Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

Molecular Phylogenetics and Evolution

Volumn 63, Issue 3, 2012, Pages 714-723

  Nishikawa, Kanto ^a   Matsui, Masafumi ^a   Yong, Hoi Sen ^b   Ahmad, Norhayati ^c   Yambun, Paul ^d   Belabut, Daicus M ^b,c   Sudin, Ahmad ^e   Hamidy, Amir ^a,f   Orlov, Nikolai L ^g   Ota, Hidetoshi ^h   Yoshikawa, Natsuhiko ^a   Tominaga, Atsushi ⁱ   Shimada, Tomohiko ^j  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF MALAYA   (Malaysia)

^c UNIVERSITI KEBANGSAAN MALAYSIA   (Malaysia)

^d Research and Education Division   (Malaysia)

^e UNIVERSITI MALAYSIA SABAH   (Malaysia)

^f Museum Zoologicum Bogoriense   (Indonesia)

^g ZOOLOGICAL INSTITUTE   (Russian Federation)

^h UNIVERSITY OF HYOGO   (Japan)

ⁱ UNIVERSITY OF THE RYUKYUS   (Japan)

^j AICHI UNIVERSITY OF EDUCATION   (Japan)

more..

Author keywords

Biogeography; Caecilians; Mitochondrial DNA; Phylogeny; Southeast Asia; Sundaland

Indexed keywords

AMPHIBIAN PROTEIN; CYTOCHROME B; RIBOSOME RNA; RNA 16S; RNA, RIBOSOMAL, 12S;

AMPHIBIA; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; GENETICS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PHYLOGEOGRAPHY; SOUTHEAST ASIA; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; STATISTICAL MODEL; SYMPATRY;

AMPHIBIAN PROTEINS; AMPHIBIANS; ANIMALS; ASIA, SOUTHEASTERN; BAYES THEOREM; CYTOCHROMES B; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PHYLOGEOGRAPHY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; SYMPATRY;

AMPHIBIA; CAUDACAECILIA; GYMNOPHIONA; ICHTHYOPHIIDAE; ICHTHYOPHIS;

EID: 84859829930     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.02.017     Document Type: Article

References (67)

1. Arifin U., Iskandar D.T., Bickford D.P., Brown R.M., Meier R., Kutty S.N. Phylogenetic relationships within the genus Staurois (Anura, Ranidae) based on 16S rRNA sequences. Zootaxa 2011, 2744:39-52.
2. Bain R.H., Nguyen Q.T., Doan V.K. New herpetofaunal records from Vietnam. Herpetol. Rev. 2007, 38:107-117.
3. Beck R.A., Burbank D.W., Sercombe W.J., Riley G.W., Barndt J.K., Berry J.R., Afzal J., Khan A.M., Jurgen H., Metje J., Lawrence R.D., Khan M.A. Stratigraphic evidence for an early collision between northwest India and Asia. Nature 1995, 373:55-57.
4. Blackburn D.C., Bickford D.P., Diesmos A.C., Iskandar D.T., Brown R.M. An ancient origin for the enigmatic flat-headed frogs (Bombinatoridae: Barbourula) from the islands of Southeast Asia. PLoS ONE 2010, 5:1-10.
5. Bossuyt F., Milinkovitch M.C. Amphibians as indicators of early Tertiary "out-of-India" dispersal of vertebrates. Science 2001, 292:93-95.
6. Brown W.C., Alcala A.C. Philippine frogs of the family Rhacophoridae. Proc. Calif. Acad. Sci. 1994, 48:185-220.
7. Brown R.M., Guttman S.I. Phylogenetic systematics of the Rana signata complex of Philippine and Bornean stream frogs: reconsideration of Huxley's modification of Wallace's line at the Oriental-Australian faunal zone interface. Biol. J. Linn. Soc. 2002, 76:393-461.
8. Brown R.M., Siler C.D., Diesmos A.R., Alcala A.C. Philippine frogs of the genus Leptobrachium (Anura; Megophryidae): phylogeny-based species delimitation, taxonomic review, and descriptions of three new species. Herpetol. Monogr. 2009, 23:1-44.
9. Brown R.M., Linkem C.W., Siler C.D., Sukumaran J., Esselstyn J.A., Diesmos A.C., Iskandar D.T., Bickford D., Evans B.J., McGuire J.A., Grismer L., Supriatna J., Andayani N. Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion?. Mol. Phylogenet. Evol. 2010, 57:598-619.
10. Das I., Jankowski A., Makmor M.I.B., Haas A. Species diversity, elevational distribution and reproductive modes in an amphibian community at the Matang Range, Sarawak (Borneo). Mitt. Hamb. Zool. Mus. Inst. 2007, 104:141-174.
11. Duellman W.E., Trueb L. Biology of Amphibians 1986, McGraw-Hill Publishing Company, New York.
12. Evans B.J., Brown R.M., McGuire J.A., Supriatna J., Andayani N., Diesmos A., Iskandar D., Melnic D.J., Cannatella D.C. Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Syst. Biol. 2003, 52:794-819.
13. Feller A.E., Hedges S.B. Molecular evidence for the early history of living amphibians. Mol. Phylogenet. Evol. 1998, 9:509-516.
14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
15. Frost, D.R., 2011. Amphibian Species of the World: an Online Reference, version 5.5. American Museum of Natural History, New York. http://research.amnh.org/herpetology/amphibia/index.php.
16. Gower D.J., Wilkinson M. Conservation biology of caecilian amphibians. Conserv. Biol. 2005, 19:45-55.
17. Gower D.J., Kupfer A., Oommen O.V., Himstedt W., Nussbaum R.A., Loader S.P., Presswell B., Krishna S.B., Müller H., Boistel R., Wilkinson M. A molecular phylogeny of ichthyophiid caecilians (Amphibia: Gymnophiona: Ichthyophiidae): out of India or out of South East Asia?. Proc. Roy. Soc. B. 2002, 269:1563-1569.
18. Gower D.J., Dharne M., Bhatta G., Giri V., Vyas R., Govindappa V., Oommen O.V., George J., Schouche Y., Wilkinson M. Remarkable genetic homogeneity in unstriped, long-tailed Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae) along 1500 km of the Western Ghats, India. J. Zool. 2007, 272:266-275.
19. Gower D.J., San Mauro D., Giri V., Bhatta G., Govindappa V., Kotharambath R., Oomen O.V., Fatih F.A., Mackenzie-Dodds J., Nussbaum R.A., Biju S.D., Shouche Y.S., Wilkinson M. Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India. Mol. Phylogenet. Evol. 2011, 59:698-707.
20. Hedges S.B., Nussbaum R.A., Maxson L.R. Caecilian phylogeny and biogeography inferred from mitochondrial DNA sequences of the 12S rRNA and 16S rRNA genes (Amphibia: Gymnophiona). Herpetol. Monogr. 1993, 7:64-76.
21. Hillis D.M., Mable B.K., Larson A., Davis S.K., Zimmer E.A. Nucleic acids IV: Sequencing and cloning. Molecular Systematics 1996, 321-378. Sinauer Associates, Sunderland. second ed. D.M. Hillis, B.K. Mable, C. Moritz (Eds.).
22. Huelsenbeck J.P., Hillis D.M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 1993, 42:247-264.
23. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
24. Inger R.F. Distribution of amphibians in Southern Asia and adjacent islands. Patterns of Distribution of Amphibians 1999, 445-482. The Johns Hopkins University Press, Baltimore and London. W.E. Duellman (Ed.).
25. Inger R.F., Voris H.K. The biogeographical relations of the frogs and snakes of Sundaland. J. Biogeogr. 2001, 28:863-891.
26. Inoue J.G., Kumazawa Y., Miya M., Nishida M. The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a Mesozonic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Mol. Phylogenet. Evol. 2009, 51:486-499.
27. Jobb, G., 2008. "TREEFINDER version of October 2008" Munich, Germany. Distributed by the author at http://www.treefinder.de.
28. Kamei R.G., Wilkinson M., Gower D.J., Biju S.D. Three new species of striped Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae) from the northeast Indian states of Manipur and Nagaland. Zootaxa 2009, 2267:26-42.
29. Kotaki M., Kurabayashi A., Matsui M., Kuramoto M., Djong T.H., Sumida M. Molecular phylogeny of the diversified frogs of genus Fejervarya (Anura: Dicroglossidae). Zool. Sci. 2010, 27:386-395.
30. Kupfer A., Müller H. On the taxonomy of ichthyophiid caecilians from southern Thailand: a reevaluation of the holotype of Ichthyophis supachaii Taylor, 1960 (Amphibia: Gymnophiona: Ichthyophiidae). Amphibia-Reptilia 2004, 25:87-97.
31. Leaché A.D., Reeder T.W. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 2002, 51:44-68.
32. Li X., Musikasinthorn P., Kumazawa Y. Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences. Ichthyol. Res. 2006, 53:148-159.
33. Matsui M. Anuran inventory in Sabah - past and future. Cur. Herpetol. 2006, 25:1-14.
34. Matsui M., Nishikawa K., Sudin A., Mohamed M. The first karyotypic report of the genus Caudacaecilia with comments on its generic validity (Amphibia, Gymnophiona, Ichthyophiidae). Copeia 2006, 2006:256-260.
35. Matsui M., Shimada T., Liu W., Maryati M., Khonsue W., Orlov N. Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae). Mol. Phylogenet. Evol. 2006, 38:659-666.
36. Matsui M., Panha S., Khonsue W., Kuraishi N. Two new species of the "kuhlii" complex of the genus Limnonectes from Thailand (Anura: Dicroglossidae). Zootaxa 2010, 2615:1-22.
37. Matsui M., Hamidy A., Murphy R.W., Khonsue W., Yambun P., Shimada T., Ahmad N., Belabut D.M., Jiang J.-P. Phylogenetic relationships of megophryid frogs of the genus Leptobrachium (Amphibia, Anura). Mol. Phylogenet. Evol. 2010, 56:259-272.
38. Matsui M., Tominaga A., Liu W., Khonsue W., Grismer L.L., Diesmos A.C., Das I., Sudin A., Yambun P., Yong H., Sukumaran J., Brown R.M. Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura; Bufonidae). Mol. Phylogenet. Evol. 2010, 54:561-570.
39. Matsui M., Hamidy A., Belabut D.M., Ahmad N., Panha S., Sudin A., Khonsue W., Oh H.-S., Yong H.-S., Jiang J.-P., Nishikawa K. Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy. Mol. Phylogenet. Evol. 2011, 61:167-176.
40. Meimberg H., Wistuba A., Dittrich P., Heubl G. Molecular phylogeny of Nepenthaceae based on cladistic analysis of plastid trnK intron sequence data. Plant Biol. 2001, 3:164-175.
41. Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., Kent J. Biodiversity hotspots for conservation priorities. Nature 2000, 403:853-858.
42. Nguyen, V.S., Ho, T.C., Nguyen, Q.T., 2009. Herpetofauna of Vietnam. Edition Chimaira, Frankfurt am Main.
43. Nussbaum R.A., Wilkinson M. On the classification and phylogeny of caecilians (Amphibia: Gymnophiona), a critical review. Herpetol. Monogr. 1989, 3:1-42.
44. Pillai R.S., Ravichandran M.S. Gymnophiona (Amphibia) of India. A taxonomic study. Rec. Zool. Survey India. Occasion. Papers 1999, 172:1-117.
45. Rambaut, A., Drummond, A.J., 2007. Tracer version 1.4. http://tree.bio.ed.ac.uk/software/tracer/.
46. Roelants K., Gower D.J., Wilkinson M., Loader S.P., Biju S.D., Guillaume K., Moriau L., Bossuyt F. Global patterns of diversification in the history of modern amphibians. Proc. Natl. Acad. Sci. USA 2007, 104:887-892.
47. Rowley J., Brown R., Bain R., Kusrini M., Inger R., Stuart B., Wogan G., Thy N., Chan-ard T., Trung C.T., Diesmos A., Iskandar D.T., Lau M., Ming L.T., Makchai S., Truong N.Q., Phimmachak S. Impending conservation crisis for Southeast Asian amphibians. Biol. Lett. 2010, 6:336-338.
48. San Mauro D., Gower D.J., Oommen O.V., Wilkinson M., Zardoya R. Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol. Phylogenet. Evol. 2004, 33:413-427.
49. Shimada T., Matsui M., Yambun P., Sudin A. A taxonomic study of Whitehead's torrent frog, Meristogenys whiteheadi, with descriptions of two new species (Amphibia: Ranidae). Zool. J. Linn. Soc. 2011, 161:157-183.
50. 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.
51. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Phylogenet. Evol. 2007, 24:1596-1599.
52. Tanabe, A.S., 2008. Phylogears2 version 2.0.2010.11.12, software distributed by the author at http://www.fifthdimension.jp/.
53. Tanabe A.S. Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Mol. Ecol. Res. 2011, 11:914-921.
54. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Mathematical Questions in Biology - DNA Sequence Analysis 1986, 57-86. American Mathematical Society, Providence. R.M. Miura (Ed.).
55. Taylor E.H. On the caecilian species Ichthyophis glutinosus and Ichthyophis monochrous, with description of related species. Univ. Kansas Sci. Bull. 1960, 40:37-120.
56. Taylor E.H. New Asiatic and African caecilians with redescriptions of certain other species. Univ. Kansas Sci. Bull. 1965, 46:253-302.
57. Taylor E.H. The Caecilians of the World: A Taxonomic Review 1968, University of Kansas Press, Kansas.
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface. flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 1997, 25:4876-4882.
59. Vences M., Thomas M., Bonett R.M., Vieites D.R. Deciphering amphibian diversity through DNA barcoding: chances and challenges. Phil. Trans. Roy. Soc. B 2005, 360:1859-1868.
60. Vences M., Thomas M., Van der Meijden A., Chiari Y., Vieites D.R. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front. Zool. 2005, 2:5.
61. Vos R.A. Accelerated likelihood surface exploration: the likelihood ratchet. Syst. Biol. 2003, 52:368-373.
62. Wilkinson M., Sheps J.A., Oomen O.V., Cohen B.L. Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences. Mol. Phylogenet. Evol. 2002, 23:401-407.
63. Wilkinson M., San Mauro D., Sherratt E., Gower D.J. A nine-family classification of caecilians (Amphibia: Gymnophiona). Zootaxa 2011, 2874:41-64.
64. Xia Y., Gu H.-F., Peng R., Chen Q., Zheng Y.-C., Murphy R.W., Zeng X.M. COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Mol. Ecol. Res. 2012, 12:48-56.
65. Zardoya R., Meyer A. Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona). Genetics 2000, 155:765-775.
66. Zhang P., Wake M.H. A mitogenomic perspective on the phylogeny and biogeography of living caecilians (Amphibia: Gymnophiona). Mol. Phylogenet. Evol. 2009, 53:479-491.
67. Zhang P., Zhou H., Chen Y.Q., Liu Y.F., Qu L.H. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst. Biol. 2005, 54:391-400.