Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania)

Molecular Phylogenetics and Evolution

Volumn 6, Issue 1, 1996, Pages 49-62

  Titus, Tom A ^a   Frost, Darrel R ^b  

^a UNIVERSITY OF OREGON   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLURUS; IGUANIA; OPLURINAE; OPLURUS; OPLURUS CUVIERI; OPLURUS CYCLURUS; OPLURUS QUADRIMACULATUS; OPLURUS SAXICOLA; SAXICOLA; SQUAMATA;

RIBOSOME RNA; RNA, RIBOSOMAL, 12S;

ANIMAL; ARTICLE; CONFORMATION; GENETICS; LIZARD; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; LIZARDS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0030208308     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1996.0057     Document Type: Article

References (70)

1. Allard, M. W., and Miyamoto, M. M. (1992). Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method. Mol. Biol. Evol. 9: 778-786.
2. Arnold, E. N. (1984). Variation in the cloacal and hemipenial muscles of lizards and its bearing on their relationships. Symp. Zool. Soc. London 52: 47-85.
3. Blanc, C. P. (1965). Etudes sur les Iguanidae de Madagascar: I. Le squellette de Charlarodon madagascariensis Peters, 1854. Mem. Mus. Natl. Hist. Nat. Paris, N.S. (A-Zool.) 33: 93-146.
4. Blanc, C. P. (1977). Reptiles, Sauriens Iguanidae. Faune Madagascar 45: 1-194.
5. Blanc, C. P. (1982). Les iguanes. Recherche 13: 1398-1408.
6. Blanc, C. P., Blanc, F., and Roualt, J. (1983). The interrelationships of the Malagasy iguanids. J. Herpetol. 17: 129-136.
7. Butts, R. E. (1989). "William Whewell's Theory of Scientific Method," revised ed. Hackett, Indianapolis, IN.
8. Desjardins, P., and Morais, R. (1990). Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212: 599-634.
9. Dixon, M. T., and Hillis, D. M. (1993). Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Mol. Biol. Evol. 10: 256-267.
10. Etheridge, R., and de Queiroz, K. (1988). A phylogeny of Iguanidae. In "Phylogenetic Relationships of Lizard Families: Essays Commemorating Charles L. Camp" (R. Estes and G. Pregill, Eds.), pp. 283-368, Stanford Univ. Press, Stanford, CA.
11. Farris, J. S. (1983). The logical basis of phylogenetic analysis. In "Advances in cladistics" (N. I. Platnick and V. A. Funk, Eds.), Vol. 2, pp. 7-36, Columbia Univ. Press, New York.
12. Farris, J. S., and Kluge, A. G. (1985). Parsimony, synapomorphy, and explanatory power: A reply to Duncan. Taxon 34: 130-135.
13. Farris, J. S., and Kluge, A. G. (1986). Synapomorphy, parsimony, and evidence. Taxon 35: 298-305.
14. Feng, D., and Doolittle, R. F. (1987). Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25: 351-360.
15. Feng, D., and Doolittle, R. F. (1990). Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol. 183: 375-387.
16. Fitch, W. M., and Smith, T. F. (1983). Optimal sequence alignments. Proc. Natl. Acad. Sci. USA 80: 1382-1386.
17. Frost, D. R. (1992). Phylogenetic analysis and toxonomy of the Tropidurus group of lizards (Iguania: Tropiduridae). Am. Mus. Novit. 3033: 1-68.
18. Frost, D. R., and Etheridge, R. (1989). A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata). Misc. Publ. Mus. Nat. Hist. Univ. Kans. 81: 1-65.
19. Frost, D. R., and Kluge, A. G. (1995). A consideration of epistemology in systematic biology, with special reference to species. Cladistics 10: 259-294.
20. Gatesy, J., DeSalle, R., and Wheeler, W. C. (1993). Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2: 152-157.
21. Gatesy, J., Hayashi, C., De Salle, R., and Vrba, E. (1994). Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes. Evolution 48: 188-196.
22. Gutell, R. R. (1994). Collection of small subunit (16S-and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 22: 3502-3507.
23. Gutell, R. R., and Fox, G. E. (1988). A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 16: r175-r247.
24. Hein, J. (1989). A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when a phylogeny in given. Mol. Biol. Evol. 6: 649-668.
25. Hein, J. (1990). Unified approach to alignment and phylogenies. Methods Enzymol. 183: 626-644.
26. Hendy, M. D., and Penny, D. (1982). Branch and bound algorithms to determine minimal evolutionary trees. Math. Biosci. 59: 277-290.
27. Hennig, W. (1966). "Phylogenetic Systematics." Univ. of Illinois Press, Urbana.
28. Hickson, R. E., Simon, C., Cooper, A., Spicer, G. S., Sullivan, J., and Penny, D. (1996). Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol. Biol. Evol. in press.
29. Higgins, D. G., and Sharp, P. M. (1989). Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5: 151-153.
30. Hillis, D. M. (1995). Approaches for assessing phylogenetic accuracy. Syst. Biol. 44: 3-16.
31. Hillis, D. M., and Dixon, M. T. (1991). Ribosomal DNA: Molecular evolution and phylogenetic inference. Q. Rev. Biol. 66: 411-453.
32. Hillis, D. M., Huelsenbeck, J. P., and Cunningham, C. W. (1994). Application and accuracy of molecular phylogenies. Science 264: 671-677.
33. Hillis, D. M., Larson, A., Davis, S. K., and Zimmer, E. A. (1990). Nucleic acids III: Sequencing. In "Molecular Systematics" (D. M. Hillis and C. Moritz, Eds.), pp. 318-370, Sinauer, Sunderland, MA.
34. Jardine, N. (1967). The concept of homology in biology. Br. J. Philos. Sci. 18: 125-139.
35. Kjer, K. M. (1995). Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phylogenetic. Evol. 4: 314-330.
36. Kluge, A. G. (1983). Cladistics and the classification of the great apes. In "New Interpretations of Ape and Human Ancestry" (R. L. Ciochon and R. S. Corruccini, Eds.), Plenum, New York.
37. Kluge, A. G. (1989). A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38: 7-25.
38. Kluge, A. G. (1993). Three-taxon transformation and phylogenetic inference: ambiguity and distortion as regards explanatory power. Cladistics 9: 246-259.
39. Kluge, A. G., and Farris, J. S. (1969). Quantitative phylogenetics and the evolution of anurans. Syst. Zool. 18: 1-32.
40. Kocher, T. D., Thomas, W. K., Edwards, S. V., Pääbo, S., Villablanca, F. X., and Wilson, A. C. (1989). Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86: 6196-6200.
41. Konings, D. A. M., Hogeweg, P., and Hesper, B. (1987). Evolution of the primary and secondary structures of the E1α mRNAs of the adenovirus. Mol. Biol. Evol. 4: 300-314.
42. Kraus, F., Jarecki, L., Miyamoto, M., Tanhauser, S., and Laipis, P. (1992). Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA. Mol. Biol. Evol. 9: 770-774.
43. Kumazawa, Y., and Nishida, M. (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. MoI. Evol. 37: 380-398.
44. Lake, J. (1991). The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 8: 378-385.
45. Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982). "Molecular Cloning: A Laboratory Manual," Cold Spring Laboratory Press, Cold Spring Harbor, NY.
46. Mickevich, M. F. (1978). Taxonomic congruence. Syst. Zool. 27: 143-158.
47. Mindell, D. P. (1991). Aligning DNA sequences: Homology and phylogenetic weighting. In "Phylogenetic Analysis of DNA Sequences" (M. M. Miyamoto and J. Cracraft, Eds.), pp. 73-89, Oxford Univ. Press, New York.
48. Mindell, D. P., and Honeycutt, R. L. (1990). Ribosomal RNA in vertebrates: Evolution and phylogenetic implications. Annu. Rev. Ecol. Syst. 21: 541-566.
49. Miyamoto, M. M., Allard, M. W., Adkins, R. M., Janecek, L. L., and Honeycutt, R. L. (1994). A congruence test of reliability using linked mitochondrial DNA sequences. Syst. Biol. 43: 236-249.
50. Miyamoto, M. M., and Fitch, W. M. (1995). Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44: 64-76.
51. Noller, H. F. (1984). Structure of ribosomal RNA. Annu. Rev. Biochem. 53: 119-162.
52. Patterson, C. (1982). Morphological characters and homology. In "Problems of Phylogenetic Reconstruction" (K. A. Joysey and A. E. Friday, Eds.), pp. 21-74, Academic Press, London.
53. Patterson, C. (1988). Homology in classical and molecular biology. Mol. Biol. Evol. 5: 603-625.
54. Reeder, T. W. (1995). Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions. Mol. Phylogenet. Evol. 4: 203-222.
55. Remane, A. (1952). "Die Grundlagen des Natürlichen Systems der Vergleichenden Anatomie und der Phylogenetik," Geest und Portig K. G., Leipzig.
56. Richards, C., and Moore, W. S. (1996). A phylogeny for the African treefrog family Hyperoliidae based on mitochondrial rDNA. Mol. Phylogenet. Evol., in press.
57. Riedl, R. (1978). "Order in Living Organisms: A Systems Analysis of Evolution," Wiley, New York.
58. Roe, B. A., Ma, D.-P., Wilson, R. K., and Wong, J. F.-H. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 17: 7959-9774.
59. Ruben, D. A., and Dores, R. M. (1995). Obtaining a more resolute teleost growth hormone phylogeny by the introduction of gaps in sequence alignment. Mol. Phylogenet. Evol. 4: 129-138.
60. Sankoff, D. D., and Cedergren, R. J. (1983). Simultaneous comparison of three or more sequences related by a tree. In "Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison" (D. Sankoff and J. B. Kruskal, Eds.), pp. 253-263, Addison-Wesley, Reading, MA.
61. Simon, C., Pääbo, S., Kocher, T., and Wilson, A. C. (1990). Evolution of the mitochondrial ribosomal RNA in insects as shown by the polymerase chain reaction. UCLA Symp. Mol. Cell. Biol. 122: 235-244.
62. Swofford, D. L. (1993). Phylogenetic analysis using parsimony, version 3.1.1. Computer software distributed by the Illinois Natural History Museum, Champaign.
63. Swofford, D. L., and Olsen, G. J. (1990). Phylogeny reconstruction. In "Molecular Systematics" (D. M. Hillis and C. Moritz, Eds.), pp. 411-501, Sinauer, Sunderland, MA.
64. Titus, T. A., and Larson, A. (1995). A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 44: 125-151.
65. Van de Peer, Y., Van den Broeck, I., De Rijk, P., and De Wachter, R. (1994). Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 22: 3488-3494.
66. Waterman, M. S. (1984). General methods of sequence comparison. Bull. Math. Biol. 46: 473-500.
67. Wheeler, W. C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44: 321-331.
68. Wheeler, W. C., Gatesy, J., and De Salle, R. (1995). Elision: A method for accomodating multiple molecular sequence alignments with alignment-ambiguous sites. Mol. Phylogenet. Evol. 4: 1-9.
69. Wheeler, W., and Gladstein, D. (1994). Malign, version 1.99. Computer program distributed by the authors, Department of Invertebrates, American Museum of Natural History, New York.
70. Wheeler, W. C., and Honeycutt, R. L. (1988). Paired sequence differences in ribosomal RNAs: Evolution and phylogenetic implications. Mol. Biol. Evol. 5: 90-96.