylogeography , and historical changes in population demography from mitochondrial DNA[J]. Evolution Int J Org Evolution. , 2004,58 : 145-159 .
[15] Jennifer L. Roberts, Jason L. Brown , Rudolf von May , et al. Wilfredo Arizabal ,Rainer Schulte, Kyle Summers.Genetic divergence and speciation in lowland and montane peruvian poison frogs[J]. Molecular Phylogenetics and Evolution ,2006,41 :149-164.
[16] HUANG Zu Hao,LIU Nai Fa, LONG Jin. Population genetic structure, haplotype distribution and genetic diversity of the rusty-necklaced partridge Alectoris magna lanzhouensis based on mtDNA control region sequences[J]. Acta Zoologica Sinica,2006, 52 (4) :738-745 .
[17]黄勤华,刘若余,吴芸等.贵州麻羊mt DNA Cytb基因遗传多样性分析[J].山地农业生物学报, 2008, 27 (5): 417-420.
[18]鲍毅新,程宏毅,周襄武等.黑麂( Muntiacus crinifrons ) 3个种群的遗传多样性[J].生态学报, 2008, 28(8): 4030-4036.
[19]祁得林,晁燕,郭松长等.黄河裸裂尻鱼五种群mtDNA控制区的遗传结构[J].动物学报, 2008, 54 (6) : 972-980.
[20]张保卫,张晨岭,陈建琴等.基于微卫星标记的中国大陆地区野猪种群结构分析与亚种分化[J].动物学报, 2008, 54 (5) : 753-761.
[21]刘文娟,刘迺发.基于线粒体Cytb基因的雉鸡甘肃亚种的种群遗传结构[J].动物学报, 2008, 54 (2) : 225 -232.
[22]陶峰勇,王小明,郑合勋,等.中国大鲵四种群的遗传结构和地理分化[J].动物学研究, 2005, 26(2): 162 -167.
[23]蔡垚.应用微卫星标记进行江豚种群遗传结构和亲缘关系判别的研究[D].南京:南京师范大学, 2004.
[24] Jiawu Xu, Tin-Yam Chan, Ling Ming Tsang, et al. Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia:Pleistocene isolation,population expansion and secondary contact[J]. MolecularPhylogenetics and Evolution, 2009, 52, 45-56.
[25]杨玉慧,张德兴,李义明,等.中国黑斑蛙种群的线粒体DNA多样性和生物地理演化过程的初探[J].动物学报, 2004, 50(2): 193 -201.
[26]张雄飞,周开亚,常青.中国大陆黑斑侧褶蛙基于mtDNA控制区序列的种群遗传结构[J].遗传学报, 2004, 31(11): 1232-1240.
[27]刘忠权.中国泽蛙线粒体基因组结构及种群系统地理学研究[D].南京:南京师范大学, 2003.
[28] Hua Zhang, Jie Yan, Guoqiang Zhang, et al. Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata):Evidence for Independent Refugia Expansion and Secondary Contact[J]. BMC Evolutionary Biology, 2008, 8:21.
[29] Mingwang Zhang, Dingqi Rao, Junxing Yang, et al. Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China[J]. Molecular Phylogenetics and Evolution, 2010, 54, 47-58.
[30] Nei M.Molecular Evolutionary Genetics[M]. New York: Columbia University Press, 1987.
[31] Lynch M., CreaseT.J. The analysis of population survey data on DNA sequence variation[J]. Mol.Biol.Evol, 1990, 7: 377-394.
[32] Husband BC, Barrett SCH. Estimates of gene flow in Eichhornia paniculata (Pontederi aceae):Effects of range substructure[J]. Heredity, 1995, 75: 549-560.
[33]李忠超,王小兰.保护生物学中若干术语的理解和辨析(2)*[J]生物学通报, 2005, 40(11): 3-5.
[34] Avise J C, Arnold J, Ball R M, et a1.Intraspecific phylogeography: the mitoc hondrial DNA bridge between population genetics and systematics[J]. Annual Review of Ecology and Systematics, 1987, 18: 489-522.
[35] Templeton A R. Nested clade analysis of phylogeographic data: testing hypotheses about gene flow and population history [J]. Molecular Ecology, 1998, 7: 381-397.
[36]钱迎倩,马克平.生物多样性研究的原理与方法[M].北京:中国科学技术出版社, 1994, 13-361.
[37] Moritz,C. ,D.M.Hillis. Molecular systematics :context and controversies[C]. In Hillis,D.M.andC.Moritz (eds.).Molecular systematics. Sunderland :Sinauer,1990,1-11.
[38] Grant ,V. The Evolutionary Process:A Critical Study of Evolutionary Theory .(2nd ed.)[M]. New York :Columbia University Press,1991.
[39] Ayala FJ,JW Valentine(胡凯译).现代综合进化论[M].成都:四川教育出版社, 1990, 114-136.
[40] Nass MMK,Nass S. Fibrous structures within the atrix of developing chick embryo mitochondria[J]. Exptl.Cell Res, 1962, 26: 424-427.
[41] Nass MMK, Nass S. Intramitochondrial fibers With DNA characteristics.I. Fixation and electron staining reactions[J] .J.Cell Bio.l, 1963, 19: 593-611.
[42] Nass MMK, Nass S. Intramitochondrial fibers With DNA characteristics.II. Enzymatic and other hydrolytic treatments[J]. J.Cell Bi0l., 1963, 19: 613-629.
[43]张亚平.从DNA序列到物种树[J].动物学研究, 1996, 17: 247-252.
[44] Sumida M, Kanamori Y, Kaneda H, et al. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata[J]. Genes Genet Syst, 2001, 76(5): 311-325.
[45] Liu,Z.Q., Wang,Y.Q., Su,B. The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate[J]. Gene, 2005, 346: 145-151.
[46] Su,X., Wu,X.B., Yan,P., et al. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus[J]. Gene, 2007, 394 (1-2):25-34.
[47] Kurabayashi,A., Igawa,T., Sumida,M. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings[J]. Gene,2008, 407 (1-2):116-129.
[48] Zhang,J.F., Nie,L.W., Wang,Y., et al. The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA[J]. Gene ,2009,442 (1-2):119-127.
[49]张际峰,聂刘旺,王洋,等.大头蛙和脆皮大头蛙线粒体3个基因的测定及两栖类亲缘关系研究[J].水生生物学报, 2007, 31(6): 822-828.
[50] Wong,J.F., Ma,D.P., Wilson,R.K., etal. DNA sequence of the Xenopus laevis mitochondrial heavy and light strand replication origins and flanking tRNA genes[J].J.Biol. Chem. ,1985, 260 (17): 9759-9774.
[51] Igawa,T., Kurabayashi,A., Usuki,C., etal. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings[J]. Gene,2008, 407 (1-2):116-129.
[52] Arnason,U., Gullberg,A., Janke,A., etal. Mitogenomic analyses of deep gnathostome divergences: a fish is a fish[J].Gene,2004,333:61-70.
[53] Zhang,P., Chen,Y.Q., Liu,Y.F., etal. The complete mitochondrial genome of the Chinese giant salamander,Andrias davidianus (Amphibia: Caudata)[J]. Gene,2003,311:93-98.
[54] Zhang,P., Chen,Y.Q., Zhou,H., et al. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny[J]. Mol. Phylogenet. Evol. ,2003,28 (3):620-626.
[55] Chang Y,Huang F., Lo T. The complete nucleotide sequence and gene organization of carp(Cyprinus carpio)mitochondrial genome[J].J.Mol.Evol.,1994,38:138-155.
[56] Stanley HF,Casey S,Carnaham JM, et al. Worldlwide patterns of mitochondrial DNA differentiation in the harbor seal hocavitulina[J].Mol Bio.Evol.,1996,13:368-382.
[57] Bonatto SL,Salzano FM. A simple and early migration for control region sequences in a marine mammal:implications for conservation and biogeography of Steller seallions Eumelopias jubatus[J].Mammal,1997,77:95-108.
[58] Vila C,Savolainen I,Maldonado JE, et al. Mutiple and ancient origins of the domestic dog[J]. Science,1997,276:1687-1689.
[59]苟德明,王智新.动物线粒体DNA特性及多态性研究[J].遗传育种, 1996, 22 (4): 7-10.
[60] Brown W. M. , Prager E . M.,Wang A . et al.Mitochondrial DNA sequences of primates:tempo and mode of evolution [J]. J.Mo l . Evol., 1982, 18: 225-239.
[61] Brown W.M..Evolution of animal mitochondrial DNA[C].In:Nei M.,Koehn R.K.eds . Evolution of Genes and Proteins.Sunderland:Sinauer,1983,62-68.
[62] Brennicke A .,Clayton D.A .Nucleotide assignment of alkili-sensitive sites in mouse mitochondrial DNA[J].Proc.Natl.Acad.Sci.,1981,83:4350-4353.
[63] Clayton DA.Transcription of the mammalian mitochondrial genome[J].Annu.Rev.Btochem,1984,53: 573 -594.
[64] Avise J .C .Mitochondrial DNA and evolutionary genetics of higher animals [J].Philos .Trans.R.Soc. London.B,1986,312:328-334.
[65] Wilson A.C . ,RL . Cann ,S. M.Carr,M.Geoge, U.B . Gyliensten, K.M. Helimbychowski,R.CxHiguchi ,S. R . Palumbi ,E.M. Prager,R.D Sage, and M.Stoneking .Mitochondrial DNA and two perspectives on evolutionary genetics [J] .Biol .J.Linnaean Sot.,1985,26:375-400.
[66] Ingman M,Kaessmann H,Paabo S,et al.Mitochondrial genome variation and the origin of modern humans [J].Nature,2000,408:708-713.
[67] Avise J. C., Lansman R. A..Polymerase of mitochondrial DNA in populations of high animals[C].In:Nei M.and Koehn R K.Ecolution of genes and protoins.Stander.,1983,65-138.
[68] Denao M.Ethnic variation in Hap I endonuclease cleavage patterns of human mitochondrial DNA[J]. Proc.Natl.Acad.Sci.,1981,78:5768-5772.
[69] Taberlet,P.,Bouvet,J. Mitochondrial DNA polymorphism,phylogeography ,and conservation genetics the brow bear(Ursus arctos) in Europe[J]. Proc. R . Soc. Lond. B , 1994,255:195-200.
[70] Wooding , S., Ward , R.. Phylogeography and pleistocene evolution in the North American Black bear[J]. Mol . Biol .Evol.,1997,14(11):1096-1105.
[71] Fermando , P. , Pfrender ,M. E. , Encalada ,S. E.et al.Mitochondrial DNA variation , phylogeography and population structure of the Asian elephant[J].Heredity,2000,3:362-372.
[72] Sumida M, Kaneda H, Kato Y, et al.. Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs[J].Genes Genet Syst,2000,75(2):79-92.
[73] Zhang XF, Zhou KY, Chang Q.Population genetic structure of Pelophylax nigromaculata in Chinese mainland, based on mtDNA control region sequences[J].Acta Genetica Sinica,2004,31(11):1232-1240.
[74] Talbot , S. L., Shields ,G. F. Phylogeography of brown bears (ursus actors) of Alaska and Paraphyly within the Ursida[J].Molecular Phylogenetics and Evolution,1996,5(3):477-494.
[75] Santucci , F.,Emerson ,B. C., Hewitt,G. M.Mitochondrial DNA phylogeography of European hedgehogs[J].Molecular Ecology,1998,7:1163-1172.
[76] Gubitz , T. , Thorpe ,R. S., Malhotra ,A..Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii:testing historical and adaptive hypotheses[J]. Molecular Ecology,2000,9:1213-1221.
[77] H. Hurston , L. Voith , J. Bonanno, et al. Effects of fragmentation on genetic diversity in island populations of the Aegean wall lizard Podarcis erhardii (Lacertidae, Reptilia)[J].MolecularPhylogenetics and Evolution,2009,52:395-405.
[78] Hua Zhang, Jie Yan, Guoqiang Zhang, et al. Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact[J].BMC Evolutionary Biology,2008,8:21.
[79] Mark P. Miller, Suan M. Haig, R. Steven Wagner. Phylogeography and Spatial Genetic Structure of the Southern Torrent Salamander: Implications for Conservation and Management[J].Journal of Heredity, 2006,97(6):561-570.
[80] Yuchi Zheng , Jinzhong Fu , Shuqiang Li. Toward understanding the distribution of Laurasian frogs:A test of Savage’s biogeographical hypothesis using the genus Bombina[J].Molecular Phylogenetics and Evolution.,2009,52:70-83.
[81] Redenbach , Z., Taylor ,E. B. Zoogeographical implications of variation in mitochondrial DNA of Arctic grayling ( Thymallus arcticus) [J].Molecular Ecology,1999,8:23-35.
[82] J. Robert Macey, Jared L, Strasburg, et al. Molecular Phylogenetics of Western North American Frogs of the Rana boylii Species Group[J].Molecular Phylogenetics and Evolution,2001,19:131-143.
[83] Brown , R. P. , Pestano ,J . Phylogeography of skinks (Chalcides) in the Canary Islands inferred f rom mitochondrial DNA sequences[J].Molecular Ecology,1998,7:1183-1191.
[84] Sharon B. Emerson,Robert F. Inger, Djoko Iskandar. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution,2000,16:131-142.
[85] Franky Bossuyt, Rafe M. Bruwn, David M. Hillis,et al. Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-Scale Endemism in the Family Ranidae[J]. Syst. Biol,2006, 55(4): 579-594.
[86] Ben J. Evans, Darcy B. Kelley,Richard C. Tinsley,et al. A mitochondrial DNA phylogeny of African clawed frogs:phylogeography and implications for polyploid evolution[J]. Molecular Phylogenetics and Evolution, 2004, 33: 197-213.
[87] Johnson,W.E.,Slattery,J.P.,Eizirik ,E.et al..Disparate phylogeographic patterns of molecular genetic variation in four closely related South American small cat species[J]. Molecular Ecology, 1999, 8: 879-894.
[88] Javier,J.B, Alvarez,Y., Tabares.E, et al. Phylogeography of African Fruitbats (Megachiroptera)[J]. Molecular Phylogenetics and Evolution, 1999, 3: 596-604.
[89] Sharon B. Emerson, Robert F. Inger, Djoko Iskandar. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution, 2000,16(1): 131-142.
[90] Ben J. Evans, Darcy B. Kelley, Richard C. Tinsley, et al. A mitochondrial DNA phylogeny of African clawed frogs:phylogeography and implications for polyploid evolution[J]. Molecular Phylogenetics and Evolution, 2004, 33: 197-213.
[91] Elizabeth K. Timpe , Sean P. Grahamb, Ronald M. Bonett. Phylogeography of the Brownback Salamander reveals patterns of local endemism in Southern Appalachian springs[J]. Molecular Phylogenetics and Evolution, 2009, 52: 368-376.
[92] Trevino,S.E., Dizon ,A. E. Phylogeography,intraspecificst ructure and sex-biased dispersal of Dall’s porpoise,Phocoenoides dalli,revealed by mitochondria and microsatellite DNA analyses[J]. Molecular Ecology, 2000, 9: 1049-1060.
[93] Hillis D.M., Moritz M., Mable K . M. Molecular systematic[M]. Sunderland:Sinauer Aaaociates, 1996.
[94]郑冬,刘学东,马建章. 12S rRNA基因及其二级结构在系统学研究中的应用[J].东北林业大学学报, 2003, 31(3): 59 -61.
[95] Hixson J . E ., Brown W. M. A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans:sequence ,structure , evolution and phylogenetic implications[J]. Mol.Biol.Evol.,1986, 3: 1-18.
[96] Springer M. S ., Emmamuel D. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules[J]. J.Mol.Evol.,1996,43:357-373.
[97] Jiang J P , Zhou KY. Evolutionary relationships among Chinese ranid frogs inferred from mitochondrial sequence 12 S rRNA gene[J]. Acta Zool.Sin., 2001, 47 (1): 38-44.
[98] Jiang J P , Zhou KY. Phylogenetic relationships of Chinese brown frogs inferred from mitochondrial DNA sequences of 12 S ribosomal RNA gene [J]. Zool.Res., 2001, 22(1): 27 - 32.
[99] Jiang J P , Yuan FR , Xie F ,et al . Phylogenetic relation of some species and genera in Megophryids inferred from partial sequences of mitochondrial 12 S and 16 S rRNA genes [J]. Zool .Res., 2003, 24(4): 241-248.
[100] Miguel Vences, Joachim Kosuch, Stefan Lotters, et al. Phylogeny and Classification of Poison Frogs(Amphibia:Dendrobatidae), Based on Mitochondrial 16S and 12S Ribosomal RNA Gene Sequences[J]. Molecular Phylogenetics and Evolution, 2000,15(1): 34-40.
[101] Sharon B. Emerson, Robert F, Inger, et al. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia[J]. Molecular Phylogenetics and Evolution,2000,16:131–142.
[102] Abeda Dawood, Alan Channing, James P. Bogart. A Molecular Phylogeny of the Frog Genus Tomopterna in Southern Africa:Examining Species Boundaries with Mitochondrial 12S rRNA Sequence Data[J]. Molecular Phylogenetics and Evolution, 2002,22: 407–413.
[103] Mark Clough, Kyle Summers. Phylogenetic systematics and biogeography of the poison frogs:evidence from mitochondrial DNA sequences[J].Biological Journal of the Linnean Society,2000,70:515–540.
[104] Hennig,W. Phylogenetic systematics[M]. University of lllinois Press,Urbana,1966.
[105] Eck,R.V, M.O. Dayhoff .1966. Atlas of Protein sequence and structure[M]. National Biomedical Research Roundation,Silver Springs,MD.1966.
[106] Fitch,W.M. Towards defining the course of evolution:Minimum change for a specific tree topology [J]. Syst Zool.,1971,20:406-416.
[107] Hartigan,J.A. Minimum evolution fits in man[J].Proc.R. Soc .Lond B.,1973,164:298-310.
[108] Miyamoto,M M., J.Cracraft. Phylogenetic inference,DNA sequence analysis,and the future of molecular systematics[C].In Phylogenetice analysis of DNA squenees(M.M.Miyamota and J. Carcartf,eds.),pp.3-17.Oxford University Press,New York.
[109] Sourdis,J, M.Nei. Relative efficiencies of the maximum parsimony anddistance-matrix methods in obtanining the correct phylogenetic tree[J].Mol. Biol.Evol., 1988,5:298-311.
[110] Nei,M. Relative efficiencies of different tree making methods for molecular data[C].In Recent advances in phylogenetic studies of DNA sequences(M.M.Miyamoto and J.L.Cracraft,eds.),pp.133-147.Oxford University Press,Oxford,U.K.,1991.
[111] Felsenstein,J. Evolutionary trees from DNA sequences:A maximum likelihood approach[J].J.Mol.Evol.,1981,17:368-376.
[112] Kishinodg,H,T.Miyata, M.Hasegawa. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts[J].J.Mol.Evol.,1990,31:151-160.
[113] Posada D, Crandall KA.1998.Modeltest:testing the model of DNA substitution[J].Bioinformatics,2000,14:817-818.
[114] Huelsenbeck J.P., Crandall K.A. .Phylogeny estimation and hypothesis testing using maximum likelihood[J].Annu.Rev.Ecol.Syst.,1997,28:437-466.
[115] Nei M.and Kumer. Molecular Evolution and Phylogenetics[M].Oxford:Oxford Univ.Press,2000.
[116]郝柏林,张淑誉.生物信息学手册[M].上海:上海科学技术出版社,2000,36-37.
[117] Posada D,Buckley TR..Model selection and model averaging in phylogenetics : advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests [J].Systems Biology ,2004,53 :793-808.
[118] Kim R.C., Stansfield W.D. A dictionary og genetics[M].NewYork: Oxofrd Universtiy Press,1997.
[119] Sambrook J, Fritscher EF, Maniatis T. .Molecular Cloning:a Laboratory Manual[M].New York:Cold Spring Harbor Laboratory Press,1989.
[120] Kocher TD, Thomas WK, Edwards SV, et al. Dynamics of mitochondrial DNA evolution in animals: amplifications and sequencing with conserved primers[J]. Proc Natl Acad Sci USA.1989,86:6196-6200.
[121] Palumbi, S., Martin, A., Romano, S.,et al.“The Simple Fool’s Guide to PCR, Version 2.”[M].Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI,1991.
[122] Jeanmougin F ,Thompson J D , Gouy M, et al. Multiple sequence alignment with Clustal X [J]. Trends Biochem Sci ,1998,23 : 403-405.
[123] Kumar S, Tamura K , Nei M .2004 .MEGA3:Integrated Software for Molecular Evolutionary Analysis and Sequence Alignment [J].Bioinformatics,5:150-163.
[124] Rozas, J., Sánchez-Delbarrio, J.C., Messeguer, X., et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics,2003,19, 2496-2497.
[125] Fu, Y. X. ,W. H. Li. Statistical tests of neutrality of mutations[J].Genetics,1993,133: 693-709.
[126] Kimura M.A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences[J].Jounal of Molecular Evolution ,1980,16:111-120.
[127] Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distanceamong DNA restriction data[J]. Genetics ,1992,131:479-491.
[128] Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies[J]. Molecular Biology and Evolution, 1999,16, 37-48.
[129] Crandall KA, Templeton AR. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny construction. Genetics,1993, 134, 959-969.
[130] Posada D,Crandall KA. .MODELTEST:Testing the model of DNA substitution [J].Bioinformatics,1998,14:817-818.
[131] Huelsenbeck JP, Ronquist F. MrBAYES:Bayesian inference of phylogeny[J].Bioinformatics,2001,17:754-755.
[132] Swofford DL.PAUP4.0b10.Phylogenetic analysis using parsimony (and other methods). Version 4[M]. Sunderland,2002, MA: Sinauer Associates.
[133] Felsenstein , J. Confidence limits on phylogenies : an approach using the bootstrap [J]. Evolution , 1985,39:783-791.
[134] Fu YX. Statistical tests of neutrality of mutations against population growth,and background selection[J].Genetics,1997,147:915-925.
[135] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics,1989,123, 585-595.
[136] Harpending, H.C., Batzer, M.A., Gurven, M.,et al.Genetic traces of ancient demography[J]. Proc. Natl. Acad. Sci. 1998, 95, 1961-1967.
[137] Avise JC. Phylogeography :the History and Formation of Species[M]. Cambridge,Massachusetts London, England: Harvard University,2000.
[138] Hewitt,G.M. Some genetic consequences of iceages,and their role in divergence and speciation[J].Biol.JLinn.Soc.,1996,58:247-276.
[139] Slatkin M. Gene flow and the geographic structure of natural populations[J]. Sci.,1987,236:787-792.
[140] Babik W, Szymura JM, Rafinski J. Nuclear markers,mitochondrial DNA and male secondary sexual traits variation in a newt hybrid zone(Triturus vulgaris×T.montandoni)[J]. Mol.Eco., 2003, 12, 1913-1930.
[141]司徒尚纪.珠江传[M].河北:河北大学出版社. 2001 24-25.
[142] Neigel J E.Is FST obsolete ? [J] Conserv Genet , 2002, 3 :167-173.
[143]江兴亮.试论新构造运动在风景地貌形成中的作用及其旅游开发———以黄山为例[J].安徽师大学报(自然科学版), 1998, 12(4): 358-360.
[144] Babik W, Rafinski J. Relationship between morphometric and genetic variation in pure and hybrid populations of the smooth and Montandon’s newt(Triturus vulgaris×T.montandoni) [J].J.Zool.,2004,262,135-143.
[145] DeChaine, E.G., Martin, A.P. Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA[J]. Evolution,2004,58, 113-127.
[146] Yuan, S.L., Lin, L.K., Oshida, T..Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal [J]. Mol. Ecol. ,2006,15, 2119-2130.