爪哇特有種Microhyla achatina粒線基因體完整序列及其親緣遣傳演化

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：63

、訪客IP：3.146.206.19

姓名

范阮海時(Pham Nguyen Hai Tho) 查詢紙本館藏

畢業系所

生命科學系

論文名稱

爪哇特有種Microhyla achatina粒線基因體完整序列及其親緣遣傳演化
(Complete mitochondrial genome sequence of Indonesian endemic frog Microhyla achatina and genetic evolution)

相關論文

★ 探討resveratrol和osajin對鼻咽癌之抗腫瘤作用及機制	★ 臺灣及鄰近地區澤蛙的地理親源演化關係
★ 白藜蘆醇對鼻咽癌中基因的異常甲基化及細胞移動的影響	★ 調控酵母菌MIG1基因表達的轉錄因子
★ 單一核甘酸差異來研究MIG1調控表現的機制	★ 利用粒腺體全基因體DNA 序列瞭解台灣小雨蛙與近親種的演化及親源關係
★ Influences of habitat adaptation and geological events on Asian Common Toad (Duttaphrynus melanostictus) distribution pattern	★ 東亞及東南亞地區貢德氏赤蛙之親緣地理關係研究
★ 利用粒腺體基因(16S rRNA & ND4) 和細胞核基因(7IβFIB & 3ITBP) 研究亞洲蝮蛇在印尼地區的地理親緣演化	★ Microhyla fissipes及其近親種在東亞及東南亞的地理親緣關係
★ 面天樹蛙全粒線體基因組序列與其親緣關係	★ 台灣東部澤蛙(Fejervarya limnocharis)完整粒線體基因組序列及其親緣演化之探討
★ 透過粒線體基因體探討盤古蟾蜍與中華蟾蜍在蟾蜍科之內的親緣關係

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

至系統瀏覽論文 (2026-1-1以後開放)

摘要(中)

利用Sanger定序的技術完成印尼爪哇的特有種Microhyla achatina的全粒線基因體之序列，並將此資料存放在NCBI的GenBank中，登錄號為MW233587。其序列之總長度為16,725 bp，包含13個protein-coding genes、22個tRNA genes及兩個rRNA genes和兩個control regions（L-strand replication origin和D-loop）。親緣關係的分析是利用M. achatina和其他同科（Microhylidae科）中的物種之全粒線基因體序列，以Neighbor-joining、Maximum likelihood 及Bayesian inferences之運算方法所建立而成；其結果支持M. achatina和M. heymonsi是姊妹種，以及兩個單系屬Kaloula和Microhyla。另外因注意到ND5和ND6 DNA序列的變異性非常高，進而進行其親緣演化的分析，結果有顯著不同的結果；因此，ND5和ND6基因不適用於親緣演化的分析。此外，亦發現在密碼子中存在高度的核苷酸使用偏差，第二密碼子的T鹼基數量顯著較高（40.3 – 41.4%），而第三密碼子的G鹼基數量極低（6.6 – 8.6%）。本研究提供Microhyla achatina完整的粒線基因體序列，可供未來對Microhyla屬及Microhylidae家族遺傳演化之探討。

摘要(英)

The complete mitochondrial genome sequence of Microhyla achatina from Java, Indonesia was obtained by Sanger-sequencing technique and deposited in GenBank on NCBI with accession number of MW233587. The total length was 16,725 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two control regions (L-strand replication origin and D-loop). Phylogenetic relationships were constructed based on the complete mitogenome data of M. achatina and others in family Microhylidae by using Neighbor-joining, Maximum likelihood and Bayesian inferences. The phylogeny suggested M. achatina as a sister taxon of M. heymonsi and two monophyletic genera Kaloula and Microhyla. Additionally, due to observing high variation of ND5 and ND6 genes, we further investigated phylogenies from these two genes, and revealed they evolved strikingly different from the mitogenome. Thus, ND5 and ND6 genes were not suitable for anuran phylogeny and evolution. Moreover, there were strong codon usage bias toward significantly high T at second codons (40.3 – 41.4%) and extremely low G at third codons (6.6 – 8.6%). The complete mitochondrial genome sequence generated in this study provides a valuable source for further phylogenetic or genetic evolutionary researches on genus Microhyla or family Microhylidae.

關鍵字(中)

★ Microhylidae
★ Microhyla achatina
★ 粒線體DNA
★ 分子系統發生學

關鍵字(英)

★ Microhylidae
★ Microhyla achatina
★ mitochondrial DNA
★ molecular phylogeny

論文目次

摘要 i
ABSTRACT ii
ACKNOWLEDGEMENT iii
Table of Contents iv
List of Figures vi
List of Tables vii
Explanation of Symbols viii
Chapter I. Introduction 1
1.1 Microhyla achatina 1
1.1.1. Taxonomy 1
1.1.2. Morphological characteristics of M. achatina 2
1.1.3. Ecological characteristics 3
1.2 Mitochondrial genome 5
1.3 Overview of phylogenetic analysis methods 6
1.3.1. Neighbor-joining 6
1.3.2. Maximum-likelihood 6
1.3.3. Bayesian inference 7
1.3.4. Substitution model of evolution 7
1.3.5. Bootstrap analysis in phylogenetic research 8
1.4 Previous studies on mitochondrial genome of genus Microhyla & purpose of this study 10
Chapter II. Material & methods 14
2.1 Taxon sampling 14
2.2 DNA extraction 15
2.3 Polymerase chain reaction (PCR) amplification 16
2.4 Sample assembly and analysis 18
2.5 Molecular and phylogenetic analyses 18
Chapter III. Results 21
3.1 Microhyla achatina complete mitochondrial genome sequence 21
3.2 Protein-coding genes (PCGs) 24
3.3 Non-coding genes 30
3.4 Non-coding regions 35
3.5 Phylogenetic analyses of 18 members in subfamily Microhylinae and Kalophryninae 39
Chapter IV. Discussion 47
4.1 Microhyla achatina mitochondrial genome structure 47
4.2 Genetic phylogeny of Microhyla achatina and subfamily Microhylinae 47
4.3 ND5 and ND6 genes could be inappropriate to use in phylogenetic analyses 48
Chapter V. Conclusion 50
Bibliography 51

參考文獻

Alikhan, N.-F., Petty, N. K., BenZakour, N. L., Beatson, S. A., Zakour, N. L.Ben, &Beatson, S. A. (2011). BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics, 12(1), 402. https://doi.org/10.1186/1471-2164-12-402
AmphibiaWeb. (2020). AmphibiaWeb: Information on amphibian biology and conservation. Berkeley, California: AmphibiaWeb. https://amphibiaweb.org/lists/Microhylidae.shtml
Aquadro, C. F., &Greenberg, B. D. (1983). Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics, 103(2), 287–312.
Arenas, M. (2015). Trends in substitution models of molecular evolution. Frontiers in Genetics, 6, 319. https://doi.org/10.3389/fgene.2015.00319
Arenas, M., &Posada, D. (2014). Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Molecular Biology and Evolution, 31(5), 1295–1301. https://doi.org/10.1093/molbev/msu078
Atmaja, V. Y., Hamidy, A., Arisuryanti, T., Matsui, M., &Smith, E. N. (2018). A new species of Microhyla (Anura: Microhylidae) from Sumatra, Indonesia. Treubia, Mus. Zool. Borgoriense, 45, 25–46. https://doi.org/10.14203/treubia.v45i0.3625
Bain, R. H., &Nguyen, Q. T. (2004). Three New Species of Narrow-Mouth Frogs (Genus: Microhyla) from Indochina, with Comments on Microhyla annamensis and Microhyla palmipes. Copeia, 2004(3), 507–524. https://doi.org/10.1643/CH-04-020R2
Bayes, T., &Price, R. (1763). An essay towards solving a problem in the doctrine of chances. By the late Rev. Mr. Bayes, F. R. S. communicated by Mr. Price, in a letter to John Canton, A. M. F. R. S. Philosophical Transactions of the Royal Society of London, 53, 370–418. https://doi.org/10.1098/rstl.1763.0053
Bernt, M., Braband, A., Schierwater, B., &Stadler, P. F. (2013). Genetic aspects of mitochondrial genome evolution. Molecular Phylogenetics and Evolution, 69(2), 328–338. https://doi.org/10.1016/j.ympev.2012.10.020
Bonaparte, C. L. (1836). Ico-nografi a della fauna italica per le quattro classi degli animali vertebrati. Tipografi a Salviucci.
Boore, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research, 27(8), 1767–1780. https://doi.org/10.1093/nar/27.8.1767
Boulenger, G. A. (1897). Descriptions of new Malay frogs. Annals and Magazine of Natural History, 19(6), 108.
Broughton, R. E., &Dowling, T. E. (1994). Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera. Genetics, 138(1), 179–190.
Bruno, W. J., Socci, N. D., &Halpern, A. L. (2000). Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Molecular Biology and Evolution, 17(1), 189–197. https://doi.org/10.1093/oxfordjournals.molbev.a026231
Castoe, T. A., deKoning, A. P. J., Kim, H.-M., Gu, W., Noonan, B. P., Naylor, G., Jiang, Z. J., Parkinson, C. L., &Pollock, D. D. (2009). Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences, 106(22), 8986–8991. https://doi.org/10.1073/pnas.0900233106
Chan, P. P., &Lowe, T. M. (2019). tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods in Molecular Biology (Clifton, N.J.), 1962, 1–14. https://doi.org/10.1007/978-1-4939-9173-0_1
Chatton, É. (1937). Titres Et Travaux Scientifiques (1906-1937) De Edouard Chatton. Impr. E. Sottano.
daFonseca, R. R., Johnson, W. E., O’Brien, S. J., Ramos, M., &Antunes, A. (2008). The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics, 9(1), 119. https://doi.org/10.1186/1471-2164-9-119
Darriba, D., Taboada, G. L., Doallo, R., &Posada, D. (2012). ModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772–772. https://doi.org/10.1038/nmeth.2109
DeChiara, M., Friedrich, A., Barré, B., Breitenbach, M., Schacherer, J., &Liti, G. (2020). Discordant evolution of mitochondrial and nuclear yeast genomes at population level. BMC Biology, 18(1), 49. https://doi.org/10.1186/s12915-020-00786-4
Dhar, A., &Minin, V. N. (2016). Maximum Likelihood Phylogenetic Inference. In Encyclopedia of Evolutionary Biology (pp. 499–506). Elsevier. https://doi.org/10.1016/B978-0-12-800049-6.00207-9
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368–376. https://doi.org/10.1007/BF01734359
Felsenstein, J. (1985). Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39(4), 783. https://doi.org/10.2307/2408678
Fischer von Waldheim, G. (1813). Tabulis Synopticis Illustrata, in Usum Prælectionum Academiæ Imperialis Medico-Chirurgicæ Mosquensis Edita. In Zoognosia Tabulis Synopticis (3rd Editio). Nicolai Sergeidis Vsevolozsky.
Foran, D. R., Hixson, J. E., &Brown, W. M. (1988). Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis. Nucleic Acids Research, 16(13), 5841–5861. https://doi.org/10.1093/nar/16.13.5841
Frank, N., &Ramus, E. (1995). Complete Guide to Scientific and Common Names of Amphibians and Reptiles of the World. N. G. Publishing Inc.
Frost, D. R. (2020). Amphibian Species of the World: an Online Reference. Version 6.1. American Museum of Natural History, New York, USA. https://doi.org/doi.org/10.5531/db.vz.0001
Fusté, J. M., Wanrooij, S., Jemt, E., Granycome, C. E., Cluett, T. J., Shi, Y., Atanassova, N., Holt, I. J., Gustafsson, C. M., &Falkenberg, M. (2010). Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication. Molecular Cell, 37(1), 67–78. https://doi.org/10.1016/j.molcel.2009.12.021
Garg, S., Suyesh, R., Das, A., Jiang, J., Wijayathilaka, N., Amarasinghe, A. A. T., Alhadi, F., Vineeth, K. K., Aravind, N. A., Senevirathne, G., Meegaskumbura, M., &Biju, S. D. (2018). Systematic revision of Microhyla (Microhylidae) frogs of South Asia: A molecular, morphological, and acoustic assessment. Vertebrate Zoology, 69(1), 1–71. https://doi.org/10.26049/VZ69-1-2019-01
Gascuel, O., &Steel, M. (2006). Neighbor-joining revealed. Molecular Biology and Evolution, 23(11), 1997–2000. https://doi.org/10.1093/molbev/msl072
Gorin, V. A., Scherz, M. D., Korost, D.V., &Poyarkov, N. A. (2021). Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs. Zoosystematics and Evolution, 97(1), 21–54. https://doi.org/10.3897/zse.97.57968
Green, M. R., &Sambrook, J. (2001). Molecular cloning: a laboratory manual (J.Inglis, A.Boyle, &A.Gann (eds.); Fourth). Cold Spring Harbor Laboratory Press.
Grobben, K. (1908). Die systematische Einteilung des Tierreiches. In Verhandlungen der kaiserlich-königlichen zoologisch-botanischen Gesellschaft in Wien (pp. 491–511). Zool.-Bot. Ges. Österreich.
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., &Gascuel, O. (2010). New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59(3), 307–321. https://doi.org/10.1093/sysbio/syq010
Günther, A. C. L. G. (1858). On the systematic arrangement of the tailless batrachians and the structure of Rhinophrynus dorsalis. Zoological Society of London, 1858, 339–352.
Haeckel, E. (1866). Generelle Morphologie der Organismen, Allgemeine Grundzuge der Organischen Formen-Wissenschaft, Mechanisch Begründet Durch die von Charles Darwin Reformirte Descendez-Theorie. Verlag von Georg Reimer.
Haeckel, E. (1874). Anthropogenie oder Entwickelungsgeschichte des menschen. W. Engelmann.
Haeckel, E. (1894). Systematische Phylogenie. Verlag von Georg Reimer.
Han, N., Wu, Z., Zhang, L., &Wei, X. (2019). The complete mitogenome of Microhyla fissipes (Anura: Microhylidae) and phylogenetic analysis using GenBank data mining. Mitochondrial DNA Part B, 4(2), 3049–3050. https://doi.org/10.1080/23802359.2019.1666670
Hasan, M., Islam, M. M., Kuramoto, M., Kurabayashi, A., &Sumida, M. (2014). Description of two new species of Microhyla (Anura: Microhylidae) from Bangladesh. Zootaxa, 3755(5), 401. https://doi.org/10.11646/zootaxa.3755.5.1
Hebert, P. D. N., Cywinska, A., Ball, S. L., &DeWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313–321. https://doi.org/10.1098/rspb.2002.2218
Hixson, J. E., Wong, T. W., &Clayton, D. A. (1986). Both the conserved stem-loop and divergent 5’-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. The Journal of Biological Chemistry, 261(5), 2384–2390. http://www.ncbi.nlm.nih.gov/pubmed/3944140
Howlader, M. S. A., Nair, A., Gopalan, S.V., &Merilä, J. (2015). A New Species of Microhyla (Anura: Microhylidae) from Nilphamari, Bangladesh. Plos One, 10(3). https://doi.org/10.1371/journal.pone.0119825
Hurst, G. D. D., &Jiggins, F. M. (2005). Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings of the Royal Society B: Biological Sciences, 272(1572), 1525–1534. https://doi.org/10.1098/rspb.2005.3056
Igawa, T., Kurabayashi, A., Usuki, C., Fujii, T., &Sumida, M. (2008). Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings. Gene, 407(1–2), 116–129. https://doi.org/10.1016/j.gene.2007.10.001
Iskandar, D. T. (1998). The Amphibians of Java and Bali. In LIPI and GEF Biodiviersity Collections Project.
IUCN SSC Amphibian Specialist Group, . (2018). Microhyla achatina. The IUCN Red List of Threatened Species. https://doi.org/https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T79098776A79098638.en
Jaekel, O. (1911). Die Wirbeltiere : eine Übersicht über die fossilen und lebenden Formen [The Vertebrates. An Overview of the Fossil and Living Forms]. Verlag Gebrüder Borntraeger. https://doi.org/10.5962/bhl.title.119340
Janvier, P. (1997). Gnathostomata. Jawed Vertebrates. The Tree of Life Web Project. http://tolweb.org/Gnathostomata/14843/1997.01.01
Jetz, W., McPherson, J. M., &Guralnick, R. P. (2012). Integrating biodiversity distribution knowledge: toward a global map of life. Trends in Ecology & Evolution, 27(3), 151–159. https://doi.org/10.1016/j.tree.2011.09.007
Jukes, T. H., &Cantor, C. R. (1969). Evolution of Protein Molecules. In Mammalian Protein Metabolism (pp. 21–132). Elsevier. https://doi.org/10.1016/B978-1-4832-3211-9.50009-7
Khatiwada, J. R., Shu, G. C., Wang, S. H., Thapa, A., Wang, B., &Jiang, J. (2017). A new species of the genus Microhyla (Anura: Microhylidae) from Eastern Nepal. Zootaxa, 4254(2), 221. https://doi.org/10.11646/zootaxa.4254.2.4
Khatiwada, J. R., Wang, S., Shu, G., Xie, F., &Jiang, J. (2018). The mitochondrial genome of the Microhyla taraiensis (Anura: Microhylidae) and related phylogenetic analyses. Conservation Genetics Resources, 10(3), 441–444. https://doi.org/10.1007/s12686-017-0844-8
Kumar, S., Stecher, G., Li, M., Knyaz, C., &Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
Kurabayashi, A., Sumida, M., Yonekawa, H., Glaw, F., Vences, M., &Hasegawa, M. (2008). Phylogeny, Recombination, and Mechanisms of Stepwise Mitochondrial Genome Reorganization in Mantellid Frogs from Madagascar. Molecular Biology and Evolution, 25(5), 874–891. https://doi.org/10.1093/molbev/msn031
Ladoukakis, E. D., &Zouros, E. (2017). Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. Journal of Biological Research-Thessaloniki, 24(1), 2. https://doi.org/10.1186/s40709-017-0060-4
Lamarck, J. B. P. A. de M.de. (1801). Système des Animaux sans Vertèbres, ou Tableau général des classes, des ordres et des genres de ces animaux. Cambridge University Press.
Lemmon, A. R., &Moriarty, E. C. (2004). The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology, 53(2), 265–277. https://doi.org/10.1080/10635150490423520
Li, S., Pearl, D. K., &Doss, H. (2000). Phylogenetic tree construction using Markov Chain Monte Carlo. Journal of the American Statistical Association, 95(450), 493–508. https://doi.org/10.1080/01621459.2000.10474227
Lim, K. K. P., &Lim, F. L. K. (1992). A guide to the amphibians and reptiles of Singapore (1st Ed.). Singapore Science Centre.
Lin, J.-S., &Liu, F.-G. R. (2017). The complete mitochondrial genome of Microhyla fissipes (Amphidia, Anura, Microhylidae) from Taiwan. Mitochondrial DNA Part B, 2(2), 930–931. https://doi.org/10.1080/23802359.2017.1413289
Linnaeus, C.von. (1758). Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis (1st Editio). Impensis Direct. https://doi.org/10.5962/bhl.title.542
Macartney, J. (1802). Lectures on Comparative Anatomy (Cuvier’s lectures translated by W. Ross under the inspection of J. Macartney).
Marcelino, J. (2008). Microhyla achatina: Javan Chorus Frog. http://amphibiaweb.org/species/2166
Matsui, M. (2011). Taxonomic revision of one of the Old World’s smallest frogs, with description of a new Bornean Microhyla (Amphibia, Microhylidae). Zootaxa, 2814(1), 33. https://doi.org/10.11646/zootaxa.2814.1.3
Matsui, M., Hamidy, A., Belabut, D. M., Ahmad, N., Panha, S., Sudin, A., Khonsue, W., Oh, H.-S., Yong, H.-S., Jiang, J.-P., &Nishikawa, K. (2011). Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy. Molecular Phylogenetics and Evolution, 61(1), 167–176. https://doi.org/10.1016/j.ympev.2011.05.015
Matsui, M., Hamidy, A., &Eto, K. (2013). Description of a new species of Microhyla from Bali, Indonesia (Amphibia, Anura). Zootaxa, 3670(4), 579. https://doi.org/10.11646/zootaxa.3670.4.9
Matsui, M., Ito, H., Shimada, T., Ota, H., Saidapur, S. K., Khonsue, W., Tanaka-Ueno, T., &Wu, G.-F. (2005). Taxonomic relationships within the Pan-Oriental narrow-mouth toad Microhyla ornata as revealed by mtDNA analysis (Amphibia, Anura, Microhylidae). Zoological Science, 22(4), 489–495. https://doi.org/10.2108/zsj.22.489
Mau, B., Newton, M. A., &Larget, B. (1999). Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics, 55(1), 1–12. https://doi.org/10.1111/j.0006-341X.1999.00001.x
McKay, J. L. (2006). A Field Guide to the Amphibians and Reptiles of Bali. Krieger Publishing Company.
Minin, V., Abdo, Z., Joyce, P., &Sullivan, J. (2003). Performance-Based Selection of Likelihood Models for Phylogeny Estimation. Systematic Biology, 52(5), 674–683. https://doi.org/10.1080/10635150390235494
Moritz, C., Dowling, T. E., &Brown, W. M. (1987). Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology and Systematics, 18(1), 269–292. https://doi.org/10.1146/annurev.es.18.110187.001413
Nascimento, F. F., Reis, M.dos, &Yang, Z. (2017). A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology & Evolution, 1(10), 1446–1454. https://doi.org/10.1038/s41559-017-0280-x
Nelson, J. S. (1994). Fishes of the World (3rd Editio). John Wiley and Sons.
Nguyen, L. T., Poyarkov, N. A. J., Nguyen, T. T., Nguyen, T. A., Tran, V. H., Gorin, V. A., Murphy, R. W., &Nguyen, S. N. (2019). A new species of the genus Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from Tay Nguyen Plateau, Central Vietnam. Zootaxa, 4543(4), 549. https://doi.org/10.11646/zootaxa.4543.4.4
Parker, H. W. (1934). A Monograph of the Frogs of the Family Microhylidae. Trustees of the British Museum.
Posada, D., &Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics (Oxford, England), 14(9), 817–818. https://doi.org/10.1093/bioinformatics/14.9.817
Posada, David, &Crandall, K. A. (2001). Selecting the Best-Fit Model of nucleotide substitution. Systematic Biology, 50(4), 580–601. https://doi.org/10.1080/106351501750435121
Poyarkov Jr, N. A., Gorin, V. A., Zaw, T., Kretova, V. D., Gogoleva, S. S., Pawangkhanant, P., &Che, J. (2019). On the road to Mandalay: contribution to the Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) fauna of Myanmar with description of two new species. Zoological Research, 40(4), 244–276. https://doi.org/10.24272/j.issn.2095-8137.2019.044
Poyarkov, N. A., Nguyen, T.Van, Duong, T.Van, Gorin, V. A., &Yang, J.-H. (2018). A new limestone-dwelling species of Micryletta (Amphibia: Anura: Microhylidae) from northern Vietnam. PeerJ, 6, e5771. https://doi.org/10.7717/peerj.5771
Pyron, A. R., &Wiens, J. J. (2011). A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution, 61(2), 543–583. https://doi.org/10.1016/j.ympev.2011.06.012
Rand, D. M. (1993). Endotherms, ectotherms, and mitochondrial genome-size variation. Journal of Molecular Evolution, 37(3), 281–295. https://doi.org/10.1007/BF00175505
Randi, E., &Lucchini, V. (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. Journal of Molecular Evolution, 47(4), 449–462. https://doi.org/10.1007/PL00006402
Rannala, B., &Yang, Z. (1996). Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution, 43(3), 304–311. https://doi.org/10.1007/BF02338839
Reig, O. A. (1958). Proposiciones para una nueva macrosistematica de los anuros (Nota preliminar). Physis. Buenos Aires, 21, 109–118.
Ronquist, F., Teslenko, M., van derMark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., &Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61(3), 539–542. https://doi.org/10.1093/sysbio/sys029
Saitou, N., &Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
San Mauro, D., García-París, M., &Zardoya, R. (2004). Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene, 343(2), 357–366. https://doi.org/10.1016/j.gene.2004.10.001
Sbisà, E., Tanzariello, F., Reyes, A., Pesole, G., &Saccone, C. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene, 205(1–2), 125–140. https://doi.org/10.1016/S0378-1119(97)00404-6
Shaffer, H. B., &McKnight, M. L. (1996). The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex. Evolution, 50(1), 417–433. https://doi.org/10.1111/j.1558-5646.1996.tb04503.x
Shoemaker, J. S., &Fitch, W. M. (1989). Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Molecular Biology and Evolution, 6(3), 270–289. https://doi.org/10.1093/oxfordjournals.molbev.a040550
Soltis, P. S., &Soltis, D. E. (2003). Applying the Bootstrap in Phylogeny Reconstruction. Statistical Science, 18(2), 256–267. https://doi.org/10.1214/ss/1063994980
Sumner, J. G., Jarvis, P. D., Fernández-Sánchez, J., Kaine, B. T., Woodhams, M. D., &Holland, B. R. (2012). Is the General Time-Reversible model bad for molecular phylogenetics? Systematic Biology, 61(6), 1069–1074. https://doi.org/10.1093/sysbio/sys042
Swofford, D. L. (2003). PAUP*: Phylogenetic analysis using parsimony (and other methods) (No. 4). Sinauer Associates, Inc.
Swofford, D. L., Olsen, G. J., Waddell, P. J., &Hillis, D. M. (1996). Phylogenetic inference. In Molecular Systematics (Second, pp. 407–514). Sinauer Associates, Inc.
Tavaré, ‪Simon. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. In R. M.Miura (Ed.), Some Mathematical Questions in Biology - DNA Sequence Analysis (pp. 57–86). American Mathematical Society.‬‬
Thompson, J. D., Higgins, D. G., &Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680. https://doi.org/10.1093/nar/22.22.4673
Tschudi, J. J. von. (1838). Classification der Batrachier mit Berücksichtigung der fossilen Thiere dieser Abtheilung der Reptilien.
van derMeijden, A., Vences, M., Hoegg, S., Boistel, R., Channing, A., &Meyer, A. (2007). Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins. Molecular Phylogenetics and Evolution, 44(3), 1017–1030. https://doi.org/10.1016/j.ympev.2007.02.008
Vineeth, K. K., Radhakrishna, U. K., Godwin, R. D., Anwesha, S., Rajashekhar, K. P., &Aravind, N. A. (2018). A new species of Microhyla Tschudi, 1838 (Anura: Microhylidae) from West Coast of India: an integrative taxonomic approach. Zootaxa, 4420(2), 151. https://doi.org/10.11646/zootaxa.4420.2.1
Wang, S., Liu, L., &Jiang, J. (2016). The complete mitochondrial genome of Microhyla butleri (Amphibia, Anura, Microhylidae). Mitochondrial DNA Part B, 1(1), 154–155. https://doi.org/10.1080/23802359.2016.1144107
Wijayathilaka, N., Garg, S., Senevirathne, G., Karunarathna, N., Biju, S. D., &Meegaskumbura, M. (2016). A new species of Microhyla (Anura: Microhylidae) from Sri Lanka: an integrative taxonomic approach. Zootaxa, 4066(3), 331. https://doi.org/10.11646/zootaxa.4066.3.9
Wu, X., Li, Y., Zhang, H., Yan, L., &Wu, X.-B. (2016). The complete mitochondrial genome of Microhyla pulchra (Amphidia, Anura, Microhylidae). Mitochondrial DNA, 27(1), 40–41. https://doi.org/10.3109/19401736.2013.869685
Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Journal of Molecular Evolution, 39(3), 306–314. https://doi.org/10.1007/BF00160154
Yang, Z., &Rannala, B. (2012). Molecular phylogenetics: principles and practice. Nature Reviews. Genetics, 13(5), 303–314. https://doi.org/10.1038/nrg3186
Yong, H.-S., Song, S.-L., Lim, P.-E., Eamsobhana, P., &Tan, J. (2016). Complete mitochondrial genome and phylogeny of Microhyla butleri (Amphibia: Anura: Microhylidae). Biochemical Systematics and Ecology, 66, 243–253. https://doi.org/10.1016/j.bse.2016.04.004
Yu, D., Zhang, J., Li, P., Zheng, R., &Shao, C. (2015). Do cryptic species xxist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the Cyt b gene and the complete MT genome. PLOS ONE, 10(4), e0124825. https://doi.org/10.1371/journal.pone.0124825
Zhang, J.-Y., Zhang, L.-P., Yu, D.-N., Storey, K. B., &Zheng, R.-Q. (2018). Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae. BMC Evolutionary Biology, 18(1), 26. https://doi.org/10.1186/s12862-018-1140-2
Zhang, M., Fei, L., Ye, C., Wang, Y., Wang, B., &Jiang, J. (2018). A new species of genus Microhyla (Amphibia: Anura: Microhylidae) from Zhejiang Province, China. Asian Herpetological Research, 9(3), 135–148. https://doi.org/10.16373/j.cnki.ahr.180032
Zhang, P., Liang, D., Mao, R.-L., Hillis, D. M., Wake, D. B., &Cannatella, D. C. (2013). Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs. Molecular Biology and Evolution, 30(8), 1899–1915. https://doi.org/10.1093/molbev/mst091
Zhang, P., &Wake, D. B. (2009). Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution, 53(2), 492–508. https://doi.org/10.1016/j.ympev.2009.07.010
Zhang, P., Zhou, H., Chen, Y.-Q., Liu, Y.-F., &Qu, L.-H. (2005). Mitogenomic perspectives on the origin and phylogeny of living amphibians. Systematic Biology, 54(3), 391–400. https://doi.org/10.1080/10635150590945278
Zhao, Y., Meng, H., &Su, L. (2018). The complete mitochondrial genome of the mixtured pygmy frog Microhyla mixtura (Anura, Microhylidae). Conservation Genetics Resources, 10(3), 427–430. https://doi.org/10.1007/s12686-017-0841-y

指導教授

劉阜果(Liu Fu-Guo Robert)

審核日期

2021-1-27

推文