Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes

Molecular Phylogenetics and Evolution

Volumn 53, Issue 2, 2009, Pages 492-508

  Zhang, Peng ^a,b   Wake, David B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Mitochondrial genome; Molecular dating; Phylogeny; Salamander

Indexed keywords

MITOCHONDRIAL DNA;

AMPHIBIA; ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETICS; GEOGRAPHY; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME, MITOCHONDRIAL; GEOGRAPHY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; URODELA;

AMBYSTOMA; AMBYSTOMATIDAE; AMPHIBIA; AMPHIUMIDAE; CRYPTOBRANCHIDAE; CRYPTOBRANCHOIDEA; DICAMPTODONTIDAE; HYNOBIIDAE; PLETHODONTIDAE; PROTEIDAE; RHYACOTRITONIDAE; SALAMANDRIDAE; SALAMANDROIDEA; SIRENIDAE; TETRAPODA;

EID: 69249244262     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.07.010     Document Type: Article

References (97)

1. AmphibiaWeb: Information on amphibian biology and conservation [web application]. Berkeley, California: AmphibiaWeb. Available from: http://amphibiaweb.org/ (Accessed: June, 2009).
2. Anderson J.S., Reisz R.R., Scott D., Fröbisch N.B., and Sumida S.S. A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders. Nature 453 (2008) 515-518
3. Anisimova M., and Gascue O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55 (2006) 539-552
4. Arnason U., Gullberg A., Janke A., Joss J., and Elmerot C. Mitogenomic analyses of deep gnathostome divergences: a fish is a fish. Gene 333 (2004) 61-70
5. Benton M.J., and Donoghue P.C. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24 (2007) 26-53
6. Bininda-Emonds O.R., Cardillo M., Jones K.E., MacPhee R.D., Beck R.M., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., and Purvis A. The delayed rise of present-day mammals. Nature 446 (2007) 507-512
7. Briggs J.C. Global Biogeography (1995), Elsevier Science, Amsterdam
8. Brochu C.A. Patterns of calibration age sensitivity with quartet dating methods. J. Paleont. 78 (2004) 7-30
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
10. D'Erchia A.M., Gissi C., Pesole G., Saccone C., and Arnason U. The guinea pig is not a rodent. Nature 381 (1996) 597-600
11. Drummond A.J., Ho S.Y., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4 (2006) e88
12. Duellman W.E., and Trueb L. Biology of Amphibians (1986), McGraw-Hill, New York
13. Edwards A.W.F. Likelihood (1992), Johns Hopkins Univ. Press, Baltimore
14. Edwards J. Spinal nerves and their bearing on salamander phylogeny. J. Morphol. 148 (1976) 305-327
15. Ericson P.G., Anderson C.L., Britton T., Elzanowski A., Johansson U.S., Kallersjo M., Ohlson J.I., Parsons T.J., Zuccon D., and Mayr G. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol. Lett. 2 (2006) 543-547
16. Estes R. Gymnophiona, Caudata. Handbuch der Palaoherpetologie 2 (1981) 1-115
17. Evans S.E., Milner A.R., and Werner C. Sirenid salamanders and a gymnophionan amphibian from the Cretaceous of the Sudan. Palaeontology 39 (1996) 77-95
18. Evans S.E., and Waldman M. Small reptiles and amphibians from the Middle Jurassic of Skye, Scotland. Mus. Northern Arizona Bull. 60 (1996) 219-226
19. Evans S.E., and Borsuk-Bialynicka M. A stem-group frog from the Early Triassic of Poland. Acta Palaeontol. Polon. 43 (1998) 573-580
20. Evans S.E., Lally C., Chure D.C., Elder A., and Maisano J.A. A Late Jurassic salamander (Amphibia: Caudata) from the Morrison Formation of North America. Zool. J. Lin. Soc. 143 (2005) 599-616
21. Frost D.R., Grant T., Faivovich J., Bain R.H., Haas A., Haddad C.F.B., De Sa 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. Hist. 297 (2006) 1-370
22. Gao K.Q., and Shubin N.H. Late Jurassic salamanders from northern China. Nature 410 (2001) 574-577
23. Gao K.Q., and Shubin N.H. Earliest known crown-group salamanders. Nature 422 (2003) 424-428
24. Goin C.J., Goin O.B., and Zug G.R. Introduction to Herpetology (1978), W.H. Freeman, San Francisco
25. Good D.A., and Wake D.B. Geographic variation and speciation in the torrent salamanders of the genus Rhyacotriton (Caudata: Rhyacotritonidae). Univ. Calif. Public. Zool. 126 (1992) 1-91
26. Graur D., and Martin W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20 (2004) 80-86
27. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
28. Gutell R.R., Larsen N., and Woese C.R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58 (1994) 10-26
29. Hallam A. An Outline of Phanerozoic Biogeography (1994), Oxford Univ. Press, Oxford
30. Hay J.M., Ruvinsky I., Hedges S.B., and Maxson L.R. Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol. Biol. Evol. 12 (1995) 928-937
31. Hecht M.K., and Edwards J.L. The determination of parallel or monophyletic relationships: the proteid salamanders-a test case. Am. Nat. 110 (1976) 653-677
32. Hecht M.K., and Edwards J.L. The methodology of phylogenetic inference above the species level. In: Hecht M.K., Goody P.C., and Hecht B.M. (Eds). Major Patterns in Vertebrate Evolution (1977), Plenum Press, New York 3-51
33. Hedges S.B., and Maxson L.R. A molecular perspective on lissamphibian phylogeny. Herpetol. Monogr. 7 (1993) 27-42
34. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
35. Hugall A.F., Foster R., and Lee M.S.Y. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst. Biol. 56 (2007) 543-563
36. Jenkyns H.C., Forster A., Schouten S., and Sinninghe Damste J.S. High temperatures in the Late Cretaceous Arctic Ocean. Nature 432 (2004) 888-892
37. Kishino H., and Hasegawa M. 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 (1989) 170-179
38. Kjer K.M. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phylogenet. Evol. 4 (1995) 314-330
39. Kjer K.M., and Honeycutt R.L. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evol. Biol. 7 (2007) 8
40. Larson A., and Dimmick W.W. Phylogenetic relationships of the salamander families: an analysis of congruence among morphological and molecular characters. Herpetol. Monogr. 7 (1993) 77-93
41. Larson A., Weisrock D.W., and Kozak K.H. Phylogenetic systematics of salamanders (Amphibia: Urodela), a review. In: Sever D.M. (Ed). Reproductive Biology and Phylogeny of Urodela (Amphibia) (2003), NH Science Publishers, Enfield 31-108
42. Madsen O., Scally M., Douady C.J., Kao D.J., DeBry R.W., Adkins R., Amrine H.M., Stanhope M.J., de Jong W.W., and Springer M.S. Parallel adaptive radiations in two major clades of placental mammals. Nature 409 (2001) 610-614
43. Manchester S.R. Biogeographical relationships of North American Tertiary floras. Ann. Mo. Bot. Gard. 86 (1999) 472-522
44. Marjanović D., and Laurin M. Fossils, molecules, divergence times, and the origin of lissamphibians. Syst. Biol. 56 (2007) 369-388
45. Milner A.R. The biogeography of salamanders in the Mesozoic and early Cenozoic: a cladistic vicariance model. In: Sims R.W., Price J.H., and Whalley P.E.S. (Eds). Evolution, Time, and Space. The Emergence of the Biosphere (1983), Academic Press, New York 431-468
46. Milner A.R. The relationships and origin of the living amphibians. In: Benton M.J. (Ed). The Phylogeny and Classification of the Tetrapods, vol. 1. Amphibians, Reptiles, Birds Systematics Association Special Volume 23 (1988), Academic Press, New York 59-102
47. Milner A.R. Mesozoic and tertiary Caudata and Albanerpetontidae. In: Heatwole H., and Carroll R.L. (Eds). Amphibian Biology, vol. 4. Paleontology, the Evolutionary History of Amphibians (2000), Surrey Beatty, Chipping Norton, Australia 1412-1444
48. Miya M., and Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17 (2000) 437-455
49. Miya M., Kawaguchi A., and Nishida M. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18 (2001) 1993-2009
50. Moore W.S. Inferring phylogenies from mtDNA variation: Mitochondrial-gene versus nuclear-gene trees. Evolution 49 (1995) 718-726
51. Moreau C.S., Bell C.D., Vila R., Archibald S.B., and Pierce N.E. Phylogeny of the ants: diversification in the age of angiosperms. Science 312 (2006) 101-104
52. Morescalchi A. Chromosome evolution in the caudate amphibia. Evol. Biol. 8 (1975) 339-387
53. Mueller R.L., Macey J.R., Jaekel M., Wake D.B., and Boore J.L. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc. Natl. Acad. Sci. USA 101 (2004) 13820-13825
54. Müller J., and Reisz R.R. Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays 10 (2005) 1069-1075
55. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryder O.A., and O'Brien S.J. Molecular phylogenetics and the origins of placental mammals. Nature 409 (2001) 614-618
56. Naylor B.G., and Fox R.C. A new ambystomatid salamander, Dicamptodon antiquus n. sp. from the Paleocene of Alberta. Can. J. Earth Sci. 30 (1993) 814-818
57. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
58. Rage J.C., and Rocek Z. Redescription of Triadobatrachus massinoti (Piveteau, 1936), an anuran amphibian from the early Triassic. Palaeont. Abt. A 206 (1989) 1-16
59. Rannala B., and Yang Z. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56 (2007) 453-466
60. Ree R.H., Moore B.R., Webb C.O., and Donoghue M.J. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59 (2005) 2299-2311
61. Reyes A., Pesole G., and Saccone C. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly. Mol. Biol. Evol. 15 (1998) 499-505
62. Reyes A., Gissi C., Pesole G., Catzeflis F.M., and Saccone C. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. Mol. Biol. Evol. 17 (2000) 979-983
63. Roelants K., Gower D.J., Wilkinson M., Loader S.P., Biju S.D., Guillaume K., Moriau L., and Bossuyt F. Global pattern of diversification in the history of modern amphibians. Proc. Natl. Acad. Sci. USA 104 (2007) 887-892
64. Ronquist F. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 45 (1997) 195-203
65. Saccone C., Giorgi C.D., Gissi C., Pesole G., and Reyes A. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238 (1999) 195-209
66. Samuels A.K., Weisrock D.W., Smith J.J., France K.J., Walker J.A., Putta S., and Voss S.R. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes. Gene 349 (2005) 43-53
67. Sanderson M.J. R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19 (2003) 301-302
68. San Mauro D., Vences M., Alcobendas M., Zardoya R., and Meyer A. Initial diversification of living amphibians predated the breakup of Pangaea. Am. Nat. 165 (2005) 590-599
69. Scheltinga D.M., and Jamieson B.G.M. The mature spermatozoon. In: Sever D.M. (Ed). Reproductive biology and phylogeny of Urodela (Amphibia) (2003), NH Science Publishers, Enfield 203-265
70. Sever D.M., Rania L.C., and Krenz J.D. Reproduction of the salamander Siren intermedia Le Conte with especial reference to oviducal anatomy and mode of fertilization. J. Morphol. 227 (1996) 335-348
71. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
72. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
73. Springer M.S., DeBry R.W., Douady C., Amrine H.M., Madsen O., de Jong W.W., and Stanhope M.J. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol. Biol. Evol. 18 (2001) 132-143
74. Steven S.M. Earth System History (1999), W.H. Freeman and Company, New York
75. Swofford D.L. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b8 (2001), Sinauer Associates, Sunderland, Massachusetts
76. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
77. Thorne J.L., and Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51 (2002) 689-702
78. Tiffney B.H. Geographic and climatic influences on the Cretaceous and Tertiary history of Euramerican floristic similarity. Acta Univ. Carol. Geol. 44 (2000) 5-16
79. Trontelj P., and Goricki S. Monophyly of the family Proteidae (Amphibia: Caudata) tested by phylogenetic analysis of mitochondrial 12S rDNA sequences. Nat. Croat. 12 (2003) 113-120
80. Vieites D.R., Min M.S., and Wake D.B. Rapid diversification and dispersal during periods of global warming by plethodontid salamanders. Proc. Natl. Acad. Sci. USA 104 (2007) 19903-19907
81. Vieites D.R., Zhang P., and Wake D.B. Salamanders (Caudata). In: Hedges S.B., and Kumar S. (Eds). The Timetree of Life (2009), Oxford University Press 365-368
82. Wang Y. A new Mesozoic caudate (Liaoxitriton daohugoensis sp. nov.) from Inner Mongolia, China. Chinese Sci. Bull. 49 (2004) 858-860
83. Weisrock D.W., Harmon L.J., and Larson A. Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Syst. Biol. 54 (2005) 758-777
84. Wiens J.J., Bonett R.M., and Chippindale P.T. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Syst. Biol. 54 (2005) 91-110
85. Wiens J.J. Review of "The amphibian tree of life" by Frost et al. Quart. Rev. Biol. 82 (2007) 55-56
86. Wiens J.J., Kuczynski C.A., Smith S.A., Mulcahy D.G., Sites Jr. J.W., Townsend T.M., and Reeder T.W. Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst. Biol. 57 (2008) 420-431
87. Xia X., and Xie Z. DAMBE: data analysis in molecular biology and evolution. J. Hered. 92 (2001) 371-373
88. Xia X., Xie Z., Salemi M., Chen L., and Wang Y. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26 (2003) 1-7
89. Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
90. Yang Z., and Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23 (2006) 212-226
91. Zachos J., Pagani M., Sloan L., Thomas E., and Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292 (2001) 686-693
92. Zardoya R., and Meyer A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13 (1996) 933-942
93. Zhang P., Chen Y.Q., Liu Y.F., Zhou H., and Qu L.H. The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene 311 (2003) 93-98
94. Zhang P., Chen Y.Q., Zhou H., Wang X.L., and Qu L.H. The complete mitochondrial genome of a relic salamander, ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol. Phylogenet. Evol. 28 (2003) 620-626
95. Zhang P., Zhou H., Chen Y.Q., Liu Y.F., and Qu L.H. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst. Biol. 54 (2005) 391-400
96. Zhang P., Chen Y.Q., Zhou H., Liu Y.F., Wang X.L., Papenfuss T.J., Wake D.B., and Qu L.H. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae). Proc. Natl. Acad. Sci. USA 103 (2006) 7360-7365
97. Zhang P., Papenfuss T.J., Wake M.H., Qu L.H., and Wake D.B. Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Mol. Phylogenet. Evol. 49 (2008) 586-597