Abstract
We investigated phylogenetic relationships among populations of two species within the genus Leptophryne, L. cruentata and L. borbonica, using the mitochondrial 16S rRNA gene. As a result, we identified two distinct lineages within populations currently considered Leptophryne cruentata: 1) a lineage containing L. cruentata from the type locality, and 2) a lineage from Mt. Slamet and Mt. Ciremai. On the basis of genetic and morphological differences, we describe the Mt. Slamet and Mt. Ciremai populations as a new species, L. javanica sp. nov. The new species is distinguished from L. cruentata and L. borbonica by the following combination of morphological characters: the presence of distinct yellow mottling on the dorsum; relatively small body size (SVL male 22.2–24.0 mm, female 29.6 mm); relatively short hindlimbs (HLL 37.0–40.9 mm); relatively short fourth toe (4ToeL 4.3–6.0 mm); basal webbing on the hands, but well developed on toes; very protruding snout and an indistinct tympanum. In our preliminary phylogenetic analysis, we also detected four distinct lineages within Leptophryne borbonica: 1) a lineage containing true L. borbonica from west Java, 2) a lineage from Lampung (Sumatra I), 3) a lineage from northern Borneo, and 4) a lineage from Bengkulu (Sumatra II). Further studies are needed to determine taxonomic status of these lineages.
References
Arifin, U., Smart, U., Hertwig, S.T., Smith, E.N., Iskandar, D.T. & Haas, A. (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution, 94 (1), 163–193.
https://doi.org/10.1655/09-037.1Berry, P.Y. (1975) The Amphibia Fauna of Peninsular Malaysia. Tropical Press, Kuala Lumpur, x + 130 pp.
Brown, R.M., Siller, C.C., Diesmos, A.C. & Alcala, A.C. (2009) Philippine frogs of the genus Leptobrachium (Anura, Megophrydae), phylogeny-based species delimitation, taxonomic review, and description of three new species. Herpetological Monographs, 23, 1, 1–44.
https://doi.org/10.1655/09-037.1Davis, D.D. (1935) A new generic and family position for Bufo borbonica. Field Museum of Natural History Publication. Zoological Series, 20, 87–92.
Fitzinger, L.J.F.J. (1843) Systema Reptilium. Fasciculus Primus. Braumuülleret Seidel, Wien, 106 pp.
https://doi.org/10.5962/bhl.title.4694Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P.E., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M. & Wheeler, W.C. (2006) The amphibian tree of life. Bulletin of the American Museum of Natural History, 297, 1–370.
https://doi.org/10.1206/0003-0090Foquet, A., Gilles, A., Vences, M., Marty, C., Blanc, M. & Gemmel, N.J. (2007) Underestimation of species richness in Neotropical frog revelaed by mtDNA analyses. PLoSone, 2, 10, 1–10.
https://doi.org/10.1371/journal.pone.0001109
Hamidy, A., Matsui, M., Shimada, T., Nishikawa, K., Yambun, P., Sudin, A., Kusrini, M.D. & Kurniati, H. (2011) Morphological and genetic discordance in two species of Bornean Leptobrachium (Amphibia, Anura, Megophryidae). Molecular Phylogenetic and Evolution, 2011, 904–913.
https://doi.org/10.1016/j.ympev.2011.08.020Hamidy, A., Matsui, M., Nishikawa, K. & Belabut, D.M. (2012) Detection of cryptic taxa in Leptobrachium nigrops (Amphibia, Anura, Megophryidae) with description of two new species. Zootaxa, 3398, 22–39.
Hamidy, A. & Kurniati, H. (2015) A new species of tree frog genus Rhacophorus from Sumatra, Indonesia (Amphibia, Anura). Zootaxa, 3947 (1), 049–066.
https://doi.org/10.11646/zootaxa.3947.1.3Hamidy, A. & Matsui, M. (2017) Phylogenetic relationships of Leptobrachium hasseltii Tschudi, 1838 (Amphibia, Anura, Megophryidae) - Detection of a possible cryptic species. Treubia, 44, 15–28. Available from: http://e-journal.biologi.lipi.go.id/index.php/treubia/article/view/3286/2906 (Accessed 25 Jul. 2018)
Harvey, M.B., Pemberton, A.J. & Smith, E.N. (2002) New and poorly known parachuting frogs (Rhacophoridae: Rhacophorus) from Sumatra and Java. Herpetological Monographs, 16, 46–92.
https://doi.org/10.1655/0733-1347(2002)016[0046:napkpf]2.0.co;2Hedges, S.B., Nussbaum, R.A. & Maxson, L.R. (1993) Caecilian phylogeny and biogeography inferred from mitochondrial DNA sequences of the 12S rRNA and 16S rRNA genes (Amphibia, Gymnophiona). Herpetological Monographs, 7, 64–76.
https://doi.org/10.2307/1466952Inger, R.F. (1966) The systematics and zoogeography of the Amphibia of Borneo. Fieldiana Zoology, 52, 1–402.
Inger, R.F. & Iskandar, D.T. (2005) A collection of amphibians from West Sumatra, with description of new species of Megophrys (Amphibia, Anura). The Raffless Bulletin of Zoology, 53, 133–142.
Inger, R.F., Stuart, B.L. & Iskandar, D.T. (2009) Systematics of a widespread Southeast Asian frog, Rana chalconota (Amphibia, Anura, Ranidae). Zoological Journal of the Linnean Society, 155, 123–147.
https://doi.org/10.1111/j.1096-3642.2008.00440.xIskandar, D.T. (1998) The Amphibians of Java and Bali. Research and Development Center for Biology, LIPI, Bogor, 117 pp.
Iskandar, D.T & Mumpuni.(2004) Leptophryne cruentata. The IUCN Red List of Threatened Species 2004: e.T54815A1207443. International Union of Conservation Nation. Available from: http://iucnredlist.org/details/54815/0 (accessed 3 February 2017)
https://doi.org/10.2305/IUCN.UK.2004.RLTS.T54815A11207443.enKusrini, M.D., Skerratt, L., Berger, L., Garland, S. & Endarwin, W. (2008) Chytridiomycosis in frogs of Mount Gede-Pangrango, Indonesia. Disease of Aquatic Organisms, 82, 187–194.
https://doi.org/10.3354/dao01981
Kusrini, M.D., Lubis, M.I., Endarwin, W., Yazid, M., Darmawan, B., Ul-Hasanah, A.U., Sholihat, N., Tajali, A., Lestari, V., Utama, H., Nasir, D.M., Ardiansyah, D. & Rachmadi, R. (2017) Elevation shift range after 40 years: The amphibians of Mount Gede Pangrango National Park revisited. Conservation Biology, 206, 75–84.
https://doi.org/10.1016/j.biocon.2016.12.018Kurniati, H. (2003) Kodok merah Leptopryne cruentata ditemukan di Taman Nasional Gunung Halimun Jawa Barat. Fauna Indonesia, 5, 71–74.
Kurniati, H. (2006) The amphibian species in Gunung Halimun National Park, West Java, Indonesia. Zoo Indonesia, 15, 107–120.
Kurniati, H. (2016) Bioacoustics of Hylarana celebensis (Peters, 1872) (Anura: Ranidae) From Sulawesi. Jurnal Biology Indonesia, 12, 1–7.
Liem, D.S.S. (1971) The frogs and toads of Tjibodas National Park, Mount Gede, Java, Indonesia. Philippine Journal of Science, 100, 131–161.
Manthey, U. & Grosmann, W. (1997) Amphibien und Repetilien Südostasiens. Natur und Tier, Verlag, 512 pp.
Matsui, M. (1984) Morphometric variation analyzes and revision of the Japanese toads (Genus Bufo, Bufonidae). Contributions from the Biological Laboratory, Kyoto University, 26, 209–428.
Matsui, M., Yambun, P. & Sudin, A. (2007) Taxonomic relationships of Ansonia anotis Inger, Tan, and Yambun, 2001 and Pedostibes maculatus (Mocquard, 1890), with a Description of a new genus (Amphibia, Bufonidae). Zoological Science, 24, 1159–1166.
https://doi.org/10.2108/zsj.24.1159Matsui, M., Hamidy, A., Murphy, R.W., Khonsue, W., Yambun, P., Shimada, T., Ahmad, N., Belabut, D.M. & Jiang, J-P. (2010) Phylogenetic relationship of megophyid frogs of the genus Leptobrachium (Amphibia, Anura) as revealed by mtDNA gene sequences. Molecular Phylogenetic and Evolution, 56, 259–272.
https://doi.org/10.1016/j.ympev.2010.03.014Matsui, M., Nishikawa, K., Yeo, S.T. & Eto, K. (2012) Notes on a rare Bornean Bufonid Ansonia latidisca Inger, 1966, with special reference to its phylogenetic position. Current Herpetology, 31, 87–96.
https://doi.org/10.5358/hsj.31.87Matsui, M., Kuraishi, N., Eto, K., Hamidy, A., Nishikawa, K., Shimada, T., Yambun, P., Vairappan, C.S. & Hossman, M.Y. (2016) Unusually high genetic diversity in the Bornean Limnonectes kuhlii-like fanged frogs (Anura, Dicroglossidae). Molecular Phylogenetic and Evolution, 102, 305–319.
https://doi.org/10.1016/j.ympev.2016.06.009McLeod, S.M., Horner, A.J., Husted, C., Barley, A. & Iskandar, D.T. (2011) “Same-same, but different”, an unusual new species of the Limnonectes kuhlii complex from West Sumatra (Anura, Dicroglossidae). Zootaxa, 2883 (1), 52–64.
https://doi.org/10.11646/zootaxa.2883.1.4Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) “Creating the CIPRES Science Gateway for inference of large phylogenetic trees” in Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 14 November 2010, pp. 1–8.
Matsui, M.,Tominaga, A., Liu, W., Khosue, W., Grismer, L.L., Diesmos, A.C., Das, I., Sudin, A., Yambun, P., Yong, H., Sukumaran, J. & Brown, R.M. (2010) Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetic and Evolution, 54, 561–570.
https://doi.org/10.1016/j.ympev.2009.08.003Mumpuni (2014) Keragaman amfibi dan catatan baru katak di kawasan wisata Guci, Provinsi Jawa Tengah. Zoo Indonesia, 23, 13–19.
Pettitt, B.A., Bourne, G.R. & Bee, M.A. (2012) Quantitative Acoustic analysis of the Vocal Repertoire of the Golden Rocket Frog (Anomaloglossus beebei). Journal Acoustical Society of America, 131 (6), 4811–4820.
https://doi.org/10.1121/1.4714769Pyron, R.A. & Wiens, J.J. (2011) A large-scale phylogeny of Amphibia including 2800 species, and revised classification of extant frogs, salamanders, and caecilians. Molecular and Phylogenetics Evolution, 61, 543–583.
https://doi.org/10.1016/j.ympev.2011.06.012Riyanto, A. & Kurniati, H. (2014) Three new species of Chiromantis Peters, 1854 (Anura: Rhacophoridae) from Indonesia. Russian Journal of Herpetology, 21, 65–73.
Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3, Bayesian phylogenetic inference under mix models. Bioinformatics, 19, 1572–1574.
https://doi.org/10.1093/bioinformatics/btg180Roelants, K., Gower, D.J., Wilkinson, M., Loader, S.P., Biju, S.D., Guillaume, K., Moriau, L. & Bossuyt, F. (2007) Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy Sciences, 104 (3), 887–892.
https://doi.org/10.1073/pnas.0608378104Sambrook, J., Fritschi, E.F. & Maniatis, T. (1989) Molecular Cloning, a Laboratory Manual. Cold Sprin Harbor Laboratory Press, New York, 1120 pp.
Smart, U., Sarker, G.C., Arifin, U., Harvey, M.B., Sidik, I., Hamidy, A., Kurniawan, N. & Smith, E.N. (2017) A new genus and two new species of arboreal toads from higlands of Sumatra with a phylogeny of Sundaland toad genera. Herpetologica, 73 (1), 63–75.
https://doi.org/10.1655/Herpetologica-D-16-00041Setiawan, I., Rakhman, Z., Muzakkir, A., Saputro, B.P. & Zulkarnaen, I. (2014) Kajian Biodiversitas dan Pembuatan Kebun Koleksi Anggrek di Taman Nasional Gunung Ciremai. Unpublished fieldwork report, Laporan Akhir-Pusat Informasi Lingkungan Indonesia, Bogor, 115 pp. [in Indonesian]
Stamatakis, A. (2014) RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312–1313.
https://doi.org/10.1093/bioinformatics/btu033Streicher, J.W., Hamidy, A., Harvey, M.B., Andres, B., Shaney, K.J., Kurniawan, N. & Smith, E.N. (2014) Mitochondrial DNA reveals a new species of parachuting frog (Rhacophoridae: Rhacophorus) from Sumatra. Zootaxa, 3878 (4), 351–356.
https://doi.org/10.11646/zootaxa.3878.4.2Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6, Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.
https://doi.org/10.1093/molbev/mst197Tanabe, A.S. (2007) Kakusan, a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data. Molecular Ecology, 7, 962–964.
https://doi.org/10.1111/j.1471-8286.2007.01807.xTaylor, E.H. (1962) The amphibian fauna of Thailand. The University of Kansas Science Bulletin, 42 (8), 265–599.
Tschudi, J. (1838) Classification der Batrachier mit Berücksichtigung der fossilen Thiere dieser Abtheilung der Reptilien. Neuchâtel, 1–99.
van Kampen, P.N. (1910) Eine neue Nectophryne-Art und andere Amphibien von Deli (Sumatra). Natuurkundig tijdschrifr voor Nederlandsch Indië, 69, 18–24.
van Kampen, P.N. (1912) Javanische Amphibien gesammelt von Edw. Jacobson. Notes from The Leyden Museum, 34, 75–79.
van Kampen, P.N. (1923) The Amphibia of the Indo-Australian Archipelago. E.J. Brill, Leiden, xii + 304 pp.
van Bocxlaer, I., Biju, S.D., Loader, S.P. & Bossuyt, F. (2009) Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot. BMC Evolution Biology, 9 (131), 1–10
https://doi.org/10.1186/1471-2148-9-131Vences, M., Thomas, M., Van der Meijden, A., Chiari, Y. & Vieites, D.R. (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology, 2, 1.
https://doi.org/10.1186/1742-9994-2-5Wostl, E., Riyanto, A., Hamidy, A., Kurniawan, N., Smith, E.N. & Harvey, M.B. (2017) A taxonomic revision of the Philautus (Anura: Rhacophoridae) of Sumatra with the description of four new species. Herpetological Monographs, 31 (1), 70–113.
https://doi.org/10.1655/HERPMONOGRAPHS-D-16-00007Zhang, 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 Evolution, 30 (8), 1899–1915.
https://doi.org/10.1093/molbev/mst091