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贵州黎平地区沼水蛙的分子鉴定
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Abstract:
于2015年8月在贵州省黔东南州黎平县德凤镇南泉山采集到2个蛙类标本，经初步形态鉴定为沼水蛙(Sylvirana guentheri)，但之前并没有该物种在黎平县分布的文献记载，因此有必要使用分子手段对其分类地位进行准确界定。本文对采自贵州黎平县的沼水蛙标本进行DNA提取，并克隆其线粒体16S rRNA基因片段，使用分子系统发育学研究方法对其物种进行初步的分子鉴定。结果表明，黎平采蛙类样本16S rRNA基因序列与31条沼水蛙同源序列聚为一个支持率较高的单系，支系内序列间平均遗传距离为0.0056，且对应序列单倍型均在同一个单倍型网络内。自测序列与沼水蛙近模式产地(福建福州)一标本的16S rRNA基因序列遗传距离较小。因此，初步判断该标本属沼水蛙(Sylvirana guentheri)。初步的种群中性检验分析表明，沼水蛙种群最近可能发生过种群扩张。另外，本文探讨了较短的同源序列对相关系统发育分析结果的影响。
In August 2015, two frogspecimens were collected from Nanquan Mountain of Defeng Township, Liping County, Qiandongnan Prefecture in Guizhou Province. They were identified as Sylvirana guentheri by preliminary morphological identification. However, it was not documented the distribution of this species in Liping County, so it is necessary to use molecular means to accurately define their taxonomic status. In this paper, DNA extraction and cloning of mitochondrial 16S rRNA gene fragment of Sylvirana guentheri from Liping County, Guizhou Province were carried out. The preliminary molecular identification of this population was carried out by using the research method of molecular phylogeny. The results showed that the 16S rRNA gene sequences of Liping frogs and the homologous sequences of 31 Sylvirana guentheri frogs were clustered into a monophyletic clade with high support rates. The average genetic distance between sequences in the branch was 0.0056, and the corresponding haplotypes were all in the same haplotype network. The genetic distance between the 16S rRNA gene sequence of Liping frogs and the homologous sequence of a sample collected near type localitiy (Fuzhou, Fujian) was 0.008. Therefore, it is preliminarily determined that this specimen belongs to Sylvirana guentheri. The neutrality tests of S. guentheri population showed that the population may have expanded recently in history. In addition, the influence of shorter homologous sequences on the results of related phylogenetic analysis was discussed.
| [1] | Boulenger, G.A. (1882) Catalogue of the Batrachia Salientia s. Ecaudata in the Collection of the British Museum. Trustees of the British Museum, London, 495. |
| [2] | Gee, N.G. and Boring, A.M. (1930) A Check List of Chinese Amphibia with Notes on Geographical Distribution. Yenching University, Beijing. |
| [3] | Boulenger, G.A. (1920) A Monograph of the South Asian, Papuan, Melanesian and Australian Frogs of the Genus Rana. Records of the Indian Museum, 20, 1-226. https://doi.org/10.26515/rzsi/v20/i1/1920/163533 |
| [4] | Deckert, K. (1938) Beitr？ge zur Osteologie und Systematik ranider Froschlurche. Sitzungsberichte der Gesellschaft Naturforschender Freunde zu Berlin, 1938, 127-184. |
| [5] | 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: 364. |
| [6] | Dubois, A. (1992) Notes sur la classification des Ranidae (Amphibiens anoures). Bulletin Mensuel de la Société Linnéenne de Lyon, 61, 305-352. https://doi.org/10.3406/linly.1992.11011 |
| [7] | 费梁, 胡淑琴, 叶昌媛, 田婉淑, 江建平, 钟盛先, 李健, 王宜生. 《中国动物志》两栖纲(下卷)无尾目蛙科[M]. 北京: 科学出版社, 2009: 1246-1251. |
| [8] | 费梁, 叶昌媛, 江建平. 中国两栖动物及其分布彩色图鉴[M]. 成都: 四川科学技术出版社, 2012: 620. |
| [9] | Oliver, L.A., Prendini, E., Kraus, F. and Raxworthy, C.J. (2015) Systematics and Biogeography of the Hylarana Frog (Anura: Ranidae) Radiation across Tropical Australasia, Southeast Asia, and Africa. Molecular Phylogenetics and Evolution, 90, 176-192. https://doi.org/10.1016/j.ympev.2015.05.001 |
| [10] | Che, J., Chen, H.M., Yang, J.X., Jin, J.Q., Jiang, K., Yuan, Z.Y., Murphy, R.W. and Zhang, Y.P. (2012) Universal COI Primers for DNA Barcoding Amphibians. Molecular Ecology Resources, 12, 247-258. https://doi.org/10.1111/j.1755-0998.2011.03090.x |
| [11] | 熊荣川, 田应洲, 李松, 陈红, 于振. 贵州高原分布沼水蛙系统发育地位的初步研究[J]. 六盘水师范学院学报, 2014, 26(4): 55-59. |
| [12] | 熊荣川, 李明, 田应洲, 李松, 陈红. 贵州兴义华西雨蛙的分子鉴定[J]. 湖北农业科学, 2015, 54(19): 4865-4867. |
| [13] | 熊荣川, 田应洲, 李松, 陈红, 于振. 威宁中华蟾蜍的分子鉴定[J]. 贵州农业科学, 2014, 42(12): 32-36. |
| [14] | 熊荣川, 田应洲, 李松, 陈红. 泸县沼水蛙16SrRNA基因克隆与系统发育分析[J]. 六盘水师范学院学报, 2013, 25(5): 38-42. |
| [15] | Chen, L., Murphy, R.W., Lathrop, A., Ngo, A., Orlov, N.L., Ho, C.T. and Somorjai, I.L.M. (2005) Taxonomic Chaos in Asian Ranid Frogs: An Initial Phylogenetic Resolution. The Herpetological Journal, 15, 231-243. |
| [16] | Jiang, J.P. and Zhou, K.Y. (2005) Phylogenetic Relationships among Chinese Ranids Inferred from Sequence Data Set of 12S and 16S rDNA. The Herpetological Journal, 15, 1-8. |
| [17] | Che, J., Pang, J., Zhao, H., Wu, G.-F., Zhao, E.-M. and Zhang, Y.-P. (2007) Phylogeny of Raninae (Anura: Ranidae) Inferred from Mitochondrial and Nuclear Sequences. Molecular Phylogenetics and Evolution, 43, 1-13. https://doi.org/10.1016/j.ympev.2006.11.032 |
| [18] | Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F., De Sa, R.O., Channing, A., Wilkinson, M. and Donnellan, S.C. (2006) The Amphibian Tree of Life. Bulletin of the American Museum of natural History, 2006, 1-291. https://doi.org/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2 |
| [19] | Ziegler, T. (2009) Larval Morphology in Four Species of Hylarana from Vietnam and Thailand with Comments on the Taxonomy of H. nigrovittata Sensu Latu (Anura: Ranidae). Zootaxa, 2051, 1-25. https://doi.org/10.11646/zootaxa.2051.1.1 |
| [20] | Chen, X.H., Chen, Z., Jiang, J.P., Qiao, L., Lu, Y.Q., Zhou, K.Y., Zheng, G.M., Zhai, X.F. and Liu, J.X. (2013) Molecular Phylogeny and Diversification of the Genus Odorrana (Amphibia, Anura, Ranidae) Inferred from Two Mitochondrial Genes. Molecular Phylogenetics and Evolution, 69, 1196-1202. https://doi.org/10.1016/j.ympev.2013.07.023 |
| [21] | Grosjean, S., Ohler, A., Chuaynkern, Y., Cruaud, C. and Hassanin, A. (2015) Improving Biodiversity Assessment of Anuran Amphibians Using DNA Barcoding of Tadpoles. Case Studies from Southeast Asia. Comptes Rendus Biologies, 338, 351-361. https://doi.org/10.1016/j.crvi.2015.03.015 |
| [22] | Goutte, S., Dubois, A., Howard, S.D., Marquez, R., Rowley, J.J., Dehling, J.M., Grandcolas, P., Rongchuan, X. and Legendre, F. (2016) Environmental Constraints and Call Evolution in Torrent-Dwelling Frogs. Evolution, 70, 811-826. https://doi.org/10.1111/evo.12903 |
| [23] | Yuan, Z.Y., Zhou, W.W., Chen, X., Jr, P.N., Chen, H.M., Jang-Liaw, N.H., Chou, W.H., Matzke, N.J., Iizuka, K. and Min, M.S. (2016) Spatiotemporal Diversification of the True Frogs (Genus Rana): A Historical Framework for a Widely Studied Group of Model Organisms. Systematic Biology, 65, 824-842. https://doi.org/10.1093/sysbio/syw055 |
| [24] | Jiang, L., Wu, B., Luo, J., Xu, Z. and Huang, N. (2020) Characterization of Complete Mitochondrial Genome of Hylarana guentheri (Anura: Ranidae) and Its Phylogenetic Implication. Mitochondrial DNA Part B, 5, 616-618. https://doi.org/10.1080/23802359.2019.1711216 |
| [25] | Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35, 1547-1549. https://doi.org/10.1093/molbev/msy096 |
| [26] | Zhang, D., Gao, F., Jakovli？, I., Zou, H., Zhang, J., Li, W.X. and Wang, G.T. (2020) PhyloSuite: An Integrated and Scalable Desktop Platform for Streamlined Molecular Sequence Data Management and Evolutionary Phylogenetics Studies. Molecular Ecology Resources, 20, 348-355. https://doi.org/10.1111/1755-0998.13096 |
| [27] | Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A. and Jermiin, L.S. (2017) ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nature Methods, 14, 587-589. https://doi.org/10.1038/nmeth.4285 |
| [28] | Nguyen, L.-T., Schmidt, H.A., Von Haeseler, A. and Minh, B.Q. (2015) IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32, 268-274. https://doi.org/10.1093/molbev/msu300 |
| [29] | Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., H？hna, S., Larget, B., Liu, L., Suchard, M.A. and Huelsenbeck, J.P. (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. Systematic Biology, 61, 539-542. https://doi.org/10.1093/sysbio/sys029 |
| [30] | Paradis, E. (2010) pegas: An R Package for Population Genetics with an Integrated-Modular Approach. Bioinformatics, 26, 419-420. https://doi.org/10.1093/bioinformatics/btp696 |
| [31] | Librado, P. and Rozas, J. (2009) DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data. Bioinformatics, 25, 1451-1452. https://doi.org/10.1093/bioinformatics/btp187 |
| [32] | Ramos-Onsins, S.E. and Rozas, J. (2002) Statistical Properties of New Neutrality Tests against Population Growth. Molecular Biology and Evolution, 19, 2092-2100. https://doi.org/10.1093/oxfordjournals.molbev.a004034 |
