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Type: Article
Published: 2022-06-09
Page range: 591-599
Abstract views: 414
PDF downloaded: 36

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana)

Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA 2Zoologisches Museum Hamburg, Leibniz-Institut zur Analyse des Biodiversitaetswandels, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Department of Biology, Victor Valley College, Victorville, California 92395, USA; and Leibniz-Institut zur Analyse des Biodiversitätswandels, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia, Gd. Widyasatwaloka Jl. Raya Jakarta-Bogor Km 46, Cibinong, Bogor 16911, West Java, Indonesia
School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung 40132, Indonesia 6Basic Sciences Commission, Indonesian Academy of Sciences. 11, Jl. Medan Merdeka Selatan Jakarta 10110
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Amphibia Amphibians Biogeography Lesser Sundas Moluccas Phylogeography

Abstract

Frogs in the family Ranidae are diverse in Asia and are thought to have dispersed to the Sahul Shelf approximately 10 million years ago, where they radiated into more than a dozen species. Ranid species in the intervening oceanic islands of Wallacea, such as Hylarana florensis and H. elberti from the Lesser Sundas and H. moluccana from eastern Wallacea, are assumed to belong to the subgenus Papurana, yet this has not been confirmed with molecular data. We analyzed mitochondrial DNA of Hylarana species from five islands spanning the reported ranges of H. florensis and H. elberti and compared them to confirmed Papurana species and closely related subgenera within Hylarana. We find that the Lesser Sunda H. florensis and H. elberti form a clade that is sister to the rest of the Australo-Papuan Papurana assemblage. Species delimitation analyses and divergence time estimates suggest that populations of H. florensis on Lombok may be distinct from those on Flores at the species level. Likewise, populations of H. elberti on Sumba and Timor may be distinct from each other and from those on Wetar, tshe type locality of H. elberti. Samples from Babar Island thought to be members of H. elberti in fact belong to the wide-ranging H. daemeli, which occurs in northern Australia, across New Guinea, and on the neighboring island of Tanimbar. These results suggest that the Lesser Sundas may have served as a stepping-stone for colonization of the Sahul Shelf and that species diversity of Papurana frogs is underestimated in the Lesser Sundas.

 

References

  1. AmphibiaWeb (2021) University of California, Berkeley, CA, USA. Available from: https://amphibiaweb.org (accessed 23 December 2021)
    Blom, M.P.K., Matzke, N.J., Bragg, J.G., Arida, E., Austin, C.C., Backlin, A.R., Carretero, M.A., Fisher, R.N., Glaw, F., Hathaway, S.A., Iskandar, D.T., McGuire, J.A., Karin, B.R., Reilly, S.B., Rittmeyer, E.N., Rocha, S., Sanchez, M., Stubbs, A.L., Vences, M. & Moritz, C. (2019) Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proceedings of the Royal Society B, 286, 20182575. https://doi.org/10.1098/rspb.2018.2575
    Boettger, O. (1895) Liste der Reptilien und Batrachier der Insel Halmaheira nach den Sammlungen Prof. Dr. W. Kükenthal’s. Zoologischer Anzeiger, 18, 129–138.
    Boulenger, G.A. (1897) A list of the reptiles and batrachians collected by Mr. Alfred Everett in Lombok, Flores, Sumba, and Savu, with descriptions of new species. Annals and Magazine of Natural History, 19, 503–509. https://doi.org/10.1080/00222939708680570
    Chan, K.O., Hutter, C.R., Wood Jr, P.L., Grismer, L.L. & Brown, R.M. (2020) Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Molecular Phylogenetics and Evolution, 151, 106899. https://doi.org/10.1016/j.ympev.2020.106899
    Darlington, P.J. (1957) Zoogeography: the geographical distribution of animals. Harvard University Press, Cambridge, 675 pp.
    Deng, W., Maust, B.S., Nickle, D.C., Learn, G.H., Liu, Y., Heath, L., Kosakovsky Pond, S.L. & Mullins, J.I. (2010) DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. BioTechniques, 48, 405–408. https://doi.org/10.2144/000113370
    Dubois, A. (1992) Notes sur la classification des Ranidae (Amphibiens, Anoures). Publications de la Société Linnéenne de Lyon, 61, 305–352. https://doi.org/10.3406/linly.1992.11011
    Dubois, A., Ohler, A. & Pyron, A. (2021) New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia). Megataxa, 5, 1–738. https://doi.org/10.11646/megataxa.5.1.1
    Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797. https://doi.org/10.1093/nar/gkh340
    Evans, B.J., Brown, R.M., McGuire, J.A., Supriatna, J., Andayani, N., Diesmos, A., Iskandar, D., Melnick, D.J. & Cannatella, D.C. (2003) Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Systematic Biology, 52, 794–819. https://doi.org/10.1093/sysbio/52.6.794
    Fortuin, A.R., Van derWerff, W. & Wensink, H. (1997) Neogene basin history and paleomagnetism of a rifted and inverted forearc region, on-and offshore Sumba, Eastern Indonesia. Journal of Asian Earth Sciences, 15, 61–88. https://doi.org/10.1016/S0743-9547(96)00081-5
    Frost, D.R. (2021) Amphibian Species of the World: an Online Reference. Version 6.1. Available from: https://amphibiansoftheworld.amnh.org/index.php (accessed 12 December 2021)
    Haig, D.W. & McCartain, E. (2007) Carbonate pelagites in the post-Gondwana succession (Cretaceous – Neogene) of East Timor. Australian Journal Earth Sciences, 54, 875–897. https://doi.org/10.1080/08120090701392739
    Hall, R. (2009) Southeast Asia’s changing paleogeography. Blumea, 54, 148–161. https://doi.org/10.3767/000651909X475941
    Hall, R. (2011) Australia-SE Asia collision: plate tectonics and crustal flow. Geological Society Special Publications, 355, 75–109. https://doi.org/10.1144/SP355.5
    Hoang, D.T., Chernomor, O., Von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35, 518–522. https://doi.org/10.1093/molbev/msx281
    Kaiser, H., Carvalho, V.L., Ceballos, J., Freed, P., Heacox, S., Lester, B., Richards, S.J., Trainor, C.R., Sanchez, C. & O’Shea, M. (2011) The herpetofauna of Timor-Leste: a first report. ZooKeys, 109, 19–86. https://doi.org/10.3897/zookeys.109.1439
    Karin, B.R., Stubbs, A.L., Arifin, U., Iskandar, D.T., Arida, E., Austin, C.C. & McGuire, J.A. (2020) Crossing Lydekker’s Line: Northern Water Dragons (Tropicagama temporalis) Colonized the Mollucan Islands of Indonesia from New Guinea. Herpetologica, 76, 344–350. https://doi.org/10.1655/Herpetologica-D-19-00033
    Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K., Von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589. https://doi.org/10.1038/nmeth.4285
    Kraus, F. & Allison, A. (2007) Taxonomic notes on frogs of the genus Rana from Milne Bay Province, Papua New Guinea. Herpetological Monographs, 21, 33–75. https://doi.org/10.1655/06-004.1
    Lohman, D.J., de Bruyn, M., Page, T., von Rintelen, K., Hall, R., Ng, P.K.L., Shih, H.-T., Carvalho, G.R. & von Rintelen, T. (2011) Biogeography of the Indo-Australian archipelago. Annual Review of Ecology, Evolution, and Systematics, 42, 205–226. https://doi.org/10.1146/annurev-ecolsys-102710-145001
    Macey, J.R., Strasburg, J.L., Brisson, J.A., Vredenburg, V.T., Jennings, M. & Larson, A. (2001) Molecular phylogenetics of western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution, 19, 131–143. https://doi.org/10.1006/mpev.2000.0908
    Maryanto, I., Hisheh, S., Maharadatunkamsi, How, R.A. & Schmitt, L.H. (2021) The impact of Pleistocene glaciations on population structure and systematics in five snake species in the Banda Arc islands of southern Wallacea: the views from genes, morphology and species assemblages. Journal of the Royal Society of Western Australia, 104, 65–84.
    Mayr, E. (1944) Wallace’s line in the light of recent zoogeographic studies. The Quarterly Review of Biology, 19, 1–14. https://doi.org/10.1086/394684
    Menzies, J.I. (1987) A taxonomic revision of Papuan Rana (Amphibia: Ranidae). Australian Journal of Zoology, 35, 373–418. https://doi.org/10.1071/ZO9870373
    Mertens, R. (1967) Die herpetologische Sektion des Natur-Museums und Forschungs-Institutes Senckenberg in Frankfurt a. M. nebst einem Verzeichnis ihrer Typen. Senckenbergiana Biologica, 48, 1–106.
    Nguyen, L.T., Schmidt, H.A., Von Haeseler, A. & 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
    Nguyen, N., Duffy, B., Shulmeister, J. & Quigley, M. (2013) Rapid Pliocene uplift of Timor. Geology, 41, 179–182. https://doi.org/10.1130/G33420.1
    Ogilvie, H.A., Bouckaert, R.R. & Drummond, A.J. (2017) StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Molecular Biology and Evolution, 34, 2101–2114. https://doi.org/10.1093/molbev/msx126
    Oliver, L.A., Prendini, E., Kraus, F. & 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
    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 document compiled by S. Palumbi, Dept. Zoology, University of Hawaii, Honolulu, 44 pp.
    Pelseneer, P. (1904) La “Ligne de Weber,” limite zoologique de l’Asie et de l’Australie. Bulletin de la Classe des Sciences Academie Royale de Belgique, 1904, 1001–1022.
    Puillandre, N., Brouillet, S. & Achaz, G. (2021) ASAP: assemble species by automatic partitioning. Molecular Ecology Resources, 21, 609–620. https://doi.org/10.1111/1755-0998.13281
    Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67, 901–904. https://doi.org/10.1093/sysbio/syy032
    Reilly, S.B. (2016) Historical biogeography of reptiles and amphibians from the Lesser Sunda Islands of Indonesia. Doctoral Dissertation, University of California, Berkeley, 176 pp.
    Reilly, S.B., Stubbs, A.L., McGuire, J.A., Arifin, U., Arida, E. & Iskandar, D.T. (2016) Papurana elberti and Duttaphrynus melanostictus (Asian Common Toad). Interspecific Amplexus. Herpetological Review, 47, 114–115.
    Reilly, S.B., Wogan, G.O., Stubbs, A.L., Arida, E., Iskandar, D.T. & McGuire, J.A. (2017) Toxic toad invasion of Wallacea: A biodiversity hotspot characterized by extraordinary endemism. Global Change Biology, 23, 5029–5031. https://doi.org/10.1111/gcb.13877
    Reilly, S.B., Stubbs, A.L., Karin, B.R., Bi, K., Arida, E., Iskandar, D.T. & McGuire, J.A. (2019a) Leap-frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea. Journal of Biogeography, 46, 757–769. https://doi.org/10.1111/jbi.13526
    Reilly, S.B., Stubbs, A.L., Karin, B.R., Arida, E., Iskandar, D.T. & McGuire, J.A. (2019b) Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species. Zoologica Scripta, 48, 614–626. https://doi.org/10.1111/zsc.12368
    Reilly, S.B., Stubbs, A.L., Karin, B.R., Arifin, U., Arida, E., Iskandar, D.T. & McGuire, J.A. (2021) Genetic divergence of the Sunda ratsnake (Coelognathus subradiatus) across the Lesser Sunda Islands (Squamata: Colubridae). Amphibia-Reptilia, 42, 269–273. https://doi.org/10.1163/15685381-bja10048
    Reilly, S.B., Stubbs, A.L., Karin, B.R., Arifin, U., Arida, E., Kaiser, H., Bi, K., Iskandar, D.T. & McGuire, J.A. (2022) Phylogenomics reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda flying lizards (Genus Draco). Systematic Biology, 71, 221–241. https://doi.org/10.1093/sysbio/syab043
    Roux, J. (1911) Elbert-Sunda-Expedition des Frankfurter Vereins für Geographie und Statistik. Reptilien und Amphibien. Zoologische Jahrbücher. Abteilung für Systematik, Geographie und Biologie der Tiere, 30, 495–508.
    Tate, G.W., McQuarrie, N., van Hinsbergen, D.J.J., Bakker, R.R., Harris, R., Willett, S., Reiners, P.W., Fellin, M.G., Ganerød M. & Zachariasse W.J. (2014) Resolving spatial heterogeneities in exhumation and surface uplift in Timor-Leste: constraints on deformation processes in young orogens. Tectonics, 33, 1089–1112. https://doi.org/10.1002/2013TC003436
    Van Kampen, P.N. & Brongersma, L.D. (1931) Notes on a small collection of Amphibia from Sumba. Treubia, 13, 15–18.
    Whittaker, R.J. & Fernández-Palacios, J.M. (2007) Island biogeography: ecology, evolution, and conservation. 2nd Edition. Oxford University Press, 416 pp.