Molecular phylogeny of the diversified frogs of genus fejervarya (Anura: Dicroglossidae)

Zoological Science

Volumn 27, Issue 5, 2010, Pages 386-395

  Kotaki, Manabu ^a   Kurabayashi, Atsushi ^a   Matsui, Masafumi ^b   Kuramoto, Mitsuru ^c   Djong, Tjong Hon ^a,d   Sumida, Masayuki ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c Hikarigaoka   (Japan)

^d ANDALAS UNIVERSITY   (Indonesia)

Author keywords

Fejervarya; Mitochondrial genes; Molecular phylogeny; Nuclear genes; Sequence divergence

Indexed keywords

RNA 16S;

ANIMAL; ARTICLE; ASIA; CLASSIFICATION; FROGS AND TOADS; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; ANURA; ASIA; EVOLUTION, MOLECULAR; GENETIC VARIATION; HAPLOTYPES; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ANURA; FEJERVARYA; FEJERVARYA LIMNOCHARIS;

EID: 77952018408     PISSN: 02890003     EISSN: 02890003     Source Type: Journal    
DOI: 10.2108/zsj.27.386     Document Type: Article

References (46)

1. Alam MS, Igawa T, Khan MMR, Islam MM, Kuramoto M, Matsui M, Kurabayashi A, Sumida M (2008) Genetic divergence and evolutionary relationships in six species of genera Hoplobatrachus and Euphlyctis (Amphibia: Anura) from Bangladesh and other Asian countries revealed by mitochondrial gene sequences. Mol Phylogenet Evol 48: 515-527
2. Bossuyt F, Milinkovitch MC (2000) Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits. Proc Natl Acad Sci USA 97: 6585-6590
3. Bossuyt F, Brown RM, Hillis DM, Cannatella DC, Milinkovitch MC (2006) Phylogeney and biogeography of a cosmopolitan frog radiation: Late Cretaceous diversification resulted in continentscale endemism in the family Ranidae. Syst Biol 55: 579-594
4. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552
5. Djong TH, Islam MM, Nishioka M, Matsui M, Ota H, et al. (2007a) Genetic relationships and reproductive isolation mechanism among the Fejervarya limnocharis complex from Indonesia (Java) and other Asian countries. Zool Sci 24: 360-375
6. Djong TH, Matsui M, Kuramoto M, Daicus MB, Yong HS, Nishioka M, Sumida M (2007b) Morphological divergence, reproductive isolation mechanism, and molecular phylogenetic relationships among Indonesia, Malaysia, and Japan populations of the Fejervarya limnocharis complex (Anura, Ranidae). Zool Sci 24: 1197-1212
7. Dubois A (1975) Un nouveau complexe d'especes jumelles distinguees par le chant: les grenouilles du Nepal voisines de Rana limnocharis Boie (Amphibiens: Anoures). C R Acad Sci D 281: 1717-1720
8. Farris JS, Kallersjo M, Kluge AG, Bult C (1995) Testing significance of incongruence. Cladistics 10: 315-319
9. Fouquet A, Gilles A, Vences M, Marty C, Blanc M, Gemmell NJ (2007) Underestimation of species richness in Neotropical frogs revealed by mtDNA analyses. PLoS One 2: e1109
10. Frost DR (1985) Amphibian Species of the World. Allen Press, Lawrence
11. Frost DR (2009) Amphibian Species of the World: An Online Reference, V3.0. Electronic database available at http:// research.amnh.org/herpetology/ amphibia/index.html
12. Frost DR, Grant T, Faivovich J, Bain R, Haas A, et al. (2006) The amphibian tree of life. Bull Am Mus Nat Hist 297: 11-291
13. Hallowell E (1861) Report upon the Reptilia of North Pacific exploring expedition, under command of Capt. John Rogers, USN. Proc Acad Nat Sci Philadelphia 1860: 480-510
14. Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003a) Biological identification through DNA barcodes. Proc R Soc Lond B 270: 313-321
15. Hebert PDN, Ratnasingham S, de Waard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B (Suppl) 270: S96-S99
16. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004a) Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101: 14812-14817
17. Hebert PDN, Stoekle MY, Zemlak TS, Francis CM (2004b) Identification of birds through CO1 DNA barcodes. Phil Trans R Soc Lond B 359: 669-679
18. Hoegg S, Vences M, Brinkmann H, Meyer A (2004) Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes. Mol Biol Evol 21: 1188-1200
19. Huelsenbeck JR, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754
20. Iskandar DT (1998) The Amphibians of Java and Bali. LIPI, Yayasan Kehati, Bogor
21. Islam MM, Khan MMR, Djong TH, Alam MS, Sumida M (2008a) Genetic differentiation of the Fejervarya limnocharis complex from Bangladesh and other Asian countries elucidate by allozyme analyses. Zool Sci 25: 261-272
22. Islam MM, Kurose N, Khan MMR, Nishizawa T, Kuramoto M, Alam MS, Hasan M, Kurniawan N, Nishioka M, Sumida M (2008b) Genetic divergence and reproductive isolation in the genus Fejervarya (Amphibia: Anura) from Bangladesh inferred from morphological observations, crossing experiments, and molecular analyses. Zool Sci 25: 1084-1105
23. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29: 170-179
24. Kotaki M, Kurabayashi A, Matsui M, Khonsue W, Djong TH, Tandon M, Sumida M (2008) Genetic divergences and phylogenetic relationships among the Fejervarya limnocharis complex in Thailand and neighboring countries revealed by mitochondrial and nuclear genes. Zool Sci 25: 381-390
25. Kurabayashi A, Sumida M (2009) PCR primers for the neobatrachian mitochondrial genome. Curr Herpetol 28: 1-11
26. Kurabayashi A, Kuramoto M, Joshy H, Sumida M (2005) Molecular phylogeny of the ranid frogs from the Southwest India based on the mitochondrial ribosomal RNA gene sequences. Zool Sci 22: 525-534
27. Kurabayashi A, Sumida M, Yonekawa H, Glaw F, Vences M, Hasegawa M (2008) Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Mol Biol Evol 25: 874-891
28. Kuramoto M, Joshy SH (2001) Advertisement call structures of frogs from southwestern India, with some ecological and taxonomic notes. Curr Herpetol 20: 85-95
29. Kuramoto M, Joshy SH, Kurabayashi A, Sumida M (2007) The genus Fejervarya (Anura: Ranidae) in central western Ghats, India, with description of four new cryptic species. Curr Herpetol 26: 81-105
30. Kurniawan N, Islam MM, Djong TH, Igawa T, Daicus MB, et al. (2009) Genetic divergence and evolutionary relationship in Fejervarya cancrivora from Indonesia and other Asian countries inferred from allozyme and mtDNA sequence analyses. Zool Sci 26: 222-233
31. Matsui M, Toda M, Ota H (2007) A new species of frog allied to Fejervarya limnocharis from the southern Ryukyus, Japan (Amphibia: Ranidae). Curr Herpetol 26: 65-79
32. Okada N, Shedlock MA, Nikaido M (2003) Retroposon mapping in molecular systematics. Method Mol Biol 260: 189-226
33. Posada D, Crandall KA (1998) MODEL TEST: testing the model of DNA substitution. Bioinformatics 14: 817-818
34. Schleich HH, Kastle W (2002) Amphibians and Reptiles of Nepal. ARG Ganther Verlag KG, Ruggell
35. Shimodaira H, Hasegawa M (1999) Multiple comparison of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116
36. Stuart BL, Chuaynkern Y, Chan-ard T, Inger RF (2006) Three new species of frogs and a new tadpole from eastern Thailand. Fieldiana Zool NS 1543: 1-19
37. Sumida M, Ogata M, Kaneda H, Yonekawa H (1998) Evolutionary relationships among Japanese pond frogs infeπed from mitochondrial DNA sequences of cytochrome b and 12S ribosomal RNA genes. Genes Genet Syst 73: 121-133
38. Sumida M, Kondo Y, Kanamori Y, Nishioka M (2002) Inter- and intraspecific evolutionary relationships of the rice frog Rana limnocharis and the allied species R. cancrivora inferred from crossing experiments and mitochondrial DNA sequences of the 12S and 16S rRNA genes. Mol Phylogenet Evol 25: 293-305
39. Sumida M, Kotaki M, Islam MM, Djong TH, Igawa T, Kondo Y, Matsui M, De Silva A, Khonsue W, Nishioka M (2007) Evolutionary relationships and reproductive isolating mechanisms in the rice frog (Fejervarya limnocharis) species complex from Sri Lanka, Thailand, Taiwan and Japan, inferred from mtDNA gene sequences, allozymes, and crossing experiments. Zool Sci 24: 547-562
40. Swofford DL (2002) PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), Beta Version 4.0b10. Sinauer, Sunderland, MA
41. Thompson JD, Higgins DG, Gilbson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
42. Toda M, Nishida M, Matsui M, Ota H (1998) Genetic divergence among Southeast and East Asian population of Rana limnocharis (Amphibia:Anura), with species reference to sympatric cryptic species in Java. Zool Sci 14: 607-613 (Pubitemid 128367826)
43. Veith M, Kosuch J, Ohler A, Dubois A (2001) Systematics of Fejervarya limnocharis (Gravenhorst, 1829) (Amphibia, Anura, Ranidae) and related species. 2. Morphological and molecular variation in frogs from the Greater Sunda Islands (Sumatra, Java, Borneo) with the definition of two species. Alytes 19: 5-28
44. Vences M, Thomas M, Meijden AVD, Chiari Y, Vieites DR (2005a) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2: 5
45. Vences M, Thomas M, Bonett RM, Vieites DR (2005b) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Phil Trans R Soc B 360: 1859-1868
46. Vieites DR, Wollenberg KC, Andreone F, Glaw F, Vences M (2009) Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory. Proc Natl Acad Sci USA 106: 8267-8272