Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 5584 No. 3: 10 Feb. 2025
Type: Article
Published: 2025-02-10
DOI: 10.11646/zootaxa.5584.3.1
Page range: 301-338
Abstract views: 113
PDF downloaded: 9

Systematic evaluation of molecular genetic, morphological and acoustic variation reveals three species in the Litoria revelata complex (Anura: Pelodryadidae)

School of Biological Sciences; The University of Adelaide; Adelaide; 5005 Australia
College of Science and Engineering; James Cook University; Townsville; 4811 Australia
School of Environmental and Life Sciences; The University of Newcastle; University Drive; Callaghan; 2308; Australia
South Australian Museum; North Terrace; Adelaide; 5000; Australia; Australian Museum Research Institute; Australian Museum; 1 William St; Sydney 2010; Australia
Amphibia anura single nucleotide polymorphisms SNP taxonomy eungella Wet tropics

Abstract

We used a combination of nuclear and mitochondrial genetic data, body measurements and colouration, and male advertisement calls to analyse the systematic implications of variation in the whirring treefrog Litoria revelata complex, which occurs in three allopatric populations—north-eastern New South Wales/south-eastern Queensland, mid-eastern Queensland, and northern Queensland. The three populations each form divergent lineages for both the nuclear (single nucleotide polymorphisms; SNP) and mitochondrial datasets and are diagnosable also on the basis of morphology and advertisement calls. In combination, we use these lines of data to recognise three species: L. revelata in north-eastern New South Wales/south-eastern Queensland, L. eungellensis sp. nov. in mid-eastern Queensland, and the resurrected L. corbeni in northern Queensland. We provide a preliminary conservation assessment for each species, with the latter two species being localised to very small upland areas and warranting conservation listing and attention.

 

References

  1. Amey, A.P. & Couper, P.J. (2022) Herpetological type specimens held at the Queensland Museum: a catalogue. Memoirs of the Queensland Museum: Nature, 6, 19–259. https://doi.org/10.17082/j.2204-1478.64.2022.2020-12
  2. Anderson, E.C. & Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics, 160, 1217−1229. https://doi.org/10.1093/genetics/160.3.1217
  3. Anstis, M. (2017) Tadpoles and frogs of Australia. New Holland Publishers Pty Limited, Chatswood, 848 pp.
  4. Anstis, M., Price, L.C., Roberts, J.D., Catalano, S., Doughty, P., Hines, H.B. & Donnellan, S.C. (2016) Revision of the Australian water holding frog (Cyclorana platycephala, Anura: Hylidae), with a description of a new species and subspecies. Zootaxa, 4126 (1), 451–479. https://doi.org/10.11646/zootaxa.4126.4.1
  5. Beeman, K. (1998) Digital signal analysis, editing, and synthesis. In: Hopp, S.L., Owren, M.J. & Evans, C.S. (Eds.), Animal acoustic communication. Springer, Berlin and Heidelberg, pp. 59–103. https://doi.org/10.1007/978-3-642-76220-8_3
  6. Bryant, L.M. & Krosch, M.N. (2016) Lines in the land: a review of evidence for eastern Australia’s major biogeographical barriers to closed forest taxa. Biological Journal of the Linnean Society, 119, 238–264. https://doi.org/10.1111/bij.12821
  7. Chan, K.O. & Grismer, L.L. (2022) Correcting for body size variation in morphometric analysis. Zootaxa, 5124 (1), 471–482. https://doi.org/10.11646/zootaxa.5124.4.4
  8. Chapple, D.G., Hoskin, C.J., Chapple, S.N.J. & Thompson, M.B. (2011) Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia. BMC Evolutionary Biology, 11, 191–208. https://doi.org/10.1186/1471-2148-11-191
  9. Chifman, J. & Kubatko, L. (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics, 30, 3317–3324. https://doi.org/10.1093/bioinformatics/btu530
  10. Covacevich, J.A. & McDonald, K.R. (1993) Distribution and conservation of frogs and reptiles of Queensland rainforests. Memoirs of the Queensland Museum, 34, 189–199.
  11. Donnellan, S.C. & Mahony, M.J. (2004) Allozyme, chromosomal and morphological variability in the Litoria lesueuri species group (Anura: Hylidae), including a description of a new species. Australian Journal of Zoology, 52, 1–28. https://doi.org/10.1071/ZO02069
  12. Donnellan, S.C., Catullo, R., Rowley, J.J.L., Doughty, P., Price, L., Hines, H.B. & Richards, S.J. (2023). Revision of Litoria rothii (Anura: Hylidae: Pelodryadinae) from northern Australia. Zootaxa, 5352 (1), 73–108. https://doi.org/10.11646/zootaxa.5352.1.3
  13. Duméril, A.M.C. (1853) Mémoire sur les batraciens anoures, de la famille des hylaeformes ou rainettes. Annales des Sciences Naturelles, Paris, 3 19 (Zoology), 135–179. https://doi.org/10.5962/bhl.part.22065
  14. Duméril, A.M.C. & Bibron, G. (1841) Erpétologie Générale ou Histoire Naturelle Complète des Reptiles. Vol. 8. Roret, Paris, ii + 792 pp.
  15. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, 32, 1792–97. https://doi.org/10.1093/nar/gkh340
  16. Georges, A., Gruber, B., Pauly, G., White, D., Adams, M., Young, M., Kilian, A., Zhang, X., Shaffer, H. & Unmack, P. (2018) Genome‐wide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia. Molecular Ecology, 27, 5195–5213. https://doi.org/10.1111/mec.14925
  17. Gruber, B., Unmack, P.J., Berry, O.F. & Georges, A. (2018) dartr: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Molecular Ecology Resources, 18, 691–699. https://doi.org/10.1111/1755-0998.12745
  18. Guirguis, J., Finn, C., Johnson, J.V. & Pincheira-Donoso, D. (2023) Risk of extinction increases towards higher elevations across the world’s amphibians. Global Ecology and Biogeography, 32, 1952–1963. https://doi.org/10.1111/geb.13746
  19. Hines, H.B., Brook, M., Wilson, J., McDonald, W.J.F. & Hargreaves, J. (2020) The extent and severity of the Mackay highlands 2018 wildfires and the potential impact on natural values, particularly in the mesic forests of the Eungella-Crediton area. Proceedings of the Royal Society of Queensland, 125, 139–157.
  20. Hero, J-M., Fickling, S. & Retallick, R. (1996) The tadpole of Litoria revelata Ingram, Corben & Hosmer 1982 (Anura: Hylidae). Transactions of the Royal Society of South Australia, 120, 71–73.
  21. Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology Evolution, 35, 518–522. https://doi.org/10.1093/molbev/msx281
  22. Ingram, G.J., Corben, C.J. & Hosmer, W. (1982) Litoria revelata: a new species of tree-frog from eastern Australia. Memoirs of the Queensland Museum, 20, 635–637.
  23. IUCN (2012) IUCN Red List categories and criteria. Version 3.1. 2nd Edition. International Union for Conservation of Nature (IUCN) Species Survival Commission, Gland and Cambridge, 32 pp.
  24. 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
  25. Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., 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
  26. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Mentjies, P. & Drummond, A. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
  27. Kilian, A., Wenzl, P., Huttner, E., Carling, J., Xia, L., Blois, H., Caig, V., Heller-Uszynska, K., Jaccoud, D., Hopper, C., Aschenbrenner-Kilian, M., Evers, M., Peng, K., Cayla, C., Hok, P. & Uszynski, G. (2012) Diversity Arrays Technology: a generic genome profiling technology on open platforms. Methods in Molecular Biology, 888, 67–89. https://doi.org/10.1007/978-1-61779-870-2_5
  28. Kitching, R. (2020) Eungella–the land of clouds revisited. Proceedings of the Royal Society of Queensland, 125, 1–3.
  29. Köhler, J., Jansen, M., Rodríguez, A., Kok, P., Toledo, L., Emmrich, M., Glaw, F., Haddad, C. & Rödel, M. & Vences, M. (2017) The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice. Zootaxa, 4251 (1), 1–124. https://doi.org/10.11646/zootaxa.4251.1.1
  30. Leaché, A.D., Banbury, B.L., Felsenstein, J., de Oca, A.N. & 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
  31. Lleonart, J., Salat, J. & Torres, G.J. (2000) Removing allometric effects of body size in morphological analysis. Journal of Theoretical Biology, 205, 85–93. https://doi.org/10.1006/jtbi.2000.2043
  32. Luedeling, E. (2019) chillR: statistical methods for phenology analysis in temperate fruit trees. R package Version 0.70.21. [program]
  33. Luedtke, J.A., Chanson, J., Neam, K., Hobin, L., Maciel, A.O., Catenazzi, A., Borzée, A., Hamidy, A., Aowphol, A., Jean, A., Sosa-Bartuano, Á., Fong, G.A., de Silva, A., Fouquet, A., Angulo, A., Kidov, A.A., Muñoz Saravia, A., Diesmos, A.C., Tominaga, A., Shrestha, B., Gratwicke, B., Tjaturadi, B., Martínez Rivera, C.C., Vásquez Almazán, C.R., Señaris, C., Chandramouli, S.R., Strüssmann, C., Cortez Fernández, C.F., Azat, C., Hoskin, C.J., Hilton-Taylor, C., Whyte, D.L., Gower, D.J., Olson, D.H., Cisneros-Heredia, D.F., Santana, D.J., Nagombi, E., Najafi-Majd, E., Quah, E.S.H., Bolaños, F., Xie, F., Brusquetti, F., Álvarez, F.S., Andreone, F., Glaw, F., Castañeda, F.E., Kraus, F., Parra-Olea, G., Chaves, G., Medina-Rangel, G.F., González-Durán, G., Ortega-Andrade, H.M., Machado, I.F., Das, I., Dias, I.R., Urbina-Cardona, J.N., Crnobrnja-Isailović, J., Yang, J.H., Jianping, J., Wangyal, J.T., Rowley, J.J.L., Measey, J., Vasudevan, K., Chan, K.O., Gururaja, K.V., Ovaska, K., Warr, L.C., Canseco-Márquez, L., Toledo, L.F., Díaz, L.M., Khan, M.M.H., Meegaskumbura, M., Acevedo, M.E., Napoli, M.F., Ponce, M.A., Vaira, M., Lampo, M., Yánez-Muñoz, M.H., Scherz, M.D., Rödel, M.O., Matsui, M., Fildor, M., Kusrini, M.D., Ahmed, M.F., Rais, M., Kouamé, N.G., García, N., Gonwouo, N.L., Burrowes, P.A., Imbun, P.Y., Wagner, P., Kok, P.J.R., Joglar, R.L., Auguste, R.J., Brandão, R.A., Ibáñez, R., von May, R., Hedges, S.B., Biju, S.D., Ganesh, S.R., Wren, S., Das, S., Flechas, S.V., Ashpole, S.L., Robleto-Hernández, S.J., Loader, S.P., Incháustegui, S.J., Garg, S., Phimmachak,, S., Richards, S.J., Slimani, T., Osborne-Naikatini, T., Abreu-Jardim, T.P.F., Condez, T.H., De Carvalho, T.R., Cutajar, T.P., Pierson, T.W., Nguyen, T.Q., Kaya, U., Yuan, Z., Long, B., Langhammer, P. & Stuart, S.N. . (2023) Status and trends of the world’s amphibians: emerging threats and ongoing declines. Nature, 622, 308–314. https://doi.org/10.1038/s41586-023-06578-4
  34. Mahony, M.J., Moses, B., Mahony, S., Lemckert, F. & Donnellan, S.C. (2020) A new species of frog in the Litoria ewingii species group (Anura: Pelodryadidae) from south-eastern Australia. Zootaxa, 4858 (2), 201–230. https://doi.org/10.11646/zootaxa.4858.2.3
  35. Meyer, E.A. Hines, H.B., Clarke, J.M. & Hoskin, C.J. (2020) An update on the status of wet forest stream-dwelling frogs of the Eungella region. Proceedings of the Royal Society of Queensland, 125, 97–115.
  36. Mitchell, B.A., Callaghan, C.T. & Rowley, J.J.L. (2020) Continental-scale citizen science data reveal no changes in acoustic responses of a widespread treefrog to an urbanisation gradient. Journal of Urban Ecology, 2020, 1–12. https://doi.org/10.1093/jue/juaa002
  37. Murray, K., Retallick, R., McDonald, K.R., Mendez, D., Aplin, K., Kirkpatrick, P., Berger, L., Hunter, D., Hines, H.B., Campbell, R., Pauza, M., Driessen, M., Speare, R., Richards, S.J., Mahony, M., Freeman, A., Phillott, A.D., Hero, J.-M., Kriger, K., Driscoll, D., Felton, A., Puschendorf, R. & Skerratt, L.F. (2010) The distribution and host range of the pandemic disease chytridiomycosis in Australia, spanning surveys from 1956–2007. Ecology, 91, 1557–1558. https://doi.org/10.1890/09-1608.1
  38. 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 Evolution, 32, 268–274. https://doi.org/10.1093/molbev/msu300
  39. Parkin, T., Rowley, J.J.L., Elliott-Tate, J., Mahony, M.J., Sumner, J., Melville, J. & Donnellan, S.C. (2024) Systematic assessment of the brown tree frog (Anura: Pelodryadidae: Litoria ewingii) reveals two endemic species in South Australia. Zootaxa, 5406 (1), 1–36. https://doi.org/10.11646/zootaxa.5406.1.1
  40. Peters, W. (1874) Ueber neue Amphibien. Monatsberichte der Königlichen Preussischen Akademie der Wissenschaften zu Berlin, 1874, 616–624.
  41. Renner, S.S. (2016) Return to Linnaeus’s focus on diagnosis, not description: the use of DNA characters in the formal naming of species. Systematic Biology, 65, 1085–1095. https://doi.org/10.1093/sysbio/syw032
  42. Retallick, R.W. (1998) Population monitoring of stream-dwelling frogs at Eungella National Park. Final Report to ANCA/QDOE, June 1998, 1–51.
  43. Retallick, R.W., Hero, J.-M. & Alford, R.A. (1997) Adult population monitoring and larval ecology of the stream-dwelling frogs at Eungella National Park. Final Report to ANCA/QDOE, February 1997, 1–60.
  44. Retallick, R.W., McCallum, H. & Speare, R. (2004) Endemic infection of amphibian chytrid fungus in a frog community post-decline. PLoS Biology, 2 (e351), 1966–1971. https://doi.org/10.1371/journal.pbio.0020351
  45. Rosauer, D.F., Catullo, R.A., VanDerWal, J., Moussalli, A., Hoskin, C.J. & Moritz, C. (2017) Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PLoS ONE 12, e0169726. https://doi.org/10.1371/journal.pone.0126274
  46. Rowley, J.J.L., Callaghan, C.T., Cutajar, T., Portway, C., Potter K., Mahony, S, Trembath, D.F., Flemons, P. & Woods, A. (2019) FrogID: Citizen scientists provide validated biodiversity data on frogs of Australia. Herpetological Conservation and Biology, 14, 155–170. https://doi.org/10.3897/zookeys.912.38253
  47. Schäuble, C.S. & Moritz, C. (2001) Comparative phylogeography of two open forest frogs from eastern Australia. Biological Journal of the Linnean Society, 74, 157–170. https://doi.org/10.1111/j.1095-8312.2001.tb01384.x
  48. Schäuble, C.S., Moritz, C. & Slade, R.W. (2000) A molecular phylogeny for the frog genus Limnodynastes (Anura: Myobatrachidae), Molecular Phylogenetics and Evolution, 16, 379–391. https://doi.org/10.1006/mpev.2000.0803
  49. Sparks, A.H., Padgham, M., Parsonage, H. & Pembleton, K. (2017) bomrang: Fetch Australian Government Bureau of Meteorology Weather Data. The Journal of Open Source Software, 2, 411. https://doi.org/10.21105/joss.00411
  50. Sparks, A.H., Carroll, J., Goldie, J., Marchiori, D., Melloy, P., Padgham, M., Parsonage, H. & Pembleton, K. (2020) bomrang: Australian Government Bureau of Meteorology (BOM) Data Client. R package version 0.7.1. [https://CRAN.R-project.org/package=bomrang]
  51. Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. [program]
  52. Tamura, K., Stecher, G. & Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution, 38, 3022–3027. https://doi.org/10.1093/molbev/msab120
  53. Thorpe, R.S. (1976) Biometric analysis of geographic variation and racial affinities. Biological Reviews, 51, 407–452. https://doi.org/10.1111/j.1469-185X.1976.tb01063.x
  54. Trifinopoulos, J., Nguyen, L.T., von Haeseler, A. & Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44 (W1), W232–W235. https://doi.org/10.1093/nar/gkw256
  55. Venables, W.N. & Ripley, B.D. (2002) Modern applied statistics with S. Fourth. Springer. Available from: http://www.stats.ox.ac.uk/pub/MASS4 (accessed 9 December 2024) https://doi.org/10.1007/978-0-387-21706-2
  56. Watson, G.F., Loftus-Hills, J.J. & Littlejohn, M.J. (1971) The Litoria ewingii complex (Anura: Hylidae) in south eastern Australia. 1. A new species from Victoria. Australian Journal of Zoology, 19, 401–416. https://doi.org/10.1071/ZO9710401
  57. Webster, G.N., White, T.E. & Whiting, M.J. (2023) Male nuptial display colour and vocalisation appear to signal independent information in the Whirring Tree Frog. Behavioral Ecology and Sociobiology, 77, 1–11. https://doi.org/10.1007/s00265-023-03343-5
  58. Wells, R.W. & Wellington, C.R. (1985) A classification of the Amphibia and Reptilia of Australia. Australian Journal of Herpetology, Supplemental Series 1, 1–61.
  59. White, A.M., Whitford, R.W. & Mahony, M.J. (1994) A new species of Litoria (Anura: Hylidae) from eastern Australia. Proceedings of the Linnean Society of New South Wales, 114, 3–10.