Masafumi MATSUI,Yasuhiro KAWAHARA,Kanto NISHIKAWA,et al.Molecular Phylogeny and Evolution of Two Rhacophorus Species Endemic to Mainland Japan[J].Asian Herpetological Research(AHR),2019,10(2):86-104.[doi:10.16373/j.cnki.ahr.190015]
Click Copy

Molecular Phylogeny and Evolution of Two Rhacophorus Species Endemic to Mainland Japan
Share To:

Asian Herpetological Research[ISSN:2095-0357/CN:51-1735/Q]

2019 VoI.10 No.2
Research Field:
Publishing date:


Molecular Phylogeny and Evolution of Two Rhacophorus Species Endemic to Mainland Japan
Masafumi MATSUI1* Yasuhiro KAWAHARA2 Kanto NISHIKAWA1 Seiji IKEDA3 Koshiro ETO4 and Yusuke MIZUNO5
1 Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
2 Hagi City Museum, Horiuchi 355, Hagi, Yamaguchi 758-0057, Japan
3 Hiroshima University Museum, Kagamiyama 1-1-1, Higashi Hiroshima City, Hiroshima 739-8524, Japan
4 Kitakyushu Museum of Natural History and Human History, Higashida 2-4-1, Yahatahigashi-ku, Kitakyushu, Fukuoka 805-0071, Japan
5 Takahari 4-1002, Meito-ku, Nagoya 465-0061, Japan
glacial period mitochondrial DNA differentiation refugia Rhacophorus arboreus Rhacophorus schlegelii
We conducted molecular phylogenetic analyses of Japanese Rhacophorus species, especially of R. schlegelii and R. arboreus from the mainland, based on samples encompassing their known distribution ranges, and discussed about evolutionary history of Rhacophorus species within Japan. The common ancestor of Japanese Rhacophorus, except for R. owstoni from southern Ryukyus, was estimated to have diverged from a lineage occurring mainly in China about 7 MYBP. Both R. schlegelii and R. arboreus are genetically largely divergent between regions of eastern and western Japan, and this seems to have been promoted mainly by retreat to refugia. Retreats of the two species to different refugia sometimes in the past seem to have led restricted distribution of R. schlegelii in eastern and R. arboreus in western Japan, and brought their intraspecific variation patterns in morphology and breeding habit.


Chinzei K., Machida H. 2001. Formation history of structural landforms and tectonic landforms in Japan. 298–311. In Yonekura N., Kaizuka S., Nogami M., Chinzei K. (Eds.), Regional Geomorphology of the Japanese Islands, Introduction to Japanese Geomorphology, Vol. 1. Tokyo: University of Tokyo Press (In Japanese)
Clement M., Posada D., Crandall K. A. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol, 9: 1657–1659
Drummond A. J., Ho S. Y. W., Phillips M., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol, 4: 699–710
Drummond A. J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol, 7: 214
Dufresnes C., Litvinchuk S. N., Borzée A., Jang Y., Li J.-T., Miura I., Perrin N., St?ck M. 2016. Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs (Hyla japonica group) and complex relationships between continental and island lineages. BMC Evol Biol, 16: 1–14
Eto K., Matsui M., Sugahara T., Tanaka-Ueno T. 2012. Highly complex mitochondrial DNA genealogy in an endemic Japanese subterranean breeding brown frog Rana tagoi (Amphibia: Anura: Ranidae). Zool Sci, 29: 662–671
Excoffier L., Lischer H. E. L. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res, 10: 564–567
Felsenstein J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution, 35: 1229–1242
Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783–791
Frost D. R. 2019. Internet references. Retrieved from index.html. 17/2/2019
Fu Y. X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147: 915–925
Hasegawa M., Kishino H., Yano T. 1985. Dating of the human-ape splitting by a molecular phylogenetics. J Mol Evol, 22: 160–174
Hedges S. B. 1994. Molecular evidence for the origin of birds. Proc Nat Acad Sci, 91: 2621–2624
Hertwig S. T., Schweizer M., Das I., Haas A. 2013. Diversification in a biodiversity hotspot- the evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae). Mol Phyl Evol, 68: 567–581
Hillis D. M., Mable B. K., Larson, A., Davis, S. K., Zimmer, E. A. 1996. Nucleic acids IV: sequencing and cloning. 321–378. In Hillis D. M., Moritz C., Mable B. K. (Eds.), Molecular Systematics. Sunderland: Sinauer
Huelsenbeck J. P., Hillis M. 1993. Success of phylogenetic methods in the four taxon case. Syst Biol, 42: 247–264
Huelsenbeck J. P., Ronquist F., Nielsen R., Bollback J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294: 2310–2314
Igawa T., Kurabayashi A., Nishioka M., Sumida M. 2006. Molecular phylogenetic relationships of toads distributed in the Far East and Europe inferred from the nucleotide sequences of mitochondrial DNA genes. Mol Phyl Evol, 38: 250–260
Iizuka K., Kakegawa M., Maeda N. 1990. Nucleolus organizer regions in Japanese green tree frogs, Rhacophorus schlegelii and Rhacophorus arboreus. Jpn J Herpetol, 13: 120–125 (In Japanese)
Jobb G. 2008. TREEFINDER version of January 2008.
Jobb G. 2011. TREEFINDER version of March 2011.
Katoh K., Standley D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30: 772–780
Kim R., David J. G., Mark W., Simon P. L., Biju S. D., Karen G., Linde M., Franky B. 2007. Global patterns of diversification in the history of modern amphibians. Proc Nat Acad Sci, 104: 887–892
Kitamura A., Kimoto K. 2004. Reconstruction of the Southern Channel of the Japan Sea at 3.9–1.0 Ma. Quat Res, 43: 417–434 (In Japanese)
Leaché A. D., Reeder T. W. 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst Biol, 51: 44–68
Li J. T., Li Y., Klaus S., Rao D. Q., Hillis D. M., Zang Y. P. 2013. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. Proc Nat Acad Sci, 110: 3441–3446
Maeda N., Matsui M. 1999. Frogs and toads of Japan, revised edition. Tokyo: Bun-ichi Sogo Shuppan (In Japanese)
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). Zool Sci, 22: 489–495
Matsui M., Kuraishi, N., Jiang J.-P., Ota H., Hamidy A., Orlov N. L., Nishikawa K. 2010. Systematic reassessments of fanged frogs from China and adjacent regions (Anura: Dicroglossidae). Zootaxa, 2345: 33–42
Matsui M., Maeda N. 2018. Encyclopedia of Japanese frogs. Tokyo: Bun-ichi Sogo Shuppan (In Japanese)
Matsui M., Shimada T., Liu W.-Z., Maryati M., Khonsue W., Orlov N. 2006. Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae). Mol Phyl Evol, 38: 659–666
Mix A. C., Pisias N. G., Rugh W., Wilson J., Morey A., Hagelberg T. K. 1995. Benthic foraminifer stable isotope record from Site 849 (0–5 Ma). Local and global climate changes. Proc Ocean Drill. Prog, 138: 371–412
Nakamura K., Uéno S. 1963. Japanese Reptiles and Amphibians in Colour. Osaka: Hoikusha (In Japanese)
Nishizawa T., Kurabayashi A., Kunihara T., Sano N., Fujii T., Sumida M. 2013. Mitochondrial DNA diversification, molecular phylogeny, and biogeography of the primitive rhacophorid genus Buergeria in East Asia. Mol Phyl Evol, 59: 139–147
Okada Y. 1930. Monograph of Japanese tailless batrachians. Tokyo: Iwanami-shoten (In Japanese)
Okada Y., Kawano U. 1924. On the ecological distribution of two new varieties of Rhacophorus in Japan (2). Zool Mag, 36: 140–153 (In Japanese)
Ota Y., Koike K., Chinzei K., Koike K., Nogami M., Machida H., Matsuda T. 2010. Geomorphology of Japanese Archipelago. Tokyo: University of Tokyo Press (In Japanese)
Ota Y., Naruse,T., Tanaka S., Okada A. 2004. Regional geomorphology of the Japanese Islands, Vol. 6, Geomorphology of Kinki, Chugoku, and Shikoku Regions. Tokyo: University of Tokyo Press (In Japanese)
Palumbi S. R., Martin A., Romano S., McMillan W. O., Stice L., Grabowski G. 1991. The Simple Fool’s Guide to PCR, version 2.0. Privately Published. Compiled by Palumbi, S., Honolulu: Department of Zoology, University of Hawaii
Rambaut A. 2009. Tracer ver. 1.5.
Ronquist F., Huelsenbeck J. P. 2003. MrBayes 3: Bayesian Phylogenetic Inference under mixed models. Bioinformatics, 19: 1572–1574
Sakamaoto M., Tominaga A., Matsui M., Sakata K., Uchino A. 2009. Phylogeography of Hynobius yatsui (Amphibia: Caudata) in Kyushu, Japan. Zool Sci, 26: 35–47
Shimada T., Matsui M., Yambun P., Sudin A. 2011. A taxonomic study of Whitehead’s torrent frog, Meristogenys whiteheadi, with descriptions of two new species (Amphibia: Ranidae). Zool J Linn Soc, 161: 157–183
Sumida M., Ogata M. 1998. Intraspecific differentiation of the Japanese brown frog Rana japonica inferred from mitochondrial DNA sequences of the cytochrome b gene. Zool Sci, 15: 989–1000
Tamura K., Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol, 10: 512–526
Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 28: 2731–2739
Tanabe A. S. 2011. Kakusan4 and Aminosan: Two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Mol Ecol Res, 11: 914–921
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. Nucl Acids Res, 22: 4673–4680
Tominaga A., Matsui M., Yoshikawa N., Nishikawa K., Hayashi T., Misawa Y., Tanabe S., Ota H. 2013. Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): Taxonomic relationships and distributional changes associated with climatic oscillations. Mol Phyl Evol, 66: 654–667
Wilkinson J. A., Drewes R. C., Tatum O. L. 2002. A molecular phylogenetic analysis of the family Rhacophoridae with an emphasis on the Asian and African genera. Mol Phyl Evol, 24: 265–273
Wilkinson J. A., Matsui M., Terachi T. 1996. Geographic variation in a Japanese tree frog (Rhacophorus arboreus) revealed by PCR-aided restriction site analysis of mtDNA. J Herpetol, 30: 418–423
Zharkikh A. 1994. Estimation of evolutionary distances between nucleotide sequences. J Mol Evol, 39: 315–329


Last Update: 2019-06-25