Abstract
Using a combination of morphological and molecular data we recognize three new species of Puppet Toad, Sigalegalephrynus Smart, Sarker, Arifin, Harvey, Sidik, Hamidy, Kurniawan & Smith, a recently described genus endemic to the highland forests of Sumatra, Indonesia. Phylogenetic analysis of mitochondrial DNA sequences recovered a monophyletic relationship among all Puppet Toads, with two distinct evolutionary clades, a northern and a southern. The northern clade includes Sigalegalephrynus gayoluesensis sp. nov., and S. burnitelongensis sp. nov., and the southern clade includes S. harveyi sp. nov., S. mandailinguensis, and S. minangkabauensis. With the discovery of these three new species, Sigalegalephrynus contains more endemic species than any other genus of toad in Indonesia. We used maximum entropy, implemented in MaxEnt, to identify suitable habitats and occurrence probability of additional undescribed new species from the island. The most important predictors of Sigalegalephrynus distribution were elevation (64.5%) and land cover (7.11%). Based on the probability of presence, it is likely that there are many more species of the genus awaiting discovery in Sumatra. Our analysis, based on IUCN Red List of Threatened Species category and criteria, shows that all of the five species of Sigalegalephrynus are in great risk of extinction and should be placed into the Endangered (EN) category of IUCN Red List.
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, 163–193.
https://doi.org/10.3897/zse.94.22120
Audacity Team (2016) Audacity® Free Audio Editor and Recorder. Version 2.1.2. Available from: https://www.audacityteam.org/ (accessed 6 June 2017)
Bachman, S., Moat, J., Hill, A.W., de la Torre, J. & Scott, B. (2011) Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool. ZooKeys, 150, 117–126.
https://doi.org/10.3897/zookeys.150.2109
Bagheri, A., Fathipour, Y., Seyahooei, M.A. & Zeinalabedini, M. (2018) Ecological niche modeling of Ommatissus lybicus (Hemiptera: Tropiduchidae) De Bergevin. Annals of the Entomological Society of America, 111, 114–121.
https://doi.org/10.1093/aesa/say006
Bickford, D., Howard, S.D., Ng, D.J.J. & Sheridan, J.A. (2010) Impacts of climate on the amphibians and reptiles of Southeast Asia. Biodiversity and Conservation, 19, 1043–1062.
https://doi.org/10.1007/s10531-010-9782-4
Bioacoustics Research Program (2016) Raven lite: Interactive Sound Analysis Software. Version 2.0.0. Computer software. The Cornell Lab of Ornithology, Ithaca, New York. Available from: http://ravensoundsoftware.com/ (accessed 17 July 2017)
Bell, R.C. (2016) A New Species of Hyperolius (Amphibia: Hyperoliidae) from Príncipe Island, Democratic Republic of São Tomé and Príncipe. Herpetologica, 72, 343–351.
https://doi.org/10.1655/Herpetologica-D-16-00008.1
Berzaghi, F., Engel, J.E., Plumptre, A.J., Mugabe, H., Kujirakwinja, D., Ayebare, S. & Bates, J.M. (2018) Comparative niche modeling of two bush-shrikes (Laniarius) and the conservation of mid-elevation Afromontane forests of the Albertine Rift. The Condor, 120, 803–814.
https://doi.org/10.1650/CONDOR-18-28.1
Braunisch, V., Coppes, J., Arlettaz, R., Suchant, R., Schmid, H. & Bollmann, K. (2013) Selecting from correlated climate variables: a major source of uncertainty for predicting species distribution under climate change. Ecography, 36, 971–983. https://doi.org/10.1111/j.1600-0587.2013.00138.x
Brito, D., Moreira, D.O., Coutinho, B.R. & Opera, M. (2012) Ill Disease: Disease hotspots as threats to biodiversity. Journal of Nature Conservation, 20, 72–75.
https://doi.org/10.1016/j.jnc.2011.10.003
Brothers, J.R. & Lohmann, K.J. (2018) Evidence that magnetic navigation and geographic imprinting shape spatial genetic variation in sea turtles. Current Biology, 28, 1325–1329.
https://doi.org/10.1016/j.cub.2018.03.022
Brown, J.L. (2014) SDMtoolbox: a GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. Methods in Ecology and Evolution, 7, 694–700.
https://doi.org/10.1111/2041-210X.12200
Brown. J.L., Bennett, J.R. & French, C.M. (2017) SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. PeerJ, e4095, 1–12.
https://doi.org/10.7717/peerj.4095
Brown, R.M. & Stuart, B.L. (2012) Patterns of biodiversity discovery through time: an historical analysis of amphibian species discoveries in the Southeast Asian mainland and adjacent island archipelagos. In: Gower, D.J., Johnson, K.G., Richardson, J.E., Rosen, B.R., Rüber, L. & Williams, S.T. (Eds.), Biotic Evolution and Environmental Change in Southeast Asia. Cambridge University Press, Cambridge, pp. 348–389.
https://doi.org/10.1017/CBO9780511735882.016
Chan, K.O. & Grismer, L.L. (2019) To split or not to split? Multilocus phylogeny and molecular species delimitation of Southeast Asian toads (family: Bufonidae). BMC Evolutionary Biology, 19, 1–12.
https://doi.org/10.1186/s12862-019-1422-3
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540–552.
https://doi.org/10.1093/oxfordjournals.molbev.a026334
Coleman, J.L., Ascher, J.S., Bickford, D., Buchori, D., Cabanban, A., Chisholm, R.A., Chong, K.Y., Christie, P., Clements, G.R., dela Cruz, T.E.E., Dressler, W., Edwards, D.P., Francis, C.M., Friess, D.A., Giam, X., Gibson, L., Huang, D., Hughes, A.C., Jaafar, Z., Jain, A., Koh, L.P., Kudavidanage, E.P., Lee, B.P.Y.-H., Lee, J., Lee, T.M., Leggett, M., Leimona, B., Linkie, M., Luskin, M., Lynam, A., Meijaard, E., Nijman, V., Olsson, A., Page, S., Parolin, P., Peh, K.S.-H., Posa, M.R., Prescott, G.W., Rahman, S.A., Ramchunder, S.J., Rao, M., Reed, J., Richards, D.R., Slade, E.M., Steinmetz, R., Tan, P.Y., Taylor, D., Todd, P.A., Vo, S.T., Webb, E.L., Ziegler, A.D. & Carrasco, L.R. (2019) Top 100 research questions for biodiversity conservation in Southeast Asia. Biological Conservation, 29, 105–117.
https://doi.org/10.1016/j.biocon.2019.03.028
Crow, M.J. (2005) Tertiary volcanicity. In: Barber, A.J., Crow, M.J. & Milsom, J. (Eds.), Sumatra: Geology, Resources and Tectonic Evolution. Geological Society, Memoirs, London, pp. 98–119.
https://doi.org/10.1144/GSL.MEM.2005.031.01.08
Daszak, P., Cunningham, A.A. & Hyatt A.D. (2003) Infectious disease and amphibian population declines. Diversity and Distribution, 9, 141–150.
https://doi.org/10.1046/j.1472-4642.2003.00016.x
de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56, 879–886.
https://doi.org/10.1080/10635150701701083
Duellman, W.E. (1970) The Hylid Frogs of Middle America. Monograph of the Museum of Natural History, University of Kansas, 1, 1–753. Available from: https://archive.org/details/hylidfrogsofmidd02duel (accessed 5 September 2018)
Duellman, W.E. (2001) The Hylid Frogs of Middle America. Society for the Study of Amphibians and Reptiles, Ithaca, New York, xvi + 1159 pp.
Dufresnes, C., Mazepa, G., Rodrigues, N., Brelsford, A., Litvinchuk, S.N., Sermier, R., Lavanchy, G., Betto-Colliard, C., Blaser, O., Borzée, A., Cavoto, E., Fabre, G., Ghali, K., Grossen, C., Horn, A., Leuenberger, J., Phillips, B.C., Saunders, P.A., Savary, R., Maddalena, T., Stöck, M., Dubey, S., Canestrelli, D. & Jeffries, D.L. (2018) Genomic Evidence for cryptic speciation in tree frogs from the Apennine Peninsula, with description of Hyla perrini sp. nov. Frontiers in Ecology and Evolution, 00144, 1–18. https://doi.org/10.3389/fevo.2018.00144
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acid research, 32, 1792–1797.
https://doi.org/10.1093/nar/gkh340
Elith, J., Phillips, S.J., Hastie, T., Dudík, M., Chee, Y.E. & Yates, C.J. (2011) A statistical explanation of MaxEnt for ecologists. Diversity and Distributions, 17, 43–57.
https://doi.org/10.1111/j.1472-4642.2010.00725.x
Fick, S.E. & Hijmans, R.J. (2017) WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37, 4302–4315.
https://doi.org/10.1002/joc.5086
Fouquet, A., Gilles, A., Vences, M., Marty, C., Blanc, M. & Gemmell, N.J. (2007) Underestimation of Species Richness in Neotropical Frogs Revealed by mtDNA Analyses. PLoS One, 10, 1–10.
https://doi.org/10.1371/journal.pone.0001109
Frost, 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., 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/10.5531/sd.sp.13
Galante, P.J., Alade, B., Muscarella, R., Jansa, S.A. Goodman, S.M. & Anderson, R.P. (2018) The challenge of modeling niches and distributions for data-poor species: a comprehensive approach to model complexity. Ecography, 41, 726–736.
https://doi.org/10.1111/ecog.02909
Gridi-Papp, M. (2007) SoundRuler: Acoustic Analysis for Research and Teaching. Available from: http://soundruler.sourceforge.net (accessed 5 June 2017)
Grismer, L.L. (2006) A new species of Ansonia Stoliczka 1872 (Anura: Bufonidae) from Central Peninsular Malaysia and a revised taxonomy for Ansonia from the Malay Peninsula. Zootaxa, 1327 (1), 1–21.
https://doi.org/10.11646/zootaxa.1327.1.1
Grismer, L.L., Wood, P.L., Anur, S., Muin, M.A., Quah, E.S.H., McQuire, J.A., Brown, R.M., Tri, N.V. & Thai, P.H. (2013) Integrative taxonomy uncovers high level of cryptic species diversity in Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia. Zoological Journal of the Linnaean Society, 169, 849–880.
https://doi.org/10.1111/zoj.12064
Hamidy, A. & Kurniati, H. (2015) A new species of tree frog genus Rhacophorus from Sumatra, Indonesia (Amphibia, Anura). Zootaxa, 3947 (1), 49–66.
https://doi.org/10.11646/zootaxa.3947.1.3
Hamidy, A., Munir, M., Mumpuni, Rahmania, M. & Kholik, A.B. (2018) Detection of cryptic taxa in the genus Leptophryne (Fitzinger, 1843) (Amphibia; Bufonidae) and the description of a new species from Java, Indonesia. Zootaxa, 4450 (4), 427–444.
https://doi.org/10.11646/zootaxa.4450.4.2
Harris, N.L., Goldman, E., Garbis, C., Nordling, J., Minnemeyer, S., Ansari, S., Lippman, M., Bennett, L., Raad, M., Hansen, M. & Potapov, P. (2017) Using spatial statistics to identify emerging hot spots of forest loss. Environmental Research Letters, 12, 1–13.
https://doi.org/10.1088/1748-9326/aa5a2f
Harrison, T., Krigbaum, J. & Manser, J. (2006) Primate biogeography and ecology on the Sunda Shelf islands: a paleontological and zooarchaeological perspective. In: Lehman, S.M., Fleagle, J.G. (Eds.), Primate Biogeography. Springer, New York, pp. 331–372. Available from: https://link.springer.com/chapter/10.1007/0-387-31710-4_12 (accessed 5 September 2018)
https://doi.org/10.1007/0-387-31710-4_12
Harvey, M.B., Shaney, K., Hamidy, A., Kurniawan, N. & Smith, E.N. (2017a) A new species of Pseudocalotes (Squamata: Agamidae) from the Bukit Barisan Range of Sumatra with an Estimation of its phylogeny. Zootaxa, 4276 (2), 215–232. https://doi.org/10.11646/zootaxa.4276.2.4
O’Hanlon, S., Rieux, A., Farrer, R.A., Rosa, G.M., Waldman, B., Bataille, A., Kosch, T.A., Murry, K.A., Brankovics, B., Fumagalli, M., Martin, M.D., Wales, N., Alvarado-Rybak, M., Bates, K.A., Berger, L., Böll, S., Brookes, S., Clare, F., Courtois, E.A., Cunningham, A.A., Doherty-Bone, T.M., Ghosh, P., Gower, D.J., Hintz, W.E., Höglund, J., Jenkinson, T.S., Lin, C.F., Laurila, A., Loyau, A., Martel, A., Meurling, S., Miaud, C., Minting, P., Pasmans, F., Schmeller, D.S., Schmidt, B.R., Shelton, J.M.G., Skerratt, L.F., Smith, F., soto-Azat, C., Spagnoletti, M., Tessa, G., Toledo, L.F., Valenzuela-Sánchez, A., Verster, R., Vörös, J., Webb, R.J., Wierzbicki, C., Wombwell, E., Zamudio, K.R., Aanensen, D.M., James, T.Y., Gilbert, M.T.P., Welden, C., Bosch, J., Balloux, F., Garner, T.W.J. & Fisher, M.C. (2018) Recent Asian Origin of chytrid fungi causing global amphibian declines. Science, 360, 621–627.
https://doi.org/10.1126/science.aar1965
Harvey, M.B., Shaney, K., Sidik, I., Kurniawan, N. & Smith, E.N. (2017b) Endemic Dragons of Sumatra’s Volcanoes: New Species of Dendrogama (Squamata: Agamidae) and Status of Salea rosaceun Thominot. Herpetological Monographs, 31, 69–97.
https://doi.org/10.1655/HERPMONOGRAPHS-D-16-00012
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
Hu, H., Broennimann, O., Guisan, A., Wang, B., Huang, Y. & Jiang, J. (2016) Niche conservatism in Gynandropaa frogs on the southeastern Qinghai-Tibetan Plateau. Nature, 32624, 1–10.
https://doi.org/10.1038/srep32624
Hu, H. & Jiang, J. (2018) Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs. BMC Ecology, 18, 1–11.
https://doi.org/10.1186/s12898-018-0160-5
Huelsenbeck, J.P. & Rannala, B. (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology, 53, 904–913.
https://doi.org/10.1080/10635150490522629
Inger, R.F. (1999) Distribution of amphibians in southern Asia and adjacent islands. In: Duellman, W.E. (Ed.), Patterns of distribution of amphibians: a global perspective. The John Hopkins University Press, Baltimore, Maryland, pp. 445–480.
IUCN (2017) The IUCN Red List of Threatened Species. Version 2017-1. Available from: http://www.iucnredlist.org (accessed 27 July 2017)
IUCN Standards and Petitions Subcommittee. (2017) Guidelines for using the IUCN Red List Categories and Criteria. Version 13. Prepared by the Standards and Petitions Subcommittee. Available from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf (accessed 7 March 2018)
Jarić, I., Lennox, R.J., Kalinkat, G., Cvijanović, G. & Radinger, J. (2018) Susceptibility of European freshwater fish to climate change: Species profiling based on life-history and environmental characteristics. Global Change Biology, 25, 448–458. https://doi.org/10.1111/gcb.14518
Karrenberg, S., Liu, X., Hallander, E., Favre, A., Herforth-Rahmé, J. & Widmer, A. (2018) Ecological divergence plays important role in strong but complex reproductive isolation in campions (Silene). Evolution, 73, 245–261.
https://doi.org/10.1111/evo.13652
Kim, S.H., Cho, M.S., Li, P. & Kim, S.C. (2018) Phylogeography and ecological niche modeling reveal reduced genetic diversity and colonization patterns of Skunk Cabbage (Symplocarpus foetidus; Araceae) from glacial refugia in Eastern North America. Frontiers in Plant Science, 00648, 1-19.
https://doi.org/10.3389/fpls.2018.00648
Kodis, M., Galante, P., Sterling, E.J. & Blair, M.E. (2018) Ecological niche modeling for a cultivated plant species: a case study on taro (Colosasia esculenta) in Hawaii. Ecological Applications, 28, 967–977.
https://doi.org/10.1002/eap.1702
Kok, P.J. & Kalamandeen, M. (2008) Introduction to the Taxonomy of the Amphibians of Kaieteur National Park, Guyana. Abc Taxa, 5, 65–106.
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.2016.12.018
Lamoreux, J., Akçakaya, H.R., Bennun, L., Collar, N.J., Boitani, L., Brackett, D., Bräutigam, A., Brooks, T.M., da Fonseca, G.A.B., Mittermeier, R.A., Rylands, A.B., Gärdenfors, U., Hilton-Taylor, C., Mace, G., Stein, B.A. & Stuart, S. (2003) Value of the IUCN Red List. Trends in Ecology and Evolution, 18, 214–215.
https://doi.org/10.1016/S0169-5347(03)00090-9
Lanfear, R., Calcott, B., Ho, S.Y. & Guindon, S. (2012) PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695–1701. Available from: https://academic.oup.com/mbe/article/29/6/1695/1000514 (Accessed 1 Oct. 2019)
Lobo, J.M., Jiménez-Valverde, A. & Real, R. (2008) AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography, 17, 145–151.
https://doi.org/10.1111/j.1466-8238.2007.00358.x
Lohman, D.J., de Bruyn, M., Page, T., von Rintelen, K., Hall, R., Ng, P.K.L., Shih, H., Carvalho, G.R. & von Rintelen, T. (2011) Biogeography of the Indo-Australian Archipelago. Annuual Review of Ecology, Evolution, and Systematics, 42, 205–226. https://doi.org/10.1146/annurev-ecolsys-102710-145001
Margono, B.A., Potapov, P.V., Turubanova, S., Stolle, F. & Hansen, M.C. (2014) Primary forest cover loss in Indonesia over 2000–2012. Nature Climate Change, 4, 730–735.
https://doi.org/10.1038/nclimate2277
Matsui, M. (1984) Morphometric variation analyses and revision of the Japanese toads (Genus Bufo, Bufonidae). Contributions from the Biological Laboratory, Kyoto University, Kyoto, Japan, 26, 209–428. Available from: https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/156031/1/cbl02603-04_209.pdf (accessed 5 September 2018)
Matsui, M., Yambun, P. & Sudin, A. (2007) Taxonomic Relationship of Ansonia annotis Inger, Tan, & Yambun, 2001 and Pedostibes maculatus (Mocquard, 1980), with a Description of a New Genus (Amphibia, Bufonidae), Zoological Science, 24, 1159–1166.
https://doi.org/10.2108/zsj.24.1159
Matsui, M., Mumpuni & Hamidy, A. (2012) Description of a new species of Hylarana from Sumatra (Amphibia, Anura), Current Herpetology, 31, 38–46.
https://doi.org/10.5358/hsj.31.38
Merow, C., Smith, M.J. & Silander-Jr., J.A. (2013) A practical guide to MaxEnt for modelling species’ distributions: what it does, and why inputs and setting matter. Ecography, 36, 1058–1069.
https://doi.org/10.1111/j.1600-0587.2013.07872.x
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. New Orleans. Proceedings of the Gateway Computing Environments Workshop, 2010, 1–8.
https://doi.org/10.1109/GCE.2010.5676129
Mulcahy, D.G., Beckstead, T.H. & Sites-Jr., J.W. (2011) Molecular systematics of the Leptodeirini (Colubroidea: Dipsadidae) revisited: Species-tree analyses and multi-locus data. Copeia, 3, 407–417.
https://doi.org/10.1643/CH-10-058
Myers, C.W. & Duellman, W.E. (1982) A new species of Hyla from Cerro Colorado, and other tree frog records and geographical notes from western Panama. American Museum Novitates, 52, 1–25. Available from: http://hdl.handle.net/2246/5302 (accessed 5 September 2018)
Natusch, D.J.D. & Lyons, J.A. (2012) Exploited for pets: the harvest and trade of amphibians and reptiles from Indonesian New Guinea. Biodiversity and Conservation, 21, 2899–2911.
https://doi.org/10.1007/s10531-012-0345-8
Neal, K.M., Johnson, B.B. & Shaffer, H.B. (2018) Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the spadefoot (Spea hammondii). Conservation Genetics, 19, 937–946.
https://doi.org/10.1007/s10592-018-1066-7
Nori, J., Villalobos, F. & Loyola, R. (2018) Global priority areas for amphibian research. Journal of Biogeography, 45, 2588–2594.
https://doi.org/10.1111/jbi.13435
O’Connell, K.A, Hamidy, A., Kurniawan, N., Smith, E.N. & Fujita, M.K. (2018) Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java. Molecular Phylogenetics and Evolution, 123, 101–112.
https://doi.org/10.1016/j.ympev.2018.02.003
Osorio-Olvera L., Barve, V., Barve, N., Soberón, J. & Falconi, M. (2018) ntbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment. R package. Version 0.2.5.4. Available from: http://shiny.conabio.gob.mx:3838/nichetoolb2/ (accessed 2 February 2019)
Pearson, R.G., Raxworthy, C.J., Nakamura, M. & Peterson, A.T. (2007) Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. Journal of Biogeography, 34, 102–117.
https://doi.org/10.1111/j.1365-2699.2006.01594.x
Perger, R., Santos-Silva, A. & Guerra, F. (2017) Description of the male of Phoebe ornator (Tippmann, 1960) (Coleortera: Cerambycidae: Lamiinae: Hemilophini), analysis of the species biogeography, and first observation of chromatic gender dimorphism in Hemilophini. Zootaxa, 4250 (4), 337–346.
https://doi.org/10.11646/zootaxa.4250.4.4
Phillips, S.J. Anderson, R.P. & Schapire, R.E. (2006) Maximum entropy modelling of species geographic distributions. Ecological modelling, 190, 231–259.
https://doi.org/10.1016/j.ecolmodel.2005.03.026
Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161–175.
https://doi.org/10.1111/j.0906-7590.2008.5203.x
Phillips, S.J., Dudík, M. & Schapire, R.E. (2017) Maxent software for modeling species niches and distributions. Version 3.4.1. Available from: http://biodiversityinformatics.amnh.org/open_source/maxent/ (accessed 8 September 2017)
Proosdij, A.S., Sosef, M.S., Wieringa, J.J. & Raes, N. (2016) Minumum required number of specimen records to develop accurate species distribution models. Ecography, 39, 542–552.
https://doi.org/10.1111/ecog.01509
Rambaut A. (2012) FigTree. Version 1.4.2. Tree Figure Drawing Tool. Available from: http://tree.bio.ed.ac.uk/software/figtree (accessed 06 April 2017)
Rambaut A., Suchard, M.A., Xie, D. & Drummond, A.J. (2014) Tracer. Version 1.6. Available from: http://beast.bio.ed.ac.uk/Tracer (accessed 6 April 2017)
Ramírez-Gíl, J.G., Morales, J.G. & Townsend, P. (2018) Potential geography and productivity of “Hass” avocado crops in Colombia estimated by ecological niche modeling. Scientia Horticulturae, 237, 287–295.
https://doi.org/10.1016/j.scienta.2018.04.021
Regmi, G.R., Huettmann, F., Suwal, M.K., Nijman, V., Nekaris, K.A.I., Kandel, K., Sharma, N. & Coudart, C. (2018) First open access ensemble climate envelope predictions of Assamese macaque Macaca assamensis in Asia: a new role model and assessment of endangered species. Endangered Species Research, 36, 14–160.
https://doi.org/10.3354/esr00888
Remya, K., Ramachandran, A. & Jayakumar, S. (2015) Predicting the current and future suitable habitat distribution of Myristica dactyloides Gaertn. Using MaxEnt model in the Eastern Ghats, India. Ecological Engineering, 82, 184–188.
https://doi.org/10.1016/j.ecoleng.2015.04.053
Rödder, D., Kielgast, J., Bielby, J., Schmidtlein, S., Bosch, J., Garner, T.W.J., Veith, M., Walker, S., Fisher, M.C. & Lötters, S. (2009) Global amphibian extinction risk assessment for the panzootic chytrid fungus. Diversity, 1, 52–56.
https://doi.org/10.3390/d1010052
Rödder, D., Kielgast, J. & Lötters, S. (2010) Future potential distribution of the emerging amphibian chytrid fungus under anthropogenic climate change. Disease of Aquatic Organisms, 92, 201–207.
https://doi.org/10.3354/dao02197
Rohland, N. & Reich, D. (2012) Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Research, 22, 939–946.
https://doi.org/10.1101%2Fgr.128124.111
Rondinini, C., Marco, M.D., Visconti, P., Butchart, S.H.M. & Boitani, L. (2013) Update or Outdate: Long-term viability of the IUCN Red List. Conservation Letters, 7, 126–130.
https://doi.org/10.1111/conl.12040
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 Choice Across a Large Model Space. Systematic Biology, 61, 539–42.
https://doi.org/10.1093/sysbio/sys029
Rowley, J., Brown, R., Bain, R., Kusrini, M., Inger, R., Stuart, B., Wogan, G., Thy, N., Chand-ard, T., Trung, C.T., Diesmos, A., Iskandar, D.T., Lau, M. Ming, L.T., Makchai, S., Truong, N.Q. & Phimmachak, S. (2009) Impending conservation crisis for Southeast Asian amphibians. Biology Letters, 6, 336–338.
https://doi.org/10.1098/rsbl.2009.0793
Sabaj Perez, M.H. (Ed.) (2016) Standard Symbolic Codes for Institutional Resource Collections in Herpetology and Ichthyology: An Online Reference. Version 6.5. American Society of Ichthyologists and Herpetologists, USA. Available from: http://www.asih.org/sites/default/files/documents/symbolic_codes_for_collections_v6.5.pdf (accessed 12 September, 2017)
Savage, J.M. & Heyer,W.R. (1967) Variation and distribution in the tree-frog genus Phyllomedus in Costa Rica, Central America. Beitragezur Neotropischen Fauna, 5, 111–131.
https://doi.org/10.1080/01650526709360400
Savage, J.M. & Heyer,W.R. (1997) Digital webbing formulae for anurans: a refinement. Herpetological Review, 28,131. Available from: https://ssarherps.org/herpetological-review-pdfs (Accessed 1 Oct. 2019)
Shaney, K.J. Hamidy, A., Walsh, M., Arida, A., Arimbi, A. & Smith, E.N. (2017) Impacts of anthropogenic pressure on the contemporary biogeograpgy of threatened corcodilians in Indonesia. Oryx, 53 (3), 570–581.
https://doi.org/10.1017/S0030605317000977
Shcheglovitova, M. & Anderson, R.P. (2013) Estimating optimal complexity for ecological niche models: A jackknife approach for species with small sample size. Ecological Modelling, 269, 9–17.
https://doi.org/10.1016/j.ecolmodel.2013.08.011
Setyaningsih, C.A., Biagioni, S., Saad, A., Achnopha, Y., Sabiham, S. & Behling, H. (2018) The effect of volcanism on submontane rainforest vegetation composition: Paleoecological evidence from Danau Njalau, Sumatra (Indonesia). The Holocene, 28, 293–307.
https://doi.org/10.1177%2F0959683617721329
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 the Highlands of Sumatra with a Phylogeny of Sundaland Toad genera. Herpetologica, 73, 63–75.
https://doi.org/10.1655/Herpetologica-D-16-00041
Sodhi, N.S., Koh, L.P., Brook, B.W. & Ng, P.K.L. (2004) Southeast Asian biodiversity: an impending disaster. Trends in Ecology and Evolution, 19, 654–660.
https://doi.org/10.1016/j.tree.2004.09.006
Spear, M.J., Elgin, A.K. & Grey E.K. (2018) Current and projected distribution of the Red-eared Slider Turtle, Trachemys scripta elegans, in the Great Lakes Basin. The American Midland Naturalist, 179, 191–221.
https://doi.org/10.1674/0003-0031-179.2.191
Stamatakis, A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688–2690.
https://doi.org/10.1093/bioinformatics/btl446
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
Streicher, J.W., Hamidy, A. Harvey, M.B. Anders, 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), 351–365.
https://doi.org/10.11646/zootaxa.3878.4.2
Suprianta, J., Dwiyahrenti, A.A., Winarni, N., Mariati, S. & Margules, C. (2017) Deforestation of Primate Habitat on Sumatra and adjacent Islands, Indonesia. Primate Conservation, 31, 71–82. Available from: http://static1.1.sqspcdn.com/static/f/1200343/27795199/1515432645067/PC31_Supriatna_et_al_Deforestation_Sumatra.pdf?token=Z2dLuaEaLlWb8vUJ1%2BubSy7OsW4%3D (accessed 5 September 2018)
Talavera, G. & Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564–577.
https://doi.org/10.1080/10635150701472164
Tamura, 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/mst197
Tan, M.K., Ingrisch, S. & Wahab, R.B.H.A. (2017) First Velarifictorus (Orthoptera: Gryllidae, Gryllinae) cricket described from Borneo (Southeast Asia) and notes on a co-occurring congener. Zootaxa, 4282 (2), 374–384.
https://doi.org/10.11646/zootaxa.4282.2.10
Tapley, B., Cutajar, T., Mahony, S. Nguyen, T.C., Dau, V.Q., Nguyen, T.T., Luong, H.V. & Rowley, J.J.L. (2017) The Vietnamese population of Megophrys kuatunensis (Amphibia: Megophryidae) represents a new species of Asian horned frog from Vietnam and southern China. Zootaxa, 4344 (3), 465–492.
https://doi.org/10.11646/zootaxa.4344.3.3
Tapley, B., Michaels, C.J., Gumbs, R., Böhm, M., Luedtke, J., Pearce-Kelly, P. & Rowley, J.J.L. (2018) The disparity between species description and conservation assessment: A case study in taxa with high rates of species discovery. Biological Conservation, 220, 209–214.
https://doi.org/10.1016/j.biocon.2018.01.022
Tarkesh, M. & Jetschke, G. (2012) Comparison of six correlative models in predictive vegetation mapping on a local scale. Environmental and Ecological Statistics, 19, 437–457.
https://doi.org/10.1007/s10651-012-0194-3
Teynie, A. David, P. & Ohler, A. (2010) Note on a collection of Amphibians and Reptiles from Western Sumatra (Indonesia), with the description of a new species of the genus Bufo, Zootaxa, 2416 (1), 1–43.
https://doi.org/10.11646/zootaxa.2416.1.1
Trull, N., Böhm, M. & Carr, J. (2017) Patterns and biases of climate change threates in the IUCN Red List. Conservation Biology, 32, 135–147.
https://doi.org/10.1111/cobi.13022
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 Evolutionary Biology, 9, 1–10.
https://doi.org/10.1186/1471-2148-9-131
Vences, 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, 1–12.
https://doi.org/10.1186/1742-9994-2-5
Vieites, D.R., Wollenberg, K.C., Andreone, F., Köhler, K., Glaw, F. & Vences, M. (2009) Vast underestimation of Madagascar’s biodiversity evidenced by and integrative amphibian inventory. Proceedings of the National Academy of sciences, 106, 8267–8272.
https://doi.org/10.1073/pnas.0810821106
Walden-Schreiner, C., Leung, Y.F. & Tateosian, L. (2018) Digital footprints: Incorporating crowdsourced geographic information for protected area management. Applied Geography, 90, 44–54.
https://doi.org/10.1016/j.apgeog.2017.11.004
Wisz, M.S. Hijmans, R.J., Peterson, A.T., Graham, C.H. & Guisan, A. (2008) Effects of sample size on the performance of species distribution models. Diversity and Distributions, 14, 763–773.
https://doi.org/10.1111/j.1472-4642.2008.00482.x
Wostl, 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, 98–141. https://doi.org/10.1655/HERPMONOGRAPHS-D-16-00007
Zimkus, B.M., Lawson, L.P., Barej, M.F., Barratt, C.D., Channing, A., Dash, K.M., Dehling, J.M., Preez, L.D., Gehring, P., Greenbaum, E., Gvoždík, V., Harvey, J., Kielgast, J., Kusamba, C., Nagy, Z.T., Pabijan, M., Penner, J., Rödel, M., Vences, M. & Lötters, S. (2017) Leapfrogging into new territory: How Mascarene ridged frogs diversified across Africa and Madagascar to maintain their ecological niche. Molecular Phylogenetics and Evolution, 106, 254–269.