Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

Molecular Phylogenetics and Evolution

Volumn 50, Issue 3, 2009, Pages 571-579

  Yu, Guohua ^a   Rao, Dingqi ^a   Zhang, Mingwang ^a   Yang, Junxing ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

mtDNA; nuDNA; Phylogeny; Rhacophoridae

Indexed keywords

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

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; FROGS AND TOADS; GENETICS; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; ANURA; BAYES THEOREM; CELL NUCLEUS; CYTOCHROMES B; EVOLUTION, MOLECULAR; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MITOCHONDRIA; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ANURA; AQUIXALUS; AQUIXALUS ODONTOTARSUS; CHIROMANTIS; KURIXALUS; PHILAUTUS; POLYPEDATES; RHACOPHORIDAE; RHACOPHORUS;

EID: 60349097222     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.11.023     Document Type: Article

References (55)

1. Akaike H. Information theory as an extension of the maximum likelihood principle. In: Petrov B.N., and Csaki F. (Eds). Second International Symposium on Information Theory (1973), Budapest, Akademiai Kiado 267-281
2. Bahir, M.M., Meegaskumbura, M., Manamendra-Arachchi, K., Schneider, C.J., Pethiyagoda, R., 2005. Reproduction and terrestrial direct development in Sri Lankan shrub frogs (Ranidae: Rhacophorinae: Philautus). Raffles. B Zool. (Suppl.). 12, 339-350.
3. Biju S.D., and Bossuyt F. New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature 425 (2003) 711-714
4. Bossuyt F., Brown R.M., Hillis D.M., Cannatella D.C., and Milinkovitch M.C. Phylogeny and biogeography of a cosmopolitan frog radiation: late cretaceous diversification resulted in continent-scale endemism in the family Ranidae. Syst. Biol. 55 4 (2006) 579-594
5. Bossuyt F., and Dubois A. A review of the frog genus Philautus Gistel, 1848 (Amphibia, Anura, Ranidae, Rhcaophorinae). Zeylanica 1 (2001) 1-112
6. Bossuyt F., Meegaskumbura M., Beenaerts N., Gower D.J., Pethiyagoda R., Roelants K., Mannaert A., Wilkinson M., Bahir M.M., Manamendra-Arachchi K., Ng P.K.L., Schneider C.J., Oommen O.V., and Milinkovitch M.C. Local endemism within the Western Ghats-Sri Lanka biodiversity hotspot. Science 306 (2004) 479-481
7. Bossuyt F., and Milinkovitch M.C. Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits. Proc. Natl. Acad. Sci. USA 97 (2000) 6585-6590
8. Bossuyt F., and Milinkovitch M.C. Amphibians as indicators of early tertiary "Out-of-India" dispersal of vertebrates. Science 292 (2001) 93-95
9. Channing A. A re-evaluation of the phylogeny of Old World treefrogs. S. Afr. J. Zool. 24 (1989) 116-131
10. Darst C.R., and Cannatella D.C. Novel relationships among hyloid frogs inferred from 12S and 16S mitocondrial DNA sequences. Mol. Phylogenet. Evol. 31 (2004) 462-475
11. Delorme, M., 2004. Phylogénie des Ranidae Rhacophorinae: confrontations des analyses moléculaires et morphologiques, et etude de caractères. Unpublished thesis. Muséum National d'Histoire Naturelle, Paris, 334 pp.
12. Delorme, M., Dubois, A., Grosjean, S., Ohler, A., 2005. Une nouvelle classification generique et subgenerique de la tribu des Philautini (Amphibia, Anura, Ranidae, Rhacophorinae). Bull. Mensuel Soc. Lin. Lyon. 74, 165-171.
13. Delorme M., Dubois A., Kosuch J., and Vences M. Molecular phylogenetic relationships of Lankanectes corrugatus from Sri Lanka: endemism of South Asian frogs and the concept of monophyly in phylogenetic studies. Alytes 22 (2004) 53-64
14. Dring J.C.M. Bornean treefrogs of the genus Philautus (Rhacophoridae). Amphibian-Reptilla 8 (1987) 19-47
15. Dubois A. Miscellanea taxinomica batrachologica. Alytes 5 (1987) 7-95
16. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
17. Fei L. Atlas of Amphibians of China (1999), Henan Publishing House of Science and Technology, Zhenzhou
18. Fei L., Ye C., Jiang J., Xie F., and Huang Y. An Illustrated Key to Chinese Amphibians (2005), Sichuan Publishing House of Science and Technology, Chengdu
19. Felsenstein J.P. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
20. Frost, D.R., 2007. Amphibian Species of the World: an Online Reference, version 5.1 (1 October, 2007). Electronic database accessible at: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA.
21. Frost, D.R., 2008. Amphibian Species of the World: an Online Reference, version 5.2 (15 July, 2008). Electronic database accessible at: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA.
22. 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., and Wheeler W.C. The amphibian tree of life. Bull. Am. Mus. Nat. His. 297 (2006) 1-370
23. Grosjean S., Delorme M., Dubois A., and Ohler A. Evolution of reproduction in the Rhacophoridae (Amphibia, Anura). J. Zool. Syst. Evol. Res. 46 2 (2008) 169-176
24. Huelsenbeck J.P., and Bollback J.P. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50 (2001) 351-366
25. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
26. Kam Y.C., Chuang Z.S., and Yen C.F. Reproduction, oviposition-site selection and larval oophagy of an aboreal nester, Chirixalus eiffingeri (Rhacophoridae), from Taiwan. J. Herpetol. 30 (1996) 52-59
27. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., and Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196-6200
28. Kosuch J., Vences M., Dubois A., Ohler A., and Böme W. Out of Asia: mitochondrial DNA evidence for an oriental origin of tiger frogs, genus Hoplobatrachus. Mol. Phylogenet. Evol. 21 (2001) 398-407
29. Kou Z., Hu J., and Gao C. A new species of the genus Polypedates from Yunnan, China. Acta Zootaxonomica Sin. 26 2 (2001) 229-233
30. Kuramoto M., and Wang C. A new Rhacophorid treefrog from Taiwan, with comparisons to Chirixalus eiffingeri (Anura, Rhacophoridae). Copeia 4 (1987) 931-942
31. Leaché A.D., and Reeder T.W. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51 (2002) 44-68
32. Li J., Che J., Bain R.H., Zhao E., and Zhang Y. Molecular phylogeny of Rhacophoridae (Anura): a framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus and Philautus. Mol. Phylogenet. Evol. 48 (2008) 302-312
33. Liu, C., 1945. New frogs from West China. J. West China Border Res. Soc. 15 (B), 28-43.
34. Liu C., and Hu S. Chinese Tailless Batrachians (1961), Science Press, Beijing, China
35. Liem S.S. The morphology, systematics, and evolution of the Old World treefrogs (Rhacophoridae and Hyperoliidae). Fieldiana Zool. 57 (1970) 1-145
36. Meegaskumbura M., Bossuyt F., Pethiyagoda R., Manamendra-Arachchi K., Bahir M., Milinkovitch M.C., and Schneider C.J. Sri Lanka: an amphibian hot spot. Science 298 (2002) 379
37. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
38. Palumbi S.R., Martin A., Romano S., Owen MacMillan W., Stice L., and Grabowski G. The Simple Fool's Guide to PCR (1991), Department of Zoology, University of Hawaii, Honolulu
39. Rao D., Wilkinson J.A., and Liu H. A new species of Rhacophorus (Anura: Rhacophoridae) from Guangxi Province, China. Zootaxa 1258 (2006) 17-31
40. Richards C.M., and Moore W.S. A molecular phylogenetic study of the old world treefrog family Rhacophoridae. Herpetol. J. 8 (1998) 41-46
41. Roelants K., Gower D.J., Wilkinson M., Loader S.P., Biju S.D., Guillaume K., Moriau L., and Bossuyt F. Global patterns of diversification in the history of modern amphibians. Proc. Natl. Acad. Sci. USA 104 (2007) 887-892
42. Rambaut, A., Drummond, A.J., 2003. Tracer version 1.0.1. Available from: .
43. Sano N., Kurabayashi A., Fujii T., Yonekawa H., and Sumida M. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, Buergeria buergeri (family Rhacophoridae). Genes Genet. Syst. 79 (2004) 151-163
44. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and other Methods), Version 4.0 (2002), Sinauer Associates, Sunderland, MA
45. Swofford D.L., Olsen G.J., Waddell P.J., and Hillis D.M. Phylogenetic inference. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics. second ed. (1996), Sinauer Associates, Sunderland, Massachusetts 407-514
46. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin J., and Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
47. Van der Meijden A., Vences M., Hoegg S., and Meyer A. A previously unrecognized radiation of ranid frogs in Southern Africa revealed by nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 37 (2005) 674-685
48. Van der Meijden, A., Vences, M., Meyer, A., 2004. Novel phylogenetic relationships of the enigmatic brevicipitine and scaphiophrynine toads as revealed by sequences from the nuclear Rag-1 gene. Proc. R. Soc. Lond. B (Suppl.) 271, S378-S381.
49. Vences M., Vieites D.R., Glaw F., Brinkmann H., Kosuch J., Veith M., and Meyer A. Multiple overseas dispersal in amphibians. Proc. R. Soc. B. 270 (2003) 2435-2442
50. Wilkinson, J.A., Drewes, R.C., 2000. Character assessment, genus level boundaries, and phylogenetic analyses of the family Rhacophoridae: a review and present day status. Cont. Herpetol. 2.
51. Wilkinson J.A., Drewes R.C., and Tatum O.L. A molecular phylogenetic analysis of the family Rhacophoridae with an emphasis on the Asian and African genera. Mol. Phylogenet. Evol. 24 (2002) 265-273
52. Wu G., and Zeng X. The karyotypic differentiation of Polypedates dugritei with description of a superspecies (Rhacophoridae, Anura). Sichuan J. Zool. 13 4 (1994) 156-161
53. Ye, C., Fei, L., 1993. In: Ye, C., Fei, L., Hu, S. (Eds.), Rare and Economic Amphibians of China. Sichuan Science and Technology Press, Chengdu, pp. 320-322.
54. Yu G., Rao D., Yang J., and Zhang M. Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species. Zool. J. Lin. Soc. 153 (2008) 733-749
55. Ziegler T., and Vences M. The tadpole of Rhacophorus verrucosus Boulenger, 1983 from Vietnam (Amphibia: Anura: Rhacophoridae). Faunist. Abhandl. 22 20 (2002) 319-327