线粒体D-loop序列变异与东方鲀属鱼类系统发育
PHYLOGENETIC RELATIONSHIPS OF THE GENUSTAKIFUGU (TETRAODONTIFORM ES, TETRAODONTIDAE)TESTED BY m tDNA D-LOOP REGION SEQUENCE VARIATIONS
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摘要: 东方鲀属的红鳍东方鲀(Takifugu rubripes)是后基因组时代的一种重要模式生物。本研究中，利用东方鲀属11种鱼类(18尾)的D-loop基因序列，对东方鲀属鱼类的系统发育关系进行研究。经序列比对排定后，分析中D-loop序列有841个位点，其中395个位点为可变位点，267个位点为系统发育信息位点。分别采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯方法构建了分子系统树。研究结果表明:(1)东方鲀属鱼类为一单系类群;(2)由横纹东方鲀(T. oblongus)和铅点东方鲀(T. alboplumbeus)构成的姊妹群位于这个类群的基部。此外，本属鱼类物种分类现状还需要进一步的澄清。Abstract: The pufferfishes of the genus Takifugu are East Asian fish, mainly distribute along the coastal region in western part of the Sea of Japan and the East China. This genus is attached more and more importance to researchers, for Takifugu rubripes, which isone species in it, has been a new model fish in the post-genomic era. The detailsof the phylogenetic relationships within the genus remain unresolved. In the present paper, mitochondrial D-loop sequences of 11 species of the genus Takifugu were determined and analyzed to test the present phylogenetic hypotheses1 The sequence saturation analysis was inferred from the shape of the trend line, which indicated that the sequence was unsaturated and could be used in the following phylogenetic analysis. After alignment, the sequence compositions and variations were analyzed by using MEGA 3 software. There were 841 sites, amongwhich 395 siteswere variable, and 267 were informative1 There was significant difference in base compositional bias between the ingroup and the outgroup species1 The uncorrected p-distance matrix obtained from the analysisof the alignment of all D-loop sequences showed that the relationships among the different specieswere closely. Neighbor-joining, Maximum Parsimony, Maximum Likelihood and Bayesian methodswere employed for phylogenetics analysis, respectively. Due to the SH test about the phylogeny hypothesis, we chose the Bayesian tree as our best tree in this paper. The Bayesian tree has described a more clearly phylogeny and the analysis also has pointed out the basal species in the genus. The results indicate that the genus form a monophyletic groups, with the sister group consisted by T. oblongus and T. alboplumbeus is the basal group of the genus1 Our results also show some confusion about the taxonomy in the genus, according to the data and combined analysis with the morphological characters, we suppose some species are in fact synonymous in this genus, which suggest that the taxonomy should be clarified based on both molecular and morphological data in the future.
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[1] Santini F, TylerJ C. A phylogenyof the familiesof fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent [J]. Zoological Journal of the Linnean Society, 2003, 139: 565-617
[1] [22] Zhao K, Yang G S, Li J B, et al.Phylogenetic structure of schizopygopsis pylzovi populations from mitochondrial cytochrome bgene sequence variations [J].Acta Hydrobiologica Sinica,2006, 30 (2) : 129-133 [赵凯, 杨公社, 李俊兵, 等. 黄河裸裂尻鱼群体遗传结构和 Cyt b序列变异. 水生生物学报,2006, 30 (2) : 129-133]
[2] Masuda Y, ShinoharaN, Takahashi Y, et al. Occurrence of natural hybrid between pufferfishes, Takifugu xanthopterus and T. verm icularis, in Ariake Bay, Kyushu, Japan [J]. N ippon Suisan Gakkaishi, 1991, 57: 1247-1255
[3] Masuda H, Amaoka K, Araga C, et al. The fishes of the Japanese Archipelago [M]. Tokyo: Tokai Univ. Press.1984,363-364
[4] SongL, Liu B, Xiang J, et al. Molecular phylogeny and species identification of pufferfish of the genus Takifugu (Tetraodontiformes, Tetraodontidae) [J]. M arine B iotechnology (NY),2001, 3: 398-406
[5] Aparicio S, Chapman J, Stupka E, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes [J]. Science, 2002, 297: 1301-1310
[6] Brenner S, Elgar G, Sandford R, et al. Characterization of the pufferfish (Fugu) genome as a compactmodel vertebrate genome [J]. Nature, 1993, 366: 265-268
[7] Elmerot C, Arnason U, Gojobori T, et al. The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships [J]. Gene, 2002, 295: 163-172
[8] HolcroftN I. A molecular test of alternative hypotheses of tetraodontiform (Acanthomorpha: Tetraodontiformes) sister group relationships using data from the RAG1 gene [J]. M olecularB iology and Evolution, 2004, 32: 749-760
[9] HolcroftN I. A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes) [J].M olecularB iology and Evolution, 2005, 34: 525-544
[10] Chen W J, Orti G, Meyer A. Novel evolutionary relationship among four fish model systems [J].Trends in Genetics, 2004, 20: 424-431
[11] Fraser2Brunner A. Notes on the plectognath fishes. -Ⅷ.The classification of the suborder Tetraodontoidea, with a synopsis of the genera [J]. Annals andM agazine of Natural History, 1943, 10: 1-18
[12] Abe T. Taxonomic studies on the puffers (Tetraodontidae, Teleostei) from Japan and adjacent regions, V: Synopsis of the puffers from and adjacent regions [J]. Bulletin of the B iogeographical Society of Japan, 1949, 14 (1, 13) : 1-15, 89-140, 141-142
[13] Abe T. Taxonomic studies on the puffers (Tetraodontidae, Teleostei) from Japan and adjacent regions, Ⅶ: concluding remarks, with the introduction of two new genera, Fugu and Boesemanichthys [J]. Japanese Journal of Ichthyology, 1952, 2 (1,2, 3) : 35-44, 31-33, 93-97, 117-127
[14] Whitley G P. Studies in ichthyology [M]. publishing company,1953, 60-112
[15] ChengQ T, WangC X, TianM C, et al. Studieson the Chinese Tetraodonoid fishes of the genus Fugu [J]. Acta Zoologica Sinica, 1975, 21 (4) : 359-378 [成庆泰, 王存信, 田明诚, 等.中国东方鲀属鱼类分类研究. 动物学报, 1975, 21 (4) :359-378]
[16] Wang KL, Zhang P J, YinQ. Studieson the interspecific differences ofmyogen and cluster of the genus Fugu [J]. Oceanologia et Limnologia Sinica, 1984, 15 (5) : 493-500 [王可玲, 张培军, 尹青. 东方鲀属鱼类肌浆蛋白的种间差异及其聚类的分析. 海洋与湖沼, 1984, 15 (5) : 493-500]
[17] Miyaki K, Tebeta O, Kayano H. Karyotypes in six species of pufferfishes genus Takifugu (Tetraodontidae, Tetraodontiformes) [J]. Fisheries Sciences, 1995, 61: 594-598
[18] Chen C, Shi T, Sun S G, et al. Identification and phylogenetic relationships among four species of puffer fish in Fugu as determined by RAPD [J]. M arine Fisheries Research, 2001, 22 (3) :32-36 [陈超, 石拓, 孙曙光, 等. 应用 RAPD标记对东方鲀属进行种类鉴别及其聚类分析. 海洋水产研究, 2001, 22 (3) : 32-36]
[19] Song L S, Liu B, Wang Z, et al. Phylogenetic relationships among pufferfish of genus Takifugu by RAPD analysis [J]. Chinese Journal of Oceanology and Limnology, 2001, 19: 128-134
[20] SongL, Li H, Cui Z, et al. Population genetic structure and genetic differentiation of the pufferfish Takifugu rubripes and Takifugu pseudommus revealed by RAPD Analysis [J]. High Technology Letters, 2003, 9: 22-25
[21] Zhang Y B, He S P. Phylogenetic relationships among the Takifugu Abe and Cytochrome b and 12S rRNA variations [J]. Chinese Science Bulletin, 2007, 50 (21) : 2507-2516 [张玉波, 何舜平. 细胞色素 b和 12S rRNA基因序列变异与东方鲀属鱼类系统发育. 科学通报, 2007, 50 (21) : 2507-2516]
[23] Su J X, Li C S.Fauna Sinica, Class Teleostei, Tetraodontiformes [M]. Beijing: Science Press. 2002 [苏锦祥, 李春生.中国动物志. 北京: 科学出版社. 2002]
[24] Sambrook J, Fritsch E F, Maniatis T. Molecular cloning: a laboratorymanual 22nd[M]. New York: Cold Spring Harbor Laboratory Press. 1989
[25] Liu H Z. Phylogenetic relationshipsof the cypriniformes tested by mtDNA 12S rRNA sequence variations [J]. Journal of Genetics and Genom ics, 2004, 31: 137-142
[26] Thompson J D, Gibson TJ, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies formultiple sequence alignment aided by quality analysis tools [J]. NucleicAcids Research,1997, 25: 4876-4882
[27] Galtier N, GouyM, Gautier C. SEAV IEW and PHYLO_W IN: two graphic tools for sequence alignment and molecular phylogeny [J]. ComputerApplications in theB iosciences, 1996, 12: 543-548
[28] W iens J J. Combining data setswith different phylogenetic histories [J]. Systems B iology, 1998, 47: 568-581
[29] Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution [J]. Journal of Heredity, 2001, 92: 371-373
[30] Tamura K, NeiM. Estimation of the numberof nucleotide substitutions in the control region ofmitochondrialDNA in humans and chimpanzees [J]. MolecularB iology and Evolution, 1993, 10:512-526
[31] Kumar S, Tamura K, NeiM. MEGA3: Integrated software for Molecular Evolutionary GeneticsAnalysis and sequence alignment [J]. B riefings in B ioinformatics, 2004, 5: 150-163
[32] Swofford D L. PAUP. Phylogenetic Analysis Using Parsimony (and othermethods) [M]. Sunderland, M assachusetts: Sinauer Associates, 2002
[33] Huelsenbeck J P, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees [J]. B ioinformatics, 2001, 17: 754-755
[34] Posada D, Crandall K A. MODELTEST: testing the model of DNA substitution [J]. B ioinformatics, 1998, 14: 817-818
[35] Shimodaira H, Hasegawa M. Multiple comparisons of loglikelihoodswith applications to phylogenetic inference [J]. Molecular B iology and Evolution, 1999, 16: 1114-1116
[36] Cantatore P, RobertiM, Pesole G, et al. Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals [J]. Journal of Molecular Evolution, 1994, 39: 589-597
[37] Buckley T R, Simon C, Shimodaira H, et al. Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology [J]. MolecularB iology and Evolution, 2001, 18: 223-234
[38] LeeW J, Conroy J, HowellW H, et al. Structure and evolution of teleostmitochondrial control regions [J]. Journal ofMolecular Evolution, 1995, 41: 54-66
[39] Kadereit J W. Molecules and morphology, phylogenetics and genetics [J]. Botanica Acta, 1994, 107: 369-373
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