Abstract
Japanese tree frog, Dryophytes japonicus, formerly known as Hyla japonica, is known to include several geographic groups recognized in mitochondrial phylogeny. By analyzing genetic and morphological variations in a large number of individuals of Dryophytes, we studied their taxonomic relationships. A mitochondrial DNA phylogeny was consistent with previous studies in that a high molecular divergence existed between populations from northeastern Japan and Sakhalin (Clade A) and those from southwestern Japan and Korea (Clade B). Nuclear DNA analyses based on SNP data also support such separation, whereas hybrid populations were found at some localities near the border of mitochondrial clades in Honshu Island, forming a hybrid zone. The width of hybrid zone was estimated to be narrow (approx. 25 km) and the migration rates into/beyond it were relatively low. Those results indicate that two genetic groups have long been parapatrically maintained with a narrow hybrid zone in Honshu Island. We examined syntypes of Hyla japonica and designated lectotypes. In adult morphology, the clades could be differentiated mainly by the pattern of rear of thigh, and the lectotypes proved to be Clade B. From these results, we describe the frogs of Clade A as a new species, D. leopardus sp. nov., distinct from D. japonicus.
References
- Aihara, I., Kitahata, H., Aihara, K. & Yoshikawa, K. (2006) Periodic rhythm and anti-phase synchronization in calling behaviors of Japanese rain frogs. Mathematical Engineering Technical Reports, 2006-35, 1–10. [https://www.keisu.t.u-tokyo.ac.jp/data/2006/METR06-35.pdf]
- Basarukin, A.M. (1982) Herpetofauna of the Kunashir Island. Ekologo-Faunisticheskie Issledovaniya Nekotorykh Pozvonochnykh Sakhalina i Kurilskikh Ostrovov, Vladivostok, 1982, 3–15.
- Basarukin, A.M. (1984) On reproduction of Hyla japonica on Sakhalin.: Ekologo-Fenologicheskie Issledovaniya v Sakhalinskoi Oblasti, Vladivostok, 1984, 123–126.
- Beheld, J.L. & King, F.W. (1979) The Audubon Society Field Guide to North American Reptiles and Amphibians. Alfred A. Knopf, Inc., New York, New York, 743 pp.
- Bolger, A.M., Lohse, M. & Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
- von Bedriaga, J. (1889) Die Lurchfauna Europa's I. Anura. Froschlurche. Bulletin de la Société impériale des naturalistes de Moscou, Nouvelle Serie, 3, 210–422 + 466–622. [https://www.biodiversitylibrary.org/item/106827#page/497/mode/1up]
- Borzée, A., Messenger, K.R., Chae, S., Andersen, D., Groffen, J., Kim, Y.I., An, J., Othman, S.N., Ri, K., Nam, T.Y., Bae, Y., Ren, J.-L., Li, J.-T., Chuang, M.-F., Yi, Y., Shin, Y., Kwon, T., Jang, Y. & Min, M.-S. (2020) Yellow Sea mediated segregation between North East Asian Dryophytes species. PLoS ONE, 15, e0234299. https://doi.org/10.1371/journal.pone.0234299
- Borzée, A., Fong, J.J., Nguyen, H.Q. & Jang, Y. (2020) Large-scale hybridisation as an extinction threat to the Suweon treefrog (Hylidae: Dryophytes suweonensis). Animals, 10, 764. https://doi.org/10.3390/ani10050764
- Camerano, L. (1879) Di alcune specie di anfibii anuri esistenti nelle collezioni del R. Museo Zoologico di Torino. Atti della Reale Accademia delle scienze di Torino, 14, 886–897.
- Catchen, J., Amores, A., Hohenlohe, P., Cresko, W. & Postlethwait, J. (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1, 171–182. https://doi.org/10.1534/g3.111.000240
- Derryberry, E.P., Derryberry, G.E., Maley, J.M. & Brumfield, R.T. (2014) HZAR: Hybrid zone analysis using an R software package. Molecular Ecology Resources, 14, 652–663. https://doi.org/10.1111/1755-0998.12209
- Duellman, W.E. (2001) Hylid Frogs of Middle America. Society for the Study of Amphibians and Reptiles, Contributions to Herpetology No. 18. 2nd Edition. Society for the Study of Amphibians and Reptiles, Marceline, Missouri, xvi + x + 1159 + 94 (unnumbered pages of pls.) pp., illustrations (some color), maps.
- Duellman, W.E., Marion, A.B. & Hedges, S.B. (2016) Phylogenetics, classification, and biogeography of the treefrogs (Amphibia: Anura: Arboranae). Zootaxa, 4104 (1), 1–109. https://doi.org/10.11646/zootaxa.4104.1.1
- Dufresnes, C., Litvinchuk, S.N., Borzée, A., Jang, Y., Li, J.-T., Miura, I., Perrin, N. & Stöck, 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 Evolutionary Biology, 16, 253. https://doi.org/10.1186/s12862-016-0814-x
- Dufresnes, C., Nicieza, A.G., Litvinchuk, S.N., Rodrigues, N., Jeffries, D.L., Vences, M., Perrin, N. & Martínez-Solano, Í. (2020a) Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs. Molecular Ecology, 29 (5), 986–1000. https;//doi.org/10.1111/mec.15368
- Dufresnes, C., Pribille, M., Alard, B., Gonçalves, H., Amat, F., Crochet, P.A., Dubey, S., Perrin, N., Fumagalli, L., Vences, M. & Martínez-Solano, Í. (2020b) Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean. Heredity, 124, 423–438. https://doi.org/10.1038/s41437-020-0294-z
- Dufresnes, C. & Litvinchuk, S.N. (2022) Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zoological Journal of the Linnean Society, 195, 695–760. https://doi.org/10.1093/zoolinnean/zlab083
- Dufresnes, C. & Jablonski, D. (2022) A genomics revolution in amphibian. Science, 377, 1272. https://doi.org/10.1126/science.ade5002
- Earl, D.A. & von Holdt, B.M. (2012) STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361. https://doi.org/10.1007/s12686-011-9548-7
- Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology, 14, 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
- Fei, L. & Ye, C.Y. (2016) Amphibians of China (I). Science Press, Beijing, 1040 pp.
- Fukutani, K., Matsui, M. & Nishikawa, K. (2023) Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad (Bufo japonicus). PeerJ, 11, e16302. https://doi.org/10.7717/peerj.16302
- Gosner, K. (1960) A simplified table for staging anuran embryos and larvae with notes on identification. Herpetologica, 16, 183–190. [https://www.jstor.org/stable/3890061]
- Günther, A.C.L.G. (1859 "1858") Catalogue of the Batrachia Salientia in the Collection of the British Museum. Taylor and Francis, London, 160 pp. [https://archive.org/details/catalogueofbatra00brit/page/108/mode/2up]
- Hallowell, E. (1861) Report upon the Reptilia of the North Pacific Exploring Expedition, under command of Capt. John Rogers, U. S. N. Proceedings of the Academy of Natural Sciences of Philadelphia, 12, 480–510. [https://www.biodiversitylibrary.org/page/1801421#page/506/mode/1up]
- Hilgendorf, F. (1880) Bemerkungen über die von ihm in Japan gesammelten Schlangen nebst Beschreibungen zweier neuer Schlangenarten. Sitzungberichte der Gesellschaft Naturforschender Freunde zu Berlin, 8, 111–121. [https://www.biodiversitylibrary.org/page/8807341#page/132] https://doi.org/10.5962/bhl.part.14943
- Hillis, D.M. & Bull, J.J. (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42, 182–192. https://doi.org/10.1093/sysbio/42.2.182
- Holloway, A.K., Cannatella, D.C., Gerhardt, H.C. & Hillis, D.M. (2006) Polyploids with different origins and ancestors form a single sexual polyploid species. American Naturalist, 167, E88–E101. https://doi.org/10.1086/501079
- Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754–755. https://doi.org/10.1093/bioinformatics/17.8.754
- Jang, Y., Hahm, E.-H., Lee, H.-J., Park, S., Won, Y.-J. & Choe, J.-C. (2011) Geographic variation in advertisement calls in a tree frog species: gene flow and selection hypotheses. PLoS ONE, 6, e23297. https://doi.org/10.1371/journal.pone.0023297
- Japan Wildlife Research Center (2010) The National Survey on the Natural Environment Distributional Survey of Japanese Animals: Animal Distribution Atlas of Japan. Biodiversity Center of Japan, Nature Conservation Bureau, Ministry of the Environment, Tokyo, 289 pp. [https://www.biodic.go.jp/kiso/atlas/pdf/6.reptiles_amphibians.pdf]
- Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403–1405. https://doi.org/10.1093/bioinformatics/btn129
- Kawamura, T., Nishioka, M. & Ueda, H. (1990) Reproductive isolation in treefrogs distributed in Japan, Korea, Europe and America. Scientific Report of the Laboratory for Amphibian Biology, Hiroshima University, 10, 255–293. [https://ir.lib.hiroshima-u.ac.jp/00000300]
- Kimura, S., Imanishi, Y., Kyoya, K. & Kiyota, T. (2017) Anuran species breeding at the coastal area in Akita Pref. Bulletin of the Herpetological Society of Japan, 2017, 47–52.
- Kozlov, A.M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35, 4453–4455. https://doi.org/10.1093/bioinformatics/btz305
- Kuramoto, M. (1980) Mating calls of treefrogs (genus Hyla) in the Far East, with description of a new species from Korea. Copeia, 1980, 100–108. https://doi.org/10.2307/1444138
- Kuzmin, S., Maslova, I., Matsui, M., Liang, F. & Kaneko, Y. (2017) Dryophytes japonicus. The IUCN Red List of Threatened Species, 2017, e.T55519A112714533. https://doi.org/10.2305/IUCN.UK.2017-1.RLTS.T55519A112714533.en
- Kuzmin, S. & Maslova, I.V. (2003) The amphibians of the Russian Far East. Advances in amphibian research in the former Soviet Union 8. Pensoft, Sofia, 464 pp.
- Lee, J.-E., Yang, D.-E., Kim, Y.-R., Lee, H., Lee, H.-I., Yang, S.-Y. & Lee, H.-Y. (1999) Genetic relationships of Korean treefrogs (Amphibia; Hylidae) based on mitochondrial cytochrome b and 12S rRNA genes. Korean Journal of Biological Sciences, 3, 295–301. https://doi.org/10.1080/12265071.1999.9647499
- Leaché, A.D. & Reeder, T.W. (2002) Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology, 51, 44–68. https://doi.org/10.1080/106351502753475871
- Leaché, A.D., Banbury, B.L., Felsenstein, J., Nieto-Montes de Oca, A. & Stamatakis, A. (2015) Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Systematic Biology, 64, 1032–1047. https://doi.org/10.1093/sysbio/syv053
- Li, J.-T., Wang, J.-S., Nian, H.-H., Litvinchuk, S.N., Wang, J., Li, Y., Rao, D.-Q. & Klaus, S. (2015) Amphibians crossing the Bering Land Bridge: Evidence from holarctic treefrogs (Hyla, Hylidae, Anura). Molecular Phylogenetics and Evolution, 87, 80–90. https://doi.org/10.1016/j.ympev.2015.02.018
- Matsui, T. (1979) Nihon san kaeru no bunrui ni kansuru shomondai [Some taxonomic problems concerning Japanese frogs]. Doubutsu to Shizen, 9, 2–7, pl.
- Matsui, M. (1984) Morphometric variation analyses and revision of the Japanese toads (genus Bufo, Bufonidae). Contributions from the Biological Laboratory, Kyoto University, 26, 209–428. [http://hdl.handle.net/2433/101561]
- Matsui, M. & Maeda, N. (2018) Encyclopedia of Japanese Frogs. Bun-ichi Sogo Shuppan, Tokyo, 271 pp.
- Matsui, M. & Matsui, T. (1982) Hyla hallowelli recorded from Iriomotejima, Yaeyama group, Ryukyu Archipelago. Japanese Journal of Herpetology, 9, 79–86. [https://www.jstage.jst.go.jp/article/hsj1972/9/3/9_3_79/_pdf] https://doi.org/10.5358/hsj1972.9.3_79
- Matsui, M., Okawa, H., Nishikawa, K., Aoki, G., Eto, K., Yoshikawa, N., Tanabe, S., Misawa, Y. & Tominaga, A. (2019) Systematics of the widely distributed Japanese clouded salamander, Hynobius nebulosus (Amphibia: Caudata: Hynobiidae), and its closest relatives. Current Herpetology, 38, 32–90. https://doi.org/10.5358/hsj.38.32
- Mayr, E. (1942) Systematics and the origin of species from the viewpoint of a zoologist. Columbia Biological Series No. 13. Columbia University Press, New York, New York, xiv + 334 pp.
- Nikolski, A.M. (1905) Presmykayushchiyesya i zemnovodnyye Rossiyskoy Imperii (S 2 tablitsami) [Reptiles and amphibians of the Russian Empire. (With 2 tables)]. Zapiski Imperatorskoi akademii nauk, po Fiziko-matematicheskomu otdieleniiu, 8e Série, 17, 1–517, 2 pls.
- Nishioka, M., Sumida, M. & Borkin, L.J. (1990) Biochemical differentiation of the genus Hyla distributed in the far east. Scientific Report of the Laboratory for Amphibian Biology, Hiroshima University, 10, 93–124. [https://ir.lib.hiroshima-u.ac.jp/00000293]
- Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959. https://doi.org/10.1093/genetics/155.2.945
- Puillandre, N., Brouillet, S. & Achaz, G. (2012) ASAP: assemble species by automatic partitioning. Molecular Ecology Resources, 21, 609–620. https://doi.org/10.1111/1755-0998.13281
- R Core Team. (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available from: http://www.R-project.org/ (accessed 23 December 2024)
- Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67, 901–904. https://doi.org/10.1093/sysbio/syy032
- Rannala, B. (2007) BayesAss Edition 3.0 User’s Manual. University of California Davis, Davis, California, 14 pp.
- van Riemsdijk, I., Butlin, R.K., Wielstra, B. & Arntzen, J.W. (2019) Testing an hypothesis of hybrid zone movement for toads in France. Molecular Ecology, 28 (5), 1070–1083. https://doi.org/10.1111/mec.15005
- Sclater, W.L. (1892) List of the batrachia in the Indian Museum. Printed by order of the Trustees of the Indian Museum, London, 43 pp. [https://www.biodiversitylibrary.org/item/37318#page/44/mode/1up]
- Seto, T. (1964) The karyotype of Hyla arborea japonica with some remarks on heteromorphism of the sex chromosome. Journal of the Faculty of Science, Hokkaido University, Series 6, Zoology, 15, 366–373. [http://hdl.handle.net/2115/27382]
- Shannon, F.A. (1956) The reptiles and amphibians of Korea. Herpetologica, 12, 22–49. [https://www.jstor.org/stable/3889565]
- Shimada, T., Imamura, A. & Onishi, N. (2013) A study of larval phenologies of five anuran species in Japanese paddy fields. Bulletin of the Herpetological Society of Japan, 2013, 77–85.
- Shimada, T. (2022) Species composition and distribution patterns of Japanese anurans. Bulletin of the Herpetological Society of Japan, 2022, 292–308.
- Shimada, T., Matsui, M., Ogata, M., Miura, I., Tange, M., Min, M.-S. & Eto, K. (2022) Genetic and morphological variation analyses of Glandirana rugosa with description of a new species (Anura, Ranidae). Zootaxa, 5174, 25–45 https://doi.org/10.11646/zootaxa.5174.1.2
- Stamatakis, A. (2014) RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
- Stankowski, S. & Ravinet, M. (2021) Quantifying the use of species concepts. Current Biology, 31, R415–R429. https://doi.org/10.1016/j.cub.2021.03.060
- Takahashi, K., Shimooka, Y. & Shinohara, M. (2016) Relationships between advertisement call characteristics and body size in Japanese tree frogs, Hyla japonica. Bulletin of Teikyo University of Science, 12, 25–28. [https://tust.repo.nii.ac.jp/record/294/files/v12p25-28.pdf]
- Tanabe, A.S. (2011) Kakusan4 and Aminosan: two programs for com- paring nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Molecular Ecology Resources, 11, 914–921. https://doi.org/10.1111/j.1755-0998.2011.03021.x
- Tokuda, T. (2011) Compact picture guide to Hokkaido reptiles and amphibians. Hokkaido Shimbun Press, Sapporo, 95 pp.
- Tominaga, A. & Matsui, M. (2007) Estimation of the type locality of Hynobius naevius (Temminck and Schlegel, 1838), a salamander from Japan (Amphibia: Caudata). Zoological Science, 24, 940–944. https://doi.org/10.2108/zsj.24.940
- Wiley, E.O. (1978) The evolutionary species concept reconsidered. Systematic Biology, 27, 17–26. https://doi.org/10.2307/2412809
- Wilson, G.A. & Rannala, B. (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163, 1177–1191. https://doi.org/10.1093/genetics/163.3.1177
- Yamamoto, Y. (2012) Sound monitoring of anuran amphibians at two sites of different land usage in East Mikawa area. Scientific Report of the Toyohashi Museum of Natural History, 22, 13–18. [https://www.toyohaku.gr.jp/sizensi/06shuppan/kenkyuuho/kenpou22/22kenkyuu-houkoku13.pdf]
- Yang, S.-Y. (1962) Reconsideration on the classification of Korean anurans, family Hylidae. Korean Journal of Zoology, 5, 35–38. [https://koreascience.kr/article/JAKO196211919895576.page]
- Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869–2876. https://doi.org/10.1093/bioinformatics/btt499