Phylogenetic relationships of bufonid frogs and tests of alternate macroevolutionary hypotheses characterizing their radiation

Zoological Journal of the Linnean Society

Volumn 119, Issue 3, 1997, Pages 297-338

  Graybeal, Anna ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Bufonidae; Evolutionary radiation; Phylogenetic relationships; Phylogenetic taxonomy; Rates of molecular evolution; Total evidence

Indexed keywords

ANURA; BUFO; BUFONIDAE;

EID: 0031287225     PISSN: 00244082     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-3642.1997.tb00139.x     Document Type: Article

References (125)

1. Anderson S, Bankier AT, Barrell BG, De Bruign MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Staden R, Young IG. 1981. Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
2. Anderson S, De Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG. 1982. Complete sequence of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome. Journal of Molecular Biology 156: 683-717.
3. Arnason U, Gullberg A, Widegren B. 1991. The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. Journal of Molecular Evolution 33: 556-568.
4. Arnason U, Johnsson E. 1992. The complete mitchondrial DNA sequence of the harbor seal, Phoca vitulina. Journal of Molecular Evolution 34: 493-505.
5. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522.
6. Baldauf RJ. 1959. Morphological criteria and their use in showing bufonid phylogeny. Journal of Morphology 104: 527-560.
7. Barrett M, Donoghue MJ, Sober E. 1991. Against consensus. Systematic Zoology 40: 486-493.
8. Baum DA, Larson A. 1991. Adaptation reviewed: a phylogenetic methodology for studying character evolution. Systematic Zoology 40: 1-18.
9. Benton MJ. 1990. Phylogeny of the major tetrapod groups: morphological data and divergence dates. Journal of Molecular Evolution 30: 409-424.
10. Bibb MJ, van Etten RA, Wright CT, Walberg MW, Clayton DA. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26: 167-180.
11. Bilofsky HS, Burks C. 1988. The GenBank (R) Genetic Sequence Data Bank. Nucleic Acids Research 16: 1861-1864.
12. Blair WF. 1963. Evolutionary relationships of North American toads of the genus Bufo: a progress report. Evolution 17: 1-16.
13. Blair WF. 1966. Genetic compatibility in the Bufo valliceps and closely related groups of toads. Texas Journal of Science 18: 333-351.
14. Blair WF. 1972a. Evidence from hybridization. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 196-243.
15. Blair WF. 1972b. Summary. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 329-343.
16. Blair WF, ed. 1972c. Evolution in the genus Bufo. Austin, TX: University of Texas Press.
17. Bogart JP. 1972. Karyotypes. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 171-195.
18. Brown WM, Prager, EM, Wang A, Wilson AC. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. Journal of Molecular Evolution 18: 225-239.
19. Brun G, Dunon-Bluteau D. 1986. The secondary structures of the Xenopus laevis and human mitochondrial ribosomal subunit RNAs are similar. FEBS Letters 198: 333-335.
20. Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. 1993. Partitioning and combining data in phylogenetic analysis. Systematic Biology 42: 384-397.
21. Cannatella, DC. 1986. A new genus of bufonid (Anura) from South America, and phylogenetic relationships of the neotropical genera. Herpetologica 42: 197-205.
22. Carroll RL. 1988. Vertebrate paleontology and evolution. New York: W. H. Freeman and Co.
23. Cei JM, Erspamer V, Roseghini M. 1972. Biogenic amines. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 233-243.
24. Chang Y-S, Huang F-L, Lo T-B. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. Journal of Molecular Evolution 38: 138-155.
25. Channing A. 1978. A new bufonid genus (Amphibia: Anura) from Rhodesia. Herpetologica 34: 394-397.
26. Cope ED. 1875. On the Batrachia and Reptilia of Costa Rica, with notes on the herpetology and ichthyology of Nicaragua and Peru. Journal of the Academy of Natural Sciences, Philadelphia series 2, 8: 93-154.
27. Crump ML. 1989. Life history consequences of feeding versus non-feeding in a facultatively non-feeding toad larva. Oecologia 78: 486-489.
28. Cummings MP, Otto SP, Wakeley J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution 12: 814-822.
29. de Queiroz A. 1993. For consensus (sometimes). Systematic Biology 42: 368-372.
30. de Queiroz K, Gauthier J. 1990. Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names. Systematic Zoology 39: 307-322.
31. de Queiroz K, Gauthier J. 1992. Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23: 449-480.
32. de Queiroz K, Gauthier J. 1994. Toward a phylogenetic system of nomenclature. Trends in Ecology and Evolution 9: 27-31.
33. de Rijk P, Van de Peer Y, Chapelle S, de Wachter R. 1994. Database on the structure of large ribosomal subunit RNA. Nucleic Acids Research 22: 3495-3501.
34. Desjardins P, Morais R. 1990. Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates. Journal of Molecular Biology 212: 599-634.
35. Dixon MT, Hillis DM. 1993. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Molecular Biology and Evolution 10: 256-267.
36. Donoghue MJ. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43: 1137-1156.
37. Donoghue MJ, Olmstead RG, Smith JF, Palmer JD. 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Annals of the Missouri Botanical Garden 79: 333-345.
38. Edwards AWF. 1995. Assessing molecular phylogenies. Science 267: 253.
39. Estes R, Reig OA. 1973. The early fossil record of frogs: a review of the evidence. In: Vial, JL, ed. Evolutionary biology of the anurans: contemporary research on major problems. Columbia, MO: University of Missouri Press, 11-63.
40. Farris JS. 1970. Methods for computing Wagner trees. Systematic Zoology 19: 83-92.
41. Feder JH. 1979. Natural hybridization and genetic divergence between the toads Bufo boreas and Bufo punctatus. Evolution 33: 1089-1097.
42. Felsenstein J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.
43. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
44. Felsenstein J. 1985a. Phylogenies and the comparative method. American Naturalist 125: 1-15.
45. Felsenstein J. 1985b. Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34: 152-161.
46. Felsenstein J. 1993. PHYLIP: Phylogenetic inference package, version 3.5c. Seattle: University of Washington.
47. Ferguson JH, Lowe CH. 1969. Evolutionary relationships in the Bufo punctatus group. American Midland Naturalist 81: 435-466.
48. Ford LS, Cannatella DC. 1993. The major clades of frogs. Herpetological Monographs 7: 94-117.
49. Frost D, ed. 1985. Amphibian species of the world. Lawrence, KS: Allen Press.
50. Gadaleta G, Pepe G, de Candia G, Quagliariello C, Sbisa E, Saccone C. 1989. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. Journal of Molecular Evolution 28: 497-516.
51. Grandison, AGC. 1981. Morphology and phylogenetic position of the West African Didynamipus sjoestedti Andersson, 1903 (Anura Bufonidae). Monitore Zoologico Italiano N.S. Supplemento, 15: 187-215.
52. Graybeal A. 1993. The phylogenetic utility of cytochrome b: lessons from bufonid frogs. Molecular Phylogenetics and Evolution 2: 256-269.
53. Graybeal A. 1994. Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Systematic Biology 43: 174-193.
54. Graybeal A. 1995. Phylogenetic relationships and evolution of bufonid frogs based on molecular and morphological characters. PhD dissertation, University of California at Berkeley.
55. Graybeal A., Cannatella DC. 1995. A new taxon of Bufonidae from Peru, with descriptions of two new species and a review of the phylogenetic status of bufonid genera. Herpetologica 51: 105-131.
56. Green DM. 1984. Sympatric hybridization and allozyme variation in the toads Bufo americanus and B. fowleri in Southern Ontario. Copeia 1984: 18-26.
57. Griffiths I. 1963. The phylogeny of the Salientia. Biological Reviews 38: 241-292.
58. Gutell RR. 1994. Collection of small subunit (16S-and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Research 22: 3502-3507.
59. Gyllensten V, Erlich H. 1988. Generation of single-stranded DNA by the polymerase chain reaction and its applications to direct sequencing of the HLA DQa locus. Proceedings of the National Academy of Sciences USA 85: 7652-7656.
60. Harvey PH, Pagel MD. 1991. The comparative method in evolutionary biology. Oxford: Oxford University Press.
61. Hillis DM, Dixon MT. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411-445.
62. Huelsenbeck, JP. 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Zoology 40: 458-469.
63. Inger RF. 1967. The development of a phylogeny of frogs. Evolution 21: 369-384.
64. Inger RF. 1972. Bufo of Eurasia. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 102-118.
65. Janke A, Feldmaier-Fuchs G, Thomas WK, von Haeseler A, Paabo S. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137: 243-256.
66. Karlstrom EL. 1962. The toad genus Bufo in the Sierra Nevada of California: ecological and systematic relationships. University of California Publications in Zoology 62: 1-104.
67. 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. Journal of Molecular Evolution 29: 170-179.
68. Kjer KM. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4: 314-330.
69. Kluge AG. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38: 7-25.
70. Kluge AG, Farris JS. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18: 1-32.
71. Knight A, Mindell DP. 1993. Substitution bias, weighting of DNA sequence evolution, and the phylogenetic position of Fea's viper. Systematic Biology 42: 18-31.
72. Kumar S, Tamura K, Nei M. 1993. MEGA: molecular evolutionary genetic analysis, version 1.0. University Park: Pennsylvania State University.
73. Lessa EP, Smith MF, Orrego C. 1992. A cool hot start for PCR amplifications. Ancient DNA Newsletter 1: 40-42.
74. Li W-H, Graur D. 1991. Fundamentals of molecular evolution. Sunderland, MA: Sinauer Associates, Inc.
75. Liu CC. 1950. Amphibians of western China. Fieldiana Zoology 2: 1-400.
76. Losos JB, Miles DB. 1994. Adaptation, constraint, and the comparative method: phylogenetic issues and methods. In: Wainwright PC, Reilly SM, eds. Ecological morphology: integrative organismal biology. Chicago, IL: University of Chicago Press, 60-98.
77. Lynch, JD. 1973. The transition from archaic to advanced frogs. In: Vial, JL, ed. Evolutionary biology of the anurans: contemporary research on major problems. Columbia, MO: University of Missouri Press, 133-182.
78. Maddison WP. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5: 365-378.
79. Maddison WP. 1990. A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44: 539-557.
80. Maddison WP, Maddison DR. 1992. MacClade: analysis of phylogeny and character evolution. Sunderland, MA: Sinauer Associates.
81. Maidak, BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR. 1994. The ribosomal database project. Nucleic Acids Research 22: 3485-3487.
82. Maniatis T, Frisch EF, Sambrook J. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Publications.
83. Martin, RF. 1972. Evidence from osteology. In: Blair, WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 37-70.
84. Maxson LR. 1981a. Albumin evolution and its phylogenetic implications in African toads of the genus Bufo. Herpetologica 37: 96-104.
85. Maxson LR. 1981b. Albumin evolution and its phylogenetic implications in toads of the genus Bufo. II. Relationships among Eurasian Bufo. Copeia 1981: 579-583.
86. Maxson LR. 1984. Molecular probes of phylogeny and biogeography in toads of the widespread genus Bufo. Molecular Biology and Evolution 1: 345-356.
87. Maxson, LR, Song A-R, Lopata R. 1981. Phylogenetic relationships among North American toads, genus Bufo. Biochemical Systematics and Evolution 9: 347-350.
88. McDiarmid RW. 1971. Comparative morphology and evolution of frogs of the Neotropical genera Atelopus, Dendrophryniscus, Melanophryniscus, and Oreophrynella. Science Bulletin of the Los Angeles County Museum of Natural History 12: 1-66.
89. Medrano JF, Aasen E, Sharrow L. 1990. DNA extraction from nucleated red blood cells. Biotechniques 8: 43.
90. Mickevich MF, Farris JS. 1981. The implications of congruence in Menidia. Systematic Zoology 30: 351-370.
91. Mindell DP, Honeycutt RL. 1990. Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annual Review of Ecology and Systematics 21: 541-566.
92. Miyamoto MM, Allard MW, Adkins RM, Janecek LL, Honeycutt RL. 1994. A congruence test of reliability using linked mitochondrial DNA sequences. Systematic Biology 43: 236-249.
93. Miyamoto MM, Fitch WM. 1995. Testing species phylogenies and phylogenetic methods with congruence. Systematic Biology 44: 64-76.
94. Moritz C, Dowling TE, Brown WM. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology and Systematics 18: 269-292.
95. Mullis KB. 1991. The polymerase chain reaction in an anemic mode: how to avoid cold oligodeoxyribonuclear fusion. PCR Methods and Applications 1: 1-4.
96. Myers GS. 1942. The black toad of Deep Springs Valley, Inyo County, California. Occasional Papers of the Museum of Zoology, University of Michigan Press 460: 1-13.
97. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
98. Nevo E. 1968. Pipid frogs from the early Cretaceous of Israel and pipid evolution. Bulletin of the Museum of Comparative Zoology, Haward University 136: 225-318.
99. Novak RM, Robinson DC. 1975. Observations on the reproduction and ecology of the tropical montane toad, Bufo holdridgei Taylor in Costa Rica. Revista de Biologia Tropical 23: 213-237.
100. O'Hara RJ. 1988. Homage to Clio, or, toward an historical philosophy for evolutionary biology. Systematic Zoology 37: 142-155.
101. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R. 1994. FASTDNAML - A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. CABIOS 10: 41-48.
102. Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568-583.
103. Reeder, TW. 1995. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions. Molecular Phylogenetics and Evolution 4: 203-222.
104. Roe BA, Ma D-P, Wilson RK, Wong JF-H. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. Journal of Biological Chemistry 260: 9759-9774.
105. Sagata N, Oskarsson M, Copeland T, Brumbaugh J, Vande Woude GF. 1988. Function of c-mos protooncogene product in meiotic maturation in Xenopus oocytes. Nature 335: 519-525.
106. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
107. Sanderson MJ, Donoghue MJ. 1989. Patterns of variation in levels of homoplasy. Evolution 43: 1781-1795.
108. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA 74: 5463-5467.
109. Savage, JM. 1972. The systematic status of Bufo simus O. Schmidt with description of a new toad from western Panama. Journal of Herpetology 6: 25-33.
110. Schwarz K, Hansen-Hagge T, Bartram C. 1990. Improved yields of long PCR products using gene 32 protein. Nucleic Acids Research 18: 1079.
111. Swofford DL. 1991a. Phylogenetic Analysis Using Parsimony (PAUP). Champaign, Illinois, computer program distributed by the Illinois Natural History Survey.
112. Swofford DL. 1991b. When are phylogeny estimates from molecular and morphological data incongruent? In: Miyamoto MM, Cracraft, J, eds. Phylogenetic analysis of DNA sequences. New York: Oxford University Press, 295-333.
113. Tandy M, Keith R. 1972. Bufo of Africa. In: Blair WF, ed. Evolution in the genus Bufo. Austin, TX: University of Texas Press, 119-170.
114. Taylor EH. 1952. The frogs and toads of Costa Rica. University of Kansas Science Bulletin 35: 577-942.
115. Templeton AR. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37: 221-244.
116. Thornton WA. 1955. Interspecific hybridization in Bufo woodhousei and Bufo valliceps. Evolution 9: 455-468.
117. Tihen JA. 1960. Two new genera of African bufonids, with remarks on the phylogeny of related genera. Copeia 1960: 225-233.
118. Tihen JA. 1962. A review of New World fossil bufonids. American Midland Naturalist 68: 1-50.
119. Titus TA, Larson A. 1995. A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Systematic Biology 44: 125-151.
120. Tzeng C-S, Hui C-F, Shen S-C, Huang PC. 1992. The complete nucleotide sequence of the Crossostome lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Research 20: 4853-4858.
121. Wallis GP, Arntzen JW. 1989. Mitochondrial-DNA variation in the crested newt superspecies: limited cytoplasmic gene flow among species. Evolution 43: 88-104.
122. Waish PS, Metzger DA, Higuchi R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10: 506-513.
123. Wheeler WC, Honeycutt RL. 1988. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Molecular Biology and Evolution 5: 90-96.
124. Wiens, JJ, Reeder, TW. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Systematic Biology 558.
125. Yoneyama Y. 1987. The nucleotide sequences of the heavy and light strand replication origins of the Rana catesbiana mitochondrial genome. Nippon Ika Daigaku Zasshi 54: 429-440.