Phylogeny and cryptic diversification in Southeast Asian flying geckos

Molecular Phylogenetics and Evolution

Volumn 65, Issue 2, 2012, Pages 351-361

  Brown, Rafe M ^a   Siler, Cameron D ^a   Lee Grismer, L ^b   Das, Indraneil ^c   McGuire, Jimmy A ^d  

^a UNIVERSITY OF KANSAS   (United States)

^b LA SIERRA UNIVERSITY   (United States)

^c UNIVERSITI MALAYSIA SARAWAK   (Malaysia)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Canopy specialists; Flying geckos; Parachute geckos; Southeast Asia; Vertebrate gliders

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; LIZARD; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; SOUTHEAST ASIA;

ANIMALS; ASIA, SOUTHEASTERN; BAYES THEOREM; BIOLOGICAL EVOLUTION; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENETICS, POPULATION; LIZARDS; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA;

ANURA; GEKKONIDAE; MAMMALIA; PTYCHOZOON; SQUAMATA; VERTEBRATA;

EID: 84866281623     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.06.009     Document Type: Article

References (115)

1. Albert E.M., San Mauro D., Garcia-Paris M., Ruber L., Zardoya R. Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data. Gene 2009, 441:12-21.
2. Annandale N. Contribution to Oriental Herpetology I: the lizards of the Andamans, with the description of a gecko and a note on the reproduced tail in Ptychozoon homalocephalum. J. Asiatic Soc. Bengal 1904, 73:12-22.
3. Annandale N. Notes on some oriental geckos in the Indian Museum, Calcutta, with descriptions of new forms. Ann. Mag. Nat. Hist., Lond. 1905, 15:26-32.
4. Bauer A.M., Parham J.F., Brown R.M., Stuart B.L., Grismer L.L., Papenfuss T.J., Bohme W., Savage J., Carranza S., Grismer J., Wagner P., Ananjeva N., Inger R.F. On the availability of new Bayesian-delimited gecko names and the importance of character based definitions of species. Proc. Roy. Soc. Lond. B 2010, 278:490-492.
5. Barbour T. A contribution to the zoogeography of the East Indian Islands. Mem. Mus. Comp. Zool. 1912, 44:1-203.
6. Biswas S., Sanyal D.P. A report on the Reptilia fauna of Andaman and Nicobar Islands in the collection of Zoological Survey of India. Rec. Zool. Surv. India 1980, 77:255-292.
7. Bobrov V.V. Checklist and bibliography of the lizards of Vietnam. Smithsonian Herpetol. Infor. Ser. 1995, 105:1-28.
8. Bauer A.M., Giri V.B., Greenbaum E., Jackman T.R., Dharne M.S., Shouche Y.S. On the systematics of the gekkonid genus Teratolepis Günther, 1869: another one bites the dust. Hamadryad 2008, 33:13-27.
9. Boulenger, G.A., 1885. Catalogue of the Lizards in the British Museum (Nat. Hist.) I. Geckonidae, Eublepharidae, Uroplatidae, Pygopodidae, Agamidae. British Museum (Natural History), London.
10. Brown R.M. New species of parachute gecko (Squamata; Gekkonidae; genus Ptychozoon) from northeastern Thailand and Central Vietnam. Copeia 1999, 1999:990-1001.
11. Brown R.M., Diesmos A.C. The lizard genus Luperosaurus: taxonomy, history, and conservation prospects for some of the world's rarest lizards. Sylvatrop.: Tech. J. Philipp. Eco. Nat. Res. 2000, 10:107-124.
12. Brown R.M., Diesmos A.C. Application of lineage-based species concepts to oceanic island frog populations: the effects of differing taxonomic philosophies on the estimation of Philippine biodiversity. Silliman J. 2001 (2002), 42:133-162.
13. Brown R.M., Diesmos A.C. Philippines, biology. Encyclopedia of Islands 2009, 723-732. University of California Press, Berkeley. R. Gillespie, D. Clague (Eds.).
14. Brown R.M., Stuart B.L. Patterns of biodiversity discovery through time: an historical analysis of amphibian species discoveries in the Southeast Asian mainland and island archipelagos. Biotic Evolution and Environmental Change in Southeast Asia 2012, 348-389. Cambridge University Press. D.J. Gower, K.G. Johnson, J.E. Richardson, B.R. Rosen, L. Rüber, S.T. Williams (Eds.).
15. Brown R.M., Ferner J.W., Diesmos A.C. Definition of the Philippine parachute gecko, Ptychozoon intermedium Taylor 1915 (Reptilia: Squamata: Gekkonidae): redescription, designation of a neotype, and comparisons with related species. Herpetologica 1997, 53:357-373.
16. Brown R.M., Oliveros C., Siler C.D., Diesmos A.C. Phylogeny of Gekko from the northern Philippines, and description of a new species from Calayan Island. J. Herpetol. 2009, 43:620-635.
17. Brown R.M., Siler C.D., Das I., Pui Y.M. Testing the phylogenetic affinities of Southeast Asia's rarest geckos: flap-legged geckos (Luperosaurus), flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko. Mol. Phylogenet., Evol. 2012, 63:915-921.
18. Brown, R.M., Siler, C.D., Diesmos, D.C., Alcala, A.C., 2009b. The Philippine frogs of the genus Leptobrachium (Anura; Megophryidae): phylogeny-based species delimitation, taxonomic revision, and descriptions of three new species. Herpetol. Monogr. 23, 1-44.
19. Brown R.M., Supriatna J., Ota H. Discovery of a new species of Luperosaurus (Squamata; Gekkonidae) from Sulawesi, with a phylogenetic analysis of the genus and comments on the status of L. serraticaudus. Copeia 2000, 2000:191-209.
20. Brown, W.C., Alcala, A.C., 1978. Philippine Lizards of the family Gekkonidae. Silliman Univ. Nat. Sci. Monogr. Ser. 1, Dumaguete.
21. Bruen T.C., Philippe H., Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 2006, 172:2665-2681.
22. Bryant D., Moulton V. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004, 21:255-265.
23. Cantor, T., 1847. Catalogue of the reptiles inhabiting the Malayan Peninsula and islands, collected or observed by Theodore Cantor, Esqr., M. D. J. Asiat. Soc. Bengal 16, 607-656 (part).
24. Chan-ard T., Grossmann W., Gumprecht A., Schulz K.D. Amphibians and Reptiles of Peninsular Malaysia and Thailand - An Illustrated Checklist (bilingual English and German) 1999, Bushmaster Publications, Würselen.
25. Colbert E.H. Adaptations for gliding in the lizard Draco. Am. Mus. Novitates 1967, 2283:1-20.
26. Corbet G.B., Hill J.E. The Mammals of the Indomalayan Region 1992, Oxford University Press, New York.
27. Cox, J., van Dijk, P., Nabhitabhata, J., Thirakhupt, K., 1998. A Photographic Guide to Snakes and Other Reptiles of Peninsular Malaysia, Singapore and Thailand. New Holland Publishers Ltd., UK, London.
28. Das I. A check-list of the amphibians and reptiles of Andaman and Nicobar Islands. J. Andaman Sci. Assoc. 1994, 10:44-49.
29. Das I. The reptiles of south Asia: a checklist and distributional summary. Hamadryad 1994, 19:15-40.
30. Das, I., 2004. Lizards of Borneo. Natural History Publications (Borneo) Sdn Bhd., Kota Kinabalu.
31. Das I., Vijayakumar S.P. New species of Ptychozoon (Sauria: Gekkonidae) from the Nicobar Archipelago, Indian Ocean. Zootaxa 2009, 2095:8-20.
32. de Queiroz K. The general lineage concept of species. Species criteria, and the process of speciation. Endless Forms: Species and Speciation 1998, 57-75. Oxford University Press, New York. D.J. Howard, S.H. Berlocher (Eds.).
33. Dickerson, R.E., 1928. Distribution of Life in the Philippines. Philipp. Bur. Sci. Monogr. 21, Manila.
34. Dring J.C.M. Amphibians and reptiles from northern Trengganu, Malaysia, with descriptions of two new geckos: Cnemaspis and Cyrtodactylus. Bull. British Mus. (Natur. Hist.) Zool. Ser. 1979, 34:181-241.
35. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
36. Dudley R., Byrnes G., Yanoviak S., Borrell B., Brown R.M., McGuire J. Gliding and the functional origins of flight: biomechanical novelty or necessity?. Ann. Rev. Ecol. Syst. 2007, 38:179-201.
37. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
38. Emerson S.B., Koehl M.A.R. The interaction of behavioral and morphological change in the evolution of a novel locomotor type-flying frogs. Evolution 1990, 44:1931-1946.
39. Esselstyn J.A., Garcia H.J.D., Saulog M.G., Heaney L.R. A new species of Desmalopex (Pteropodidae) from the Philippines, with a phylogenetic analysis of the Pteropodini. J. Mammal. 2008, 89:815-825.
40. Flower S.S. Notes on a collection of reptiles and batrachians made in the Malay Peninsula in 1895-96; with a list of the species recorded from that region. Proc. Zool. Soc. Lond. 1896, 1896:856-914.
41. Frost D.R., Hillis D.M. Species in concept and practice: herpetological applications. Herpetologica 1990, 46:87-104.
42. Gadow H. Amphibia and Reptiles 1901, Macmillan and Co., London.
43. Gamble T., Bauer A.M., Greenbaum E., Jackman T.R. Evidence of Gondwanan vicariance in an ancient clade of gecko lizards. J. Biogeogr. 2008, 35:88-104.
44. Gamble T., Bauer A.M., Colli G.R., Greenbaum E., Jackman T.R., Vitt L.J., Simons A.M. Coming to America: multiple origins of New World geckos. J. Evol. 2011, 24:231-244.
45. Gamble T., Colli G.R., Rodriques M.T., Werneck F.P., Simmons A.M. Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes. Mol. Phylogenet. Evol. 2012, 62:943-953.
46. Goldingay R., Scheibe J. Biology of Gliding Mammals 2000, Filander Press, Fürth.
47. Grismer L.L. Lizards of Peninsular Malaysia, Singapore and Their Adjacent Archipelagos 2011, Edition Chimaira, Frankfurt.
48. Grismer L.L., Sumontha M., Cota M., Grismer J.L., Wood P.L., Pauwels O.S.G., Kunya K. A revision and redescription of the rock gecko Cnemaspis siamensis (Taylor 1925) (Squamata: Gekkonidae) from Peninsular Thailand with descriptions of six new species. Zootaxa 2010, 2576:1-55.
49. Grismer L.L., Thy N., Thou C., Grismer J.L. Checklist of the amphibians and reptiles of southwestern Cambodia. Cambodian J. Nat. Hist. 2008, 2008:12-28.
50. Günther, A.C.L.G., 1864. The Reptiles of British India. Ray Society, London. Reprinted 1982, Oxford and IBH Publishing Co., New Delhi.
51. Günther, A., 1885. Catalogue of Lizards in the British Museum. Geckonidae, Eublepharidae, Uroplatidae, Pygopodidae, Agamidae, vol. I, second ed. British Museum, London.
52. Heled J., Drummond A. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
53. Heyer W.R., Pongsapipatana S. Gliding speeds of Ptychozoon lionotum (Reptilia: Gekkonidae) and Chrysopelea ornata (Reptilia: Colubridae). Herpetologica 1970, 26:317-319.
54. Huson D. Splitstree-a program for analyzing and visualizing evolutionary data. Bioinformatics 1998, 14:68.
55. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:245-267.
56. Inger R.F. Distributions of amphibians in southern Asia and adjacent islands. Patterns of Distribution of Amphibians: A Global Perspective 1999, 445-482. John Hopkins University Press, Baltimore. W.E. Duellman (Ed.).
57. Inger R.F., Colwell R.K. Organization of contiguous communities of amphibians and reptiles in Thailand. Ecol. Monogr. 1977, 47:229-253.
58. Inger R.F., Voris H.K. The biogeographical relations of the frogs and snakes of Sundaland. J. Biogeogr 2001, 28:863-891.
59. IUCN, 2011. IUCN Red List of Threatened Species. Version 2011.2. (downloaded 13.01.12). http://www.iucnredlist.org.
60. Kiew B.H. The flying gecko - Ptychozoon. Nat. Malaysiana 1987, 12:18-19.
61. Leaché A.D., Fujita M.K. Bayesian species delimitation in West Aftrican forest geckos (Hemidactylus fasciatus). Proc. Roy. Soc. Lond. B 2010, 277:3071-3077.
62. Lomolino M.V., Riddle B.R., Whittaker R.J., Brown J.H. Biogeography 2010, Sinauer Associates, Sunderland. fourth ed.
63. Malkmus R., Manthey U., Vogel G., Hoffmann P., Kosuch J. Amphibians and Reptiles of Mount Kinabalu (North Borneo) 2002, A.R.G. Ganter Verlag, K.G., Rugell.
64. Manthey U. Die Gattung Ptychozoon Kuhl, 1822 (Faltengecko) Teil I mit einem Bestimmungsschlüssel für die fünf Arten. Sauria, Berlin 1985, 4:5-12.
65. Manthey U., Grossmann W. Amphibien und Reptilien Südostasiens 1997, Natur und Tier-Verlag, Münster.
66. Marcellini D.L., Keefer T.E. Analysis of the gliding behavior of Ptychozoon lionotum (Reptilia: Gekkonidae). Herpetologica 1976, 32:362-366.
67. Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
68. McLeod D.S. Of Least Concern? Systematics of a cryptic species complex: Limnonectes kuhlii (Amphiba; Anura: Dicroglossidae). Mol. Phylogenet. Evol. 2010, 56:991-1000.
69. Medway L. The function of the membranes of Ptychozoon spp. Malayan Natur. J. 1975, 29:28-30.
70. Nabhitabhata J., Chan-ard T., Chuaynkern Y. Checklist of Amphibians and Reptiles in Thailand 2000, Office of Environmental Policy and Planning, Bankok.
71. Nguyen V.S., Ho Thu Cuc, Nguyen Q.T. Herpetofauna of Vietnam 2009, Chimaira, Frankfurt am Main.
72. Pauwels O.S.G., Laohawat O.-A., Naaktae W., Puangjit C., Wisutharom T., Chimsunchart C., David P. Herpetological investigations in Phang-Nga Province, southern Peninsular Thailand, with a list of reptile species and notes on their biology. Dumerilia 2000, 4:123-154.
73. Pawar S., Biswas S. First record of the Smooth-Backed Parachute Gecko Ptychozoon lionotum Annandale 1905 from the Indian mainland. Asiatic Herpetol. Res. 2001, 9:101-106.
74. Pong T.Y. Camouflage in the flying gecko, Ptychozoon kuhli Stj. Malayan Nat. J. 1974, 28:36-37.
75. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
76. Rambaut, A., Drummond, A.J., 2005. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer.
77. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
78. de Rooij N. The Reptiles of the Indo-Australian Archipelago, I: Lacertilia, Chelonia 1915, Emydosauria. E. J. Brill, Ltd., Leiden.
79. Russell, A.P., 1972. The Foot of Gekkonid Lizards: A Study in Comparative and Functional Anatomy. Unpubl. Ph.D. Diss, Univ. of London, London.
80. Russell A.P. The origin of parachuting locomotion in gekkonid lizards (Reptilia: Gekkonidae). Zool. J. Linn. Soc. 1979, 65:233-249.
81. Russell A.P. A new species of Luperosaurus (Gekkonidae) with comments on the genus. Herpetologica 1979, 35:282-288.
82. Russell A.P., Dijkstra L.D., Powell G.L. Structural characteristics of the patagium of Ptychozoon kuhli (Reptilia:Gekkonidae) in relation to parachuting locomotion. J. Morphol. 2001, 247:252-263.
83. Setiadi M.I., McGuire J.A., Brown R.M., Zubairi M., Iskandar D.T., Andayani N., Supriatna J., Evans B.J. Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities. Amer. Natur. 2011, 178:221-240.
84. Siler C.D., Oaks J.R., Linkem C.W., Swab J., Diesmos A.C., Brown R.M. Did geckos ride the Palawan raft to the Philippines?. J. Biogeogr. 2012, 39:1217-1234.
85. Simpson G.G. Principles of Animal Taxonomy 1961, Columbia University Press, New York.
86. Smith M.A. The Reptilia and Amphibia of the Malay Peninsula. Bull. Raff. Mus. 1930, 3:1-149.
87. Smith M.A. The Fauna of British India, including Ceylon and Burma. Reptilia and Amphibia. II.-Sauria 1935, Taylor and Francis, London.
88. Sodhi N.S., Koh L.P., Brook B.W., Ng P.K. Southeast Asian biodiversity: an impending disaster. Trends Ecol. Evol. 2004, 19:654-660.
89. Stephens M., Donnelly P. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Amer. J. Human Gen. 2003, 73:1162-1169.
90. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
91. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML Web Servers. Syst. Biol. 2008, 57:758-771.
92. Stejneger L.H. Herpetology of Japan and adjacent territory. Bull. US Natl. Mus. 1907, 58:1-577.
93. Stuart, B.L., Emmett, D.A., 2006. A collection of amphibians and reptiles from the Cardamom Mountains, southwestern Cambodia. Fieldiana Zool. N.S. 109, 1-27.
94. Stuart B.L., Inger R.F., Voris H.K. High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biol. Lett. 2006, 2:470-474.
95. Taylor E.H. New species of Philippine lizards. Philipp. J. Sci. 1915, 10:89-108.
96. Taylor, E.H., 1922a. The lizards of the Philippine Islands. Philipp. Bur. Sci., Monogr. 17, Manila.
97. Taylor E.H. Additions to the herpetological fauna of the Philippine Islands, I. Philipp. J. Sci. 1922, 21:161-206.
98. Taylor, E.H., 1928. Amphibians, lizards, and snakes of the Philippines. In: Dickerson, R. (Ed.), Distribution of Life in the Philippines, pp. 214-241. Philippine Bur. Sci., Monogr. 21, Manila.
99. Taylor E.H. The lizards of Thailand. Univ. Kansas Sci. Bull. 1963, 44:687-1077.
100. Taylor, E.H., 1975. Philippine adventures: an autobiographical memoir. In: Taylor, E.H., Leonard, A.B., Smith, H.M., Pisani, G.R. (Eds.), Recollections of an Herpetologist. University of Kansas Museum of Natural History (Monogr. 4), Lawrence, pp. 1-105.
101. Tho Y.P. Camouflage in the flying gecko, Ptychozoon kuhli Stejn. Malayan Nat. J. 1974, 28:36.
102. Tiwari K.K. The eggs and flight of the gecko Ptychozoon kuhli Stejneger from Car Nicobar. J. Bombay Nat. Hist. Soc. 1961, 58:523-527.
103. Tweedie M.W.F. Notes on Malayan reptiles, no. 3. Bull. Raff. Mus. 1954, 25:107-117.
104. Venugopal P.D. An updated and annotated list of Indian lizards (Reptilia: Sauria) based on a review of distribution records and checklists of Indian reptiles. J. Threatened Taxa 2010, 2:725-738.
105. Vetter R.S., Brodie E.D. Background color selection and antipredator behavior of the flying gecko, Ptychozoon kuhli. Herpetologica 1977, 33:464-467.
106. Voris H. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J. Biogeogr. 2000, 27:1153-1167.
107. Wiley E.O. The evolutionary species concept reconsidered. Syst. Zool. 1978, 21:17-26.
108. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://ceb.csit.fsu.edu/awty.
109. Wermuth H. Gekkonidae, Pygopodidae, Xantusidae. Das Tierreich 1965, vol. 80. Walter de Gruyter & Co., Berlin.
110. Whitmore T.C. Tropical Rain Forests of the Far East 1975, Clarendon Press, Oxford.
111. Biogeographical Evolution of the Malay Archipelago 1987, Clarendon Press, Oxford. T.C. Whitmore (Ed.).
112. Whitmore T.C., Sayer J.A. Tropical Deforestation and Species Extinction 1992, Chapman and Hall, London.
113. Woodruff D.S. Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today's patterns and the future of the remaining refugial-phase biodiversity. Biodivers. Conserv. 2010, 19:919-941.
114. Yang Z., Rannala B. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. 2010, 107:9264-9269.
115. Young B.A., Lee C.E., Daley K.M. On a flap and a foot: aerial Locomotion in the "Flying" Gecko, Ptychozoon kuhli. J. Herpetol. 2002, 36:412-418.