Mitogenomic perspectives on the origin and phylogeny of living amphibians

Systematic Biology

Volumn 54, Issue 3, 2005, Pages 391-400

  Zhang, Peng ^a   Zhou, Hui ^a   Chen, Yue Qin ^a   Liu, Yi Fei ^a   Qu, Liang Hu ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Amphibian; Mitochondrial genome; Molecular dating; Phylogeny; Timescale

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

AMPHIBIA; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

AMPHIBIA; ANIMALS; BASE SEQUENCE; BAYES THEOREM; CLUSTER ANALYSIS; DNA PRIMERS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AMPHIBIA; AMPHIUMA MEANS; ANURA; CAUDATA; GYMNOPHIONA; TETRAPODA;

EID: 22844444149     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150590945278     Document Type: Article

References (57)

1. Anderson, S., M. H. DE Bruijn, A. R. Coulson, I. C. Eperon, F. Sanger, and I. G. Young. 1982. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156:683-717.
2. Andrews, R. M., I. Kubacka, P. F. Chinnery, R. N. Lightowlers, D. M. Turnbull, and N. Howell. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23:147.
3. Benton, M. J. 1990. Phylogeny of the major tetrapod groups: Morphological data and divergence dates. J. Mol. Evol. 30:409-424.
4. Benton, M. J. 1997. Vertebrate palaeontology, 2nd edition. Chapman & Hall, London, UK.
5. Biju, S. D., and F. Bossuyt. 2003. New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature 425:711-714.
6. Bolt, J. R. 1991. Lissamphibian origins. Pages 194-222 in Origins of the major groups of Tetrapods: Controversies and consensus (H. P. Schultze and L. Trueb, eds.). Cornell University Press, Ithaca, New York.
7. Cao, Y., J. Adachi, A. Janke, S. Pääbo, and M. Hasegawa. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene. J. Mol. Evol. 39:519-527.
8. Cao, Y., K. Kim, J. Ha, and M. Hasegawa. 1999. Model dependence of the phylogenetic inference: Relationship among carnivores, perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences. Genes Genet. Syst. 74:211-217.
9. Carroll, R. L. 2001. The origin and early radiation of terrestrial vertebrates. J. Paleontol. 75:1202-1213.
10. Carroll, R. L., and R. Holmes. 1980. The skull and jaw musculature as guides to the ancestry of salamanders. J. Linn. Soc. Lond. Zool. 68:1-40.
11. Carroll, R. L., A. Kuntz, and K. Albright. 1999. Vertebral development and amphibian evolution. Evol Dev. 1:36-48.
12. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
13. Chang, Y. S., F. L. Huang, and T. B. Lo. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38:138-155.
14. Coates, M. I., and A. R. Milner. 2000. Early tetrapod evolution. Trends Ecol. Evol. 15:327-328.
15. Cummings, M. P., S. P. Otto, and J. Wakeley. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
16. Delarbre, C., N. Spruyt, C. Delmarre, C. Gallut, V. Barriel, P. Janvier, V. Laudet, and G. Gachelin. 1998. The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula. Genetics 150:331-344.
17. Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome, a novel gene order in higher vertebrates. J. Mol. Biol. 212:599-634.
18. Duellman, W. E., and L. Trueb. 1986. Biology of amphibians. McGraw-Hill, New York.
19. Evans, S. E., and M. Borsuk-Bialynicka. 1998. A stem-group frog from the Early Triassic of Poland. Acta Palaeontol. Polon. 43:573-580.
20. Feller, A. E., and S. B. Hedges. 1998. Molecular evidence for the early history of living amphibians. Mol. Phylogenet. Evol. 9:509-516.
21. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410.
22. Ford, L. S., and D. C. Cannatella. 1993. The major clades of frogs. Herpetol. Monogr. 7:94-117.
23. Gao, K. Q., and N. Shubin. 2001. Late Jurassic salamanders from northern China. Nature 410:574-576.
24. Hay, J. M., I. Ruvinsky, S. B. Hedges, and L. R. Maxson. 1995. Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12:928-937.
25. Hedges, S. B., K. D. Moberg, and L. R. Maxson. 1990. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol Biol Evol. 7:607-633.
26. Huelsenbeck, J. P., and N. S. Imennov. 2002. Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison. Syst. Biol. 51:155-165.
27. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
28. Janke, A., and U. Arnason. 1997. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol. Biol. Evol. 14:1266-1272.
29. Jenkins, F. A., and D. M. Walsh. 1993. An early Jurassic caecilian with limbs. Nature 365:247-250.
30. Kishino, H., and M. Hasegawa. 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.
31. Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:197-920.
32. Larson, A. 1991. A molecular perspective on the evolutionary relationships of the salamander families. Evol. Biol. 25:211-277.
33. Laurin, M., M. Girondot, and A. de Ricqles. 2000. Early tetrapod evolution. Trends Ecol. Evol. 15:118-123.
34. Laurin, M., and R. Reisz. 1997. A new perspective on tetrapod phylogeny. Pages 9-59 in Amniote origins, (S. S. Suemida and K. L. Martin, eds.). Academic Press, New York.
35. Milner, A. R. 1983. Evolution, time and space: The emergence of the biosphere. Academic Press, New York.
36. Milner, A. R. 1988. The relationships and origin of living amphibians. Pages 59-102 in The phylogeny and classification of the Tetrapods (M. J. Benton, ed.). Clarendon Press, Oxford.
37. Philippe, H. 2000. Opinion: Long branch attraction and protist phylogeny. Protist. 151:307-316.
38. Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
39. Rage, J. C., and Z. Rocek. 1989. Redescription of Triadobatrachus massinoti (Piveteau, 1936) an anuran amphibian from the early Triassic. Palaeontographi. Abt. 206:1-16.
40. Roe, B. A., M. Din-Pow, R. K. Wilson, and J. F. Wong. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:9759-9774.
41. Roelants, K., and F. Bossuyt. 2005. Archaeobatrachian paraphyly and Pangaean diversification of crown-group frogs. Syst. Biol. 54:111-126.
42. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
43. Scotese, C. R. 2002. http;//www.scotese.com (PALEOMAP website).
44. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
45. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
46. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508.
47. Sumida, M., Y. Kanamori, H. Kaneda, Y. Kato, M. Nishioka, and H. Yonekawa. 2001. Complete nucleotide sequence and gene organization of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet. Syst. 76:311-325.
48. Swofford, D. L. 2001. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b8. Sinauer Associates, Sunderland, Massachusetts.
49. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic. Acids. Res. 24:4876-4882.
50. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
51. Trueb, L., and R. Cloutier. 1991. A phylogenetic investigation of the inter- and intrarelationships of the Lissamphibia (Amphibia: Temnospondyli). Pages 223-313 in Origins of the major groups of Tetrapods: Controversies and consensus (H. P. Schultze and L. Trueb, eds.). Cornell University Press, Ithaca, New York.
52. Zardoya, R., and A. Meyer. 1996a. The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates. Genetics 142:1249-1263.
53. Zardoya, R., and A. Meyer. 1996b. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13:933-942.
54. Zardoya, R., and A. Meyer. 2000. Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona). Genetics. 155:765-775.
55. Zardoya, R., and A. Meyer. 2001. On the origin of and phylogenetic relationships among living amphibians. Proc. Natl. Acad. Sci. USA 98:7380-7383.
56. Zhang, P., Y. Q. Chen, Y. F. Liu, H. Zhou, and L. H. Qu. 2003a. The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene 311:93-98.
57. Zhang, P., Y. Q. Chen, H. Zhou, X. L. Wang, and L. H. Qu. 2003b. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol. Phylogenet. Evol. 28:620-626.