Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes

Molecular Biology and Evolution

Volumn 21, Issue 7, 2004, Pages 1188-1200

  Hoegg, Simone ^a   Vences, Miguel ^a,b   Brinkmann, Henner ^a,c   Meyer, Axel ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Amphibia; Anura; Archaeobatrachia; Hyloidea; Neobatrachia; Rag 1; Rag 2; Ranoidea; Rhodopsin; Substitution rates

Indexed keywords

RAG1 PROTEIN; RAG2 PROTEIN; RHODOPSIN; RNA 12S; RNA 16S; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; CLADISTICS; EVOLUTIONARY RATE; FROG; GENE; GENE SEQUENCE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RAG1 GENE; RAG2 GENE; RHODOPSIN GENE; SEQUENCE ANALYSIS; TOAD; UNINDEXED SEQUENCE;

ANIMALS; ANURA; CELL NUCLEUS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; HOMEODOMAIN PROTEINS; PHYLOGENY; RHODOPSIN; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS;

AMPHIBIA; ANURA; BUFONIDAE; HELEOPHRYNIDAE; HYLIDAE; HYLOIDEA; HYPEROLIIDAE; LEPTODACTYLIDAE; MANTELLINAE; MICROHYLIDAE; NEOBATRACHIA; PELOBATIDAE; PSEUDIDAE; RANIDAE; RANOIDEA; RHACOPHORIDAE; SOOGLOSSIDAE;

EID: 3042645976     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh081     Document Type: Article

References (70)

1. AmphibiaWeb: Information on amphibian biology and conservation. [web application]. 2003. Berkeley, California: AmphibiaWeb. Available: http://amphibiaweb.org/.
2. Báez, A. M. 2000. Tertiary anurans from South America. Pp. 1388-1401 in H. Heatwole, ed. Amphibian biology, Vol. 4. Paleontology. Surrey Beatty, Chipping Norton, Australia.
3. Barnes, W. M. 1994. PCR amplification of up to 35-kb DNA with high fidelity and high yield from λ bacteriophage templates. Proc. Natl. Acad. Sci. USA 91:2216-2220.
4. Biju, S. D., and F. Bossuyt. 2003. New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature 425:711-714.
5. Bossuyt, F., and M. C. Milinkovitch. 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.
6. Brinkmann, H., and H. Philippe. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:817-825.
7. Brown, W. M., M. George, Jr., and A. C. Wilson. 1979. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76:1967-1971.
8. Cheng, S., C. Fockler, W. M. Barnes, and R. Higuchi. 1994. Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. USA 91:5695-5699.
9. Dubois, A. 1992. Notes sur la classification des Ranidae (Amphibiens Anoures). Bull. mens. Soc. linn. Lyon 61:305-352.
10. Duellman, W. E. 1975. On the classification of frogs. Occ. Pap. Mus. Nat. Hist. Univ. Kansas 42:1-14.
11. -. 2001. The hylid frogs of middle America, 2nd ed. SSAR Contrib. Herp. 18. Society for the Study of Amphibians and Reptiles, Ithaca, New York.
12. Duellman, W. E., and L. Trueb. 1986. Biology of amphibians. McGraw-Hill, New York.
13. Emerson, S. B. 1988. Convergence and morphological constraint in frogs: variation in postcranial morphology. Fieldiana: Zoology 43:1-19.
14. Emerson, S. B., C. Richards, R. C. Drewes, and K. M. Kjer. 2000. On the relationships among ranoid frogs: a review of the evidence. Herpetologica 56:209-230.
15. Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1995. Testing significance of incongruence. Cladistics 10:315-319.
16. Feller, A. E., and S. B. Hedges. 1998. Molecular evidence for the early history of living amphibians. Mol. Phylogenet. Evol. 9:509-516.
17. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
18. -. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
19. Ford, L. S., and D. C. Cannatella. 1993. The major clades of frogs. Herp. Monogr. 7:94-117.
20. Fuellen, G., J.-W. Wägele, and R. Giegerich. 2001. Minimum conflict: a divide-and-conquer approach to phylogeny estimation. Bioinformatics 17:1168-1178.
21. García-París, M., D. R. Buchholz, and G. Parra-Olea. 2003. Phylogenetic relationships of Pelobatoidea re-examined using mtDNA. Mol. Phylogenet. Evol. 28:12-34.
22. Graybeal, A. 1993. The phylogenetic utility of cytochrome b: lessons from bufonid frogs. Mol. Phylogenet. Evol. 2:256-269.
23. -. 1994. Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst. Biol. 43:174-193.
24. Griffiths, I. 1963. The phylogeny of the Salientia. Biol. Rev. 38:241-292.
25. Haas, A. 2003. Phylogeny of frogs as inferred from primarily larval characters (Amphibia: Anura). Cladistics 19:23-89.
26. 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.
27. Hedges, S. B. 1992. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol. Biol. Evol. 9:366-369.
28. Hedges, S. B., and L. R. Maxson. 1993. A molecular perspective on lissamphibian phylogeny. Herp. Monogr. 7:27-42.
29. 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.
30. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
31. Jones, D. T., W. R. Taylor, and J. B. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
32. Kumar, S. 1996. Phyltest: phylogeny hypothesis testing software. The Pennsylvania State University, Pennsylvania.
33. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
34. Laurent, R. 1979. Esquisse d'une phylogenèse des anoures. Bull. Soc. Zool. France 104:397-422.
35. Lecointre, G., H. Philippe, H. L. Van Le, and H. Le Guyader. 1994. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Mol. Phylogenet. Evol. 3:292-309.
36. Li, W. H., M. Tanimura, and P. M. Sharp. 1987. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25:330-342.
37. Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang, and T. J. Papenfuss. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:91-104.
38. Martin, A. P. 1999. Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). Mol. Biol. Evol. 16:996-1002.
39. Martin, A. P., and S. R. Palumbi. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90:4087-4091.
40. Maxson, L. R., and A. C. Wilson. 1974. Convergent morphological evolution detected by studying proteins of tree frogs in the Hyla eximia species group. Science 185:66-68.
41. Meyer, A., and R. Zardoya. 2003. The (molecular) phylogenetic relationships of vertebrates. Ann. Rev. Ecol. Evol. 34: 311-338.
42. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
43. Philippe, H., and A. Germot. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-834.
44. Philippe, H., A. Germot, and D. Moreira. 2000. The new phylogeny of eukaryotes. Curr. Op. Genet. Dev. 10:596-601.
45. Philippe, H., and J. Laurent. 1998. How good are deep phylogenetic trees? Curr. Op. Genet. Dev. 8:616-623.
46. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
47. Pugener, L. A., A.M. Maglia, and L. Trueb. 2003. Revisiting the contribution of larval characters to an analysis of phylgenetic relationships of basal anurans. Zool. J. Linnean Soc. 139:129-155.
48. Richards, C. M., and W. S. Moore. 1996. A phylogeny for the African treefrog family Hyperoliidae based on mitochondrial rDNA. Mol. Phyl. Evol. 5:522-532.
49. Richards C. M., R. A. Nussbaum, and C. J. Raxworthy. 2000. Phylogenetic relationships within the Madagassan boophids and mantellids as evidenced by mitochondrial ribosomal genes. African J. Herpet. 49:23-32.
50. Roček, Z. 2000. Mesozoic anurans. Pp. 1295-1331 in H. Heatwole, ed. Amphibian Biology, Vol. 4. Paleontology. Surrey Beatty, Chipping Norton, Australia.
51. Roček, Z., and J. C. Rage. 2000. Tertiary Anura of Europe, Africa, Asia, North America and Australia. Pp. 1332-1387 in H. Heatwole, ed. Amphibian Biology. Vol. 4, Paleontology. Surrey Beatty, Chipping Norton, Australia.
52. Ruvinsky, I., and L. R. Maxson. 1996. Phylogenetic relationships among bufonoid frogs (Anura: Neobatrachia) inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 5:533-547.
53. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
54. Sanchiz, B. 1998. Encyclopedia of palaeoherpetology, Part 4. Salientia. Pfeil, München.
55. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1231.
56. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
57. Shao, R., M. Dowton, A. Murrell, and S. C. Barker. 2003. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genome of insects. Mol. Biol. Evol. 20:1612-1613.
58. Springer, M. S., R. W. Debry, C. Douady, H. M. Amrine, O. Madsen, W. W. de Jong, and M. J. Stanhope. 2001. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol. Biol. Evol. 18: 132-143.
59. Stiller, J. W., and D. B. Hall. 1999. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16:1270-1279.
60. Sumida, M., Y. Kanamori, H. Kaneda, Y. Kato, M. Nishioka, M. Hasegawa, and H. Yonekawa. 2001. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet. Syst. 76:311-325.
61. Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
62. Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
63. Thompson, J. D., T. J. Gebson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustaIX window interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 30:109-112.
64. Vawter, L., and W. M. Brown. 1986. Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science 234:194-196.
65. Vences, M., F. Glaw, J. Kosuch, I. Das, and M. Veith. 2000a. Polyphyly of Tomopterna (Amphibia: Ranidae) based on sequences of the mitochondrial 16S and 12S rRNA genes, and ecological biogeography of Malagasy relict amphibian groups. Pp. 229-242 in W. R. Lourenço and S. M. Goodman, eds. Diversité et endémisme a Madagascar. Mémoires de la Société de Biogéographie, Paris.
66. Vences, M., J. Kosuch, S. Lötters, A. Widmer, J. Köhler, K.-H. Jungfer, and M. Veith. 2000b. Phylogeny and classification of poison frogs (Amphibia: Dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences. Mol. Phylogenet. Evol. 15:34-40.
67. Vences, M., J. Kosuch, F. Glaw, W. Böhme, and M. Veith. 2003. Molecular phylogeny of hyperoliid treefrogs: biogeographic origin of Malagasy and Seychellean taxa and re-analysis of familial paraphyly. J. Zool. Syst. Evol. Res. 41:205-215.
68. Wallace, D. G., L. R. Maxson, and A. C. Wilson. 1971. Albumin evolution in frogs: a test of the evolutionary clock hypothesis. Proc. Natl. Acad. Sci. USA 68:3127-3129.
69. Zardoya, R., E. Malaga-Trillo, M. Veith, and A. Meyer. 2003. Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani. Gene 317:17-27.
70. Zardoya, R., and A. Meyer 2001. On the origin of and phylogenetic relationships among living amphibians. Proc. Natl. Acad. Sci. USA 98:7380-7383.