The six species of mountain frogs (Philoria: Limnodynastidae: Anura) are endemic to south-eastern Australia. Five species occur in headwater systems in mountainous north-eastern New South Wales (NSW) and south-eastern Queensland (Qld), centred on the Gondwana Rainforests of Australia World Heritage Area. A previous molecular genetic analysis identified divergent genetic lineages in the central and western McPherson Ranges region of Qld and NSW, but sampling was inadequate to test the species status of these lineages. With more comprehensive geographic sampling and examination of the nuclear genome using SNP analysis, we show that an undescribed species, P. knowlesi sp. nov., occurs in the central and western McPherson Ranges (Levers Plateau and Mount Barney complex). The new species is not phylogenetically closely related to P. loveridgei in the nuclear data but is related to one of two divergent lineages within P. loveridgei in the mtDNA data. We postulate that the discordance between the nuclear and mtDNA outcomes is due to ancient introgression of the mtDNA genome from P. loveridgei into the new species. Male advertisement calls and multivariate morphological analyses do not reliably distinguish P. knowlesi sp. nov. from any of the Philoria species in northeast NSW and southeast Qld. The genetic comparisons also enable us to define further the distributions of P. loveridgei and P. kundagungan. Samples from the Lamington Plateau, Springbrook Plateau, Wollumbin (Mt Warning National Park), and the Nightcap Range, are all P. loveridgei, and its distribution is now defined as the eastern McPherson Ranges and Tweed caldera. Philoria kundagungan is distributed from the Mistake Mountains in south-eastern Qld to the Tooloom Scrub on the Koreelah Range, southwest of Woodenbong, in NSW, with two subpopulations identified by SNP analysis. We therefore assessed the IUCN threat category of P. loveridgei and P. kundagungan and undertook new assessments for each of its two subpopulations and for the new taxon P. knowlesi sp. nov., using IUCN Red List criteria. Philoria loveridgei, P. kundagungan (entire range and northern subpopulation separately) and P. knowlesi sp. nov. each meet criteria for “Endangered” (EN B2(a)(b)[i, iii]). The southern subpopulation of P. kundagungan, in the Koreelah Range, meets criteria for “Critically Endangered” (CE B2(a)(b)[i, iii]). These taxa are all highly threatened due to the small number of known locations, the restricted nature of their breeding habitat, and direct and indirect threats from climate change, and the potential impact of the amphibian disease chytridiomycosis. Feral pigs are an emerging threat, with significant impacts now observed in Philoria breeding habitat in the Mistake Mountains.
Anstis, M. (2013) Tadpoles and Frogs of Australia. New Holland Publishers, Sydney, 831pp.
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
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.
Bolitho, L.J., Rowley, J.J., Hines, H.B. & Newell, D. (2021) Occupancy modelling reveals a highly restricted and fragmented distribution in a threatened montane frog (Philoria kundagungan) in subtropical Australian rainforests. Australian Journal of Zoology, 67, 231–240. https://doi.org/10.1071/ZO20037
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
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
Dowdy, A. Abbs, D., Bhend, J., Chiew, F., Church, J., Ekström, M., Kirono, D., Lenton, A., Lucas, C., McInnes, K., Moise, A., Monselesan, D., Mpelasoka, F., Webb, L. & Whetton, P. (2015) s.n. In: Ekström, M. Whetton, P., Gerbing, C., Grose, M., Webb, L. & Risbey, J. (Eds.), East Coast Cluster Report, Climate Change in Australia Projections for Australia’s Natural Resource Management Regions: Cluster Reports. CSIRO and Bureau of Meteorology. Available from: https://www.climatechangeinaustralia.gov.au/media/ccia/2.2/cms_page_media/168/EAST_COAST_CLUSTER_REPORT_2021updated.pdf (accessed 8 February 2022) https://www.climatechangeinaustralia.gov.au/en/communication-resources/reports/
Dowdy, A.J., Ye, H., Pepler, A., Thatcher, M., Osbrough, S L., Evans, J.P., Di Virgilio, G. & McCarthy, N. (2019) Future changes in extreme weather and pyroconvection risk factors for Australian wildfires. Scientific Reports, 9, 10073. https://doi.org/10.1038/s41598-019-46362-x
Earl, D.A. (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
Evans, J.P., Ji, F., Lee, C., Smith, P., Argüeso, D. & Fita, L. (2014) Design of a regional climate modelling projection ensemble experiment—NARCliM. Geoscientific Model Development, 7, 621–629.
Familiar López, M. (2016) Distribution, ecology, disease and physiology of mountain-top endemic frogs in the face of climate change: A study on Philoria sp. PhD Dissertation, Griffith University, Brisbane. Available from: https://research-repository.griffith.edu.au/handle/10072/368164?show=full (accessed 8 February 2022)
Familiar López, M., Rebollar, E.A., Harris, R.N., Vredenburg, V.T. & Hero, J.-M. (2017) Temporal variation of the skin bacterial community and Batrachochytrium dendrobatidis infection in the terrestrial cryptic frog Philoria loveridgei. Frontiers in Microbiology, 8, 2535. https://doi.org/10.3389/fmicb.2017.02535
Georges, A., Gruber, B., Pauly, G.B., White, D., Adams, M., Young, M.J., Kilian, A., Zhang, X., Shaffer, H.B. & Unmack, P.J. (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
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
Heard, G., Bolitho, L., Newell, D., Hines, H., McCall, H., Smith, J. & Scheele, B. (2021) Post-fire impact assessment for priority frogs: northern Philoria. NESP Threatened Species Recovery Hub Project 8.1.3 report, Brisbane. Available from; https://www.nespthreatenedspecies.edu.au/media/srzerc1y/8-1-3-post-fire-impact-assessment-for-priority-frogs_v6.pdf (accessed 8 February 2022)
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
Hutley, L.B., Doley, D. & Yates, D.J. & Boonsaner, A. (1997) Water balance of an Australian subtropical rainforest at altitude: the ecological and physiological significance of intercepted cloud and fog. Australian Journal of Botany, 45, 311–329. https://doi.org/10.1071/BT96014
Ingram, G.J. & Corben, C.J. (1975) A new species of Kyarranus (Anura: Leptodactylidae) from Queensland, Australia. Memoirs of the Queensland Museum, 17, 335–339.
IUCN (2012) Guidelines for application of IUCN Red List criteria at regional and national levels. Version 4.0. Available from: https://www.iucn.org/content/guidelines-application-iucn-red-list-criteria-regional-and-national-levels-version-40 (acessed 8 February 2022)
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
Katoh, K., Kuma, K., Toh, H. & Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33, 511–518. https://doi.org/10.1093/nar/gki198
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
Kopelman, N.M., Mayzel, J., Jakobsson, M., Rosenberg, N.A. & Mayrose, I. (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15, 1179–1191. https://doi.org/10.1111/1755-0998.12387
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., Meintjes, P. & Drummond, A. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics Applications Note, 28, 1647–164. https://doi.org/10.1093/bioinformatics/bts199
Keith, D.A., Mahony, M., Hines, H., Elith, J., Regan, T.J., Baumgartner, J.B., Hunter, D., Heard, G.W., Mitchell, N.J., Parris, K.M., Penman, T., Scheele, B., Simpson, C.C., Tingley, R., Tracy, C.R., West, M. & Akcakaya, H.R. (2014) Detecting extinction risk from climate change by IUCN Red List criteria. Conservation Biology, 28, 810–819. https://doi.org/10.1111/cobi.12234
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
Knesel, K.M., Cohen, B.E., Vasconcelos, P.M. & Thiede, D.S. (2008) Rapid change in drift of the Australian plate records collision with Ontong Java plateau. Nature, 454, 754–758. https://doi.org/10.1038/nature07138
Knowles, R., Mahony, M., Armstrong, J. & Donnellan, S.C. (2004) Systematics of sphagnum frogs of the genus Philoria (Anura: Myobatrachidae) in eastern Australia. Records of the Australian Museum, 56, 57–74.
Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
Laidlaw, M.J., McDonald, W.J.F., Hunter, R.J., Putland, D.A. & Kitching, R.L. (2011) The potential impacts of climate change on Australian subtropical rainforest. Australian Journal of Botany, 59, 440–449. https://doi.org/10.1071/BT10319
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
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
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, 201–230. https://doi.org/10.11646/zootaxa.4858.2.3
Mahony, M.J., Ross, D., Newell, D., Willacy, R., Hero, J-M., Familiar-Lopez, & Lollback, G. (2013) Monitoring the effects of climate change: A survey and report on the status of endemic high altitude frogs in the Gondwana Rainforests of Australia World Heritage Area. Grant report Gondwana WHA (DECCW-720-2010). Unpublished Report for the NSW Office of Environment and Heritge, Sydney. pp. 1–97.
Moritz, C. (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic Biology, 51, 238–254. https://doi.org/10.1080/10635150252899752
Narsey, S., Laidlaw, M., Colman, R., Pearce, K., Hopkins, M. & Dowdy, A (2020) Impact of climate change on cloud forests in the Gondwana Rainforests of Australia World Heritage Area. NESP Earth Systems and Climate Change Hub. Available from; https://nespclimate.com.au/wp-content/uploads/2020/09/Gondwana-LCL-CS-TR-final.pdf (accessed 8 February 2022)
Newell, D.A (2018) An update on frog declines from the forests of subtropical eastern Australia. In: Heatwole, H. & Rowley, J. (Eds.), Status of Conservation and Decline of Amphibians. CSIRO Publishing, Melbourne, pp. 29–37.
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
Parker, H.W. (1940) The Australasian frogs of the family Leptodactylidae. Novitates Zoologicae, 42, 1–106.
Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959. https://doi.org/10.1534/genetics.116.195164
Queensland Herbarium (2021) Regional Ecosystem Description Database (REDD). Version 12. March 2021. Department of Environment and Science, Brisbane. https://apps.des.qld.gov.au/regional-ecosystems/ 21 Feb 2022
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
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
Reside, A.E., VanDerWal, J., Phillips, B., Shoo, L.P., Rosauer, D.F., Anderson, B.A., Welbergen, J., Moritz, C., Ferrier, S., Harwood, T.D., Williams, K.J., Mackey, B., Hugh, S. & Williams, S.E. (2013) Climate change refugia for terrestrial biodiversity: Defining areas that promote species persistence and ecosystem resilience in the face of global climate change. National Climate Change Adaptation Research Facility, Gold Coast, 216 pp.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
Sauer, J., Domisch, S., Nowak, C. & Haase, P. (2011) Low mountain ranges: summit traps for montane freshwater species under climate change. Biodiversity and Conservation, 20, 3133–3146. https://doi.org/10.1007/s10531-011-0140-y
Shea, G. (2005) The type location of the sphagnum frog Philoria loveridgei (Anura: Myobatrachidae). Memoirs of the Queensland Museum, 51, 524.
Spencer, B. (1901) Two new species of frogs from Victoria. Proceedings of the Royal Society of Victoria, 13, 175–178.
Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
Thorpe, R.S. (1976) Biometric analysis of geographic variation and racial affinities. Biological Reviews, 51, 407–452.
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
Willacy, R.J., Mahony, M. & Newell, D.A. (2015) If a frog calls in the forest: Bioacoustic monitoring reveals the breeding phenology of the endangered Richmond Range mountain frog (Philoria richmondensis). Austral Ecology, 40, 625–633. https://doi.org/10.1111/aec.12228