Phylogenetic relationships within Iguanidae inferred using molecular and morphological data and a phylogenetic taxonomy of iguanian lizards

Herpetologica

Volumn 59, Issue 3, 2003, Pages 399-419

  Schulte II, James A ^a,c   Valladares, John Pablo ^b   Larson, Allan ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b UNIVERSITY OF CHILE   (Chile)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

Iguania; Iguanidae; Metataxon; Phylogenetic taxonomy; Polychrotinae; Squamata; Topology test; Tropidurinae

Indexed keywords

LIZARD; MITOCHONDRIAL DNA; PHYLOGENY;

AGAMIDAE; AGAMINAE; AMPHIBIA; AMPHIBOLURINAE; ANOLIS; CHAMAELEONIDAE; CORYTOPHANINAE; CROTAPHYTINAE; DRACONINAE; HOPLOCERCINAE; HYDROSAURINAE; IGUANIA; IGUANIDAE; IGUANINAE; LEIOCEPHALUS; OPLURINAE; PHRYNOSOMATINAE; POLYCHROTINAE; POLYCHRUS; REPTILIA; SQUAMATA; TROPIDURINAE; UROMASTYCINAE;

EID: 0141673120     PISSN: 00180831     EISSN: None     Source Type: Journal    
DOI: 10.1655/02-48     Document Type: Article

References (69)

1. ANDERSON, S., A. T. BANKIER, B. G. BARRELL, M. H. L. DE BRUIJN, A. R. COULSON, J. DROUIN, I. C. EPERON, D.P. NIERLICH, B. A. ROE, F. SANGER, P. H. SCHREIER, A. J. H. SMITH, R. STADEN, AND I. G. YOUNG. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. ARCHIE, J. W. 1989. A randomization test for phylogenetic information in systematic data. Systematic Zoology 38:239-252.
3. BARTS, M., AND T. WILMS. 1997. Catalogue of Valid Species and Synonyms, Vol. 4: Agamidae. Herprint International, Bredell, South Africa.
4. BOULENGER G. A. 1884. Synopsis of the families of existing Lacertilia. Annals and Magazine of Natural History 5:117-122.
5. BREMER, K, 1994. Branch support and tree stability. Cladistics 10:295-304.
6. CAMP, C. 1923. Classification of the lizards. Bulletin of the American Museum of Natural History. 48:289-481.
7. COGGER, H. 2000. Reptiles and Amphibians of Australia. Reed New Holland, Sydney, Australia.
8. DE QUEIROZ, K., AND J. GAUTHIER. 1992. Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23:449-480.
9. DE QUEIROZ, K., AND J. GAUTHIER. 1994. Toward a phylogenetic system of biological nomenclature. Trends in Ecology and Evolution 9:27-31.
10. ESTES, R., K. DE QUEIROZ, AND J. GAUTHIER. 1988. Phylogenetic relationships within squamata. Pp. 119-281. In R. Estes and G. Pregill (Eds.), Phylogenetic Relationships of the Lizard Families, Essays Commemorating Charles L. Camp. Stanford University Press, Stanford, California, U.S.A.
11. ETHERIDGE, R., AND K. DE QUEIROZ. 1988. A Phylogeny of Iguanidae. Pp. 283-368. In R. Estes and G. Pregill (Eds.), Phylogenetic Relationships of the Lizard Families, Essays Commemorating Charles L. Camp. Stanford University Press, Stanford, California, U.S.A.
12. FAITH, D. P., AND P. S. CRANSTON. 1991. Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure. Cladistics 7:1-28.
13. FELSENSTEIN, J. 1985a. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
14. _. 1985b. Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34:152-161.
15. FELSENSTEIN, J., AND H. KISHINO. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42:193-200.
16. FROST, D. R., AND R. ETHERIDGE. 1989. A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata). University of Kansas Museum of Natural History, Miscellaneous Publications 81:1-65.
17. FROST, D. R., R. ETHERIDGE, D. JANIES, AND T. A. TITUS. 2001a. Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguania). American Museum Novitates 3343:1-38.
18. FROST, D. R., M. T. RODRIGUES, T. GRANT, AND T. A. TITUS. 2001b. Phylogenetics of the lizard genus Tropidurus (Squamata: Tropiduridae): direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology. Molecular Phylogenetics and Evolution 21:352-371.
19. GAUTHIER, J., R. ESTES, AND K. DE QUEIROZ. 1988. A phylogenetic analysis of Lepidosauromorpha, Pp. 15-98. In R. Estes and G. Pregill (Eds.), Phylogenetic Relationships of the Lizard Families, Essays Commemorating Charles L. Camp. Stanford University Press, Stanford, California, U.S.A.
20. GOLDMAN, N., J. P. ANDERSON, AND A. G. RODRIGO. 2000. Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49:652-670.
21. HARRIS, D. J., J. C. MARSHALL, AND K. A. CRANDALL. 2001. Squamate relationships based on C-mos nuclear DNA sequences: increased taxon sampling improves bootstrap support. Amphibia-Reptilia 22:235-242.
22. HILLIS, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences, Pp. 278-294. In M. M. Miyamoto and J. Cracraft (Eds.), Phylogenetic Analysis of DNA Sequences, Oxford University Press, New York, New York, U.S.A.
23. HILLIS, D. M., AND J. P. HUELSENBECK. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. Journal of Heredity 83:189-195.
24. HONDA, M., H. OTA, M. KOBAYASHI, J. NABHITABHATA, H-S. YONG, S, SENGOKU, AND T. HIKIDA. 2000. Phylogenetic relationships of the family Agamidae (Reptilia: Iguania) inferred from mitochondrial DNA sequences. Zoological Science 17:527-537.
25. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
26. JACKMAN, T. R., A. LARSON, K. DE QUEIROZ, AND J. B. LOSOS. 1999. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Systematic Biology 48:254-285.
27. KUMAZAWA, Y., AND M. NISHIDA. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Journal of Molecular Evolution 37:380-398.
28. LARSON, A. 1998. The comparison of morphological and molecular data in phylogenetic systematics, Pp 275-296. In R. DeSalle and B. Schierwater (Eds.), Molecular Approaches to Ecology and Evolution. Birkhäuser Verlag, Basel, Switzerland.
29. LEACHÉ, A. D., AND T. W. REEDER. 2002. Molecular systematics of the Eastern Fence Lizards (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology 51:44-68.
30. LEVITON, A. E., R. H. GIBBS, JR., E. HEAL, AND C. E. DAWSON. 1985. Standards in herpetology and ichthyology. Part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985:802-832.
31. MACEY, J. R., AND A. VERMA. 1997. Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Molecular Phylogenetics and Evolution 7:272-279.
32. MACEY, J. R., A. LARSON, N. B. ANANJEVA, AND T. J. PAPENFUSS. 1997a. Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. Journal of Molecular Evolution 44:600-674.
33. MACEY, J. R., A. LARSON, N. B. ANANJEVA, Z. FANG, AND T. J. PAPENFUSS. 1997b. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution 14:91-104.
34. MACEY, J. R., A. LARSON, N. B. ANANJEVA, AND PAPENFUSS, T. J. 1997c. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Molecular Biology and Evolution 14:30-39.
35. MACEY, J. R., J. A. SCHULTE II, A. LARSON, Z. FANG, Y. WANG, B. S. TUNIYEB, AND T. J. PAPENFUSS. 1998. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: a case of vicariance and dispersal. Molecular Phylogenetics and Evolution 9:80-87.
36. MACEY, J. R., A. LARSON, N. B. ANANJEVA, B. S. TUNIYEV, N. ORLOV, AND T. J. PAPENFUSS. 1999. Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families. Molecular Phylogenetics and Evolution 12:250-272.
37. MACEY, J. R., A. LARSON, N. B. ANANJEVA, N. B. ANANJEVA, Y. WANG, R. PETHIYAGODA, N. RASTEGAR-POUYANI, AND T. J. PAPENFUSS. 2000. Evaluating trans-Tethys migration: an example using acrodont lizard phylogenetics. Systematic Biology 49:233-256.
38. MADDISON, W. P., AND D. R. MADDISON. 2001. MacClade: Analysis of Phylogeny and Character Evolution, Version 4.0. Sinauer, Sunderland, Massachusetts, U.S.A.
39. MANIATIS, T., E. F. FRITSCH, AND J. SAMBROOK. 1982. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, U.S.A.
40. MANTHEY, U., AND W. GROSSMAN. 1997. Amphibien und Reptilien Südostasiens. Natur und Tier Verlag, Münster, Germany.
41. MOODY, S. M. 1980. Phylogenetic and historical biogeographical relationships of the genera in the Family Agamidae (Reptilia: Lacertilia). Ph.D. Dissertation, University of Michigan, Ann Arbor, Michigan, U.S.A.
42. NOBLE, G. K. 1924. New lizards from northwestern Peru. Occasional Papers of the Boston Society of Natural History 5:107-113.
43. PAGE, R. D. M., AND M. A. CHARLESTON, 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution 7:231-240.
44. PETERS, J. A., AND R. DONOSO-BARROS. 1970. Catalogue of the Neotropical Squamata, Part II: Lizards and Amphisbaenians. United States National Museum Bulletin 297:1-293.
45. PETREN, K., AND T. J. CASE. 1997. A phylogenetic analysis of body size evolution in chuckwallas (Sauromalus) and other iguanines. Evolution 51:206-219.
46. POSADA, D., AND K. A. CRANDALL. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
47. _. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50:580-601.
48. nd ed. Prentice Hall, Upper Saddle River, New Jersey, U.S.A.
49. RASSMANN, K. 1997. Evolutionary age of the Galápagos iguanas predates the age of the present Galápagos Islands. Molecular Phylogenetics and Evolution 7:158-172.
50. 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. Molecular Phylogenetics and Evolution 4:203-222.
51. REDDER, T. W., AND J. J. WIENS. 1996. Evolution of the lizard family Phrynosomatidae as inferred from diverse types of data. Herpetological Monographs 10:43-84.
52. RICE, J. A. 1995. Mathematical Statistics and Data Analysis. Duxbury Press, Belmont, California, U.S.A.
53. SAINT, K. M., C. C. AUSTIN, S. C. DONNELLAN, AND M. N. HUTCHINSON. 1998. C-mos, a nuclear marker useful for squamate phylogenetic analysis. Molecular Phylogenetics and Evolution 10:259-263.
54. SCHULTE, J. A. II, J. R. MACEY, A. LARSON, AND T. J. PAPENFUSS. 1998. Testing the monophyly of four iguanid subfamilies: a comparison of molecular and morphological data. Molecular Phylogenetics and Evolution 10:367-376.
55. SCHULTE, J. A. II, J. R. MACEY, R. E. ESPINOZA, AND A. LARSON. 2000. Phylogenetic relationships in the iguanid lizard genus Liolaemus: multiple origins of viviparous reproduction and evidence for recurring Andean vicariance and dispersal. Biological Journal of the Linnaean Society 69:75-102.
56. SCHWENK, K. 1994. Systematics and subjectivity: the phylogeny and classification of iguanian lizards revisited. Herpetological Review 25:53-57.
57. SHIMODAIRA, H., AND M. HASEGAWA. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 13:964-969.
58. SITES, J. w., JR., S. K. DAVIS, T. GUERRA, J. B. IVERSON, AND H. L. SNELL. 1996. Character congruence and phylogenetic signal in molecular and morphological data sets: a case study in the living iguanas (Squamata, Iguanidae). Molecular Biology and Evolution 13:1087-1105.
59. SLOWINSKI, J. B. 2001. Molecular polytomies. Molecular Phylogenetics and Evolution 19:114-120.
60. SORENSON, M. D. 1999. TreeRot, Version 2, Boston University, Boston, Massachusetts, U.S.A.
61. SUZUKI, Y., G. V. GLAZKO, AND M. NEI. 2002. Over-credibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences 99:16138-16143.
62. SWOFFORD, D. L. 2001. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0b8. Sinauer, Sunderland, Massachusetts, U.S.A.
63. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
64. TITUS, T. A., AND D. R. FROST. 1996. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Molecular Phylogenetics and Evolution 6:49-62.
65. TOWNSEND, T., AND A. LARSON. 2002. Molecular phylogenetics and mitochondrial genomic evolution in the Chamaeleonidae (Reptilia, Squamata). Molecular Phylogenetics and Evolution 23:22-36.
66. WEISROCK, D. W., J. R. MACEY, I. H. UGURTAS, A. LARSON, AND T. J. PAPENFUSS. 2001. Molecular phylogenetics and historical biogeography among salamandrids of the "true" salamander clade: rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia. Molecular Phylogenetics and Evolution 18:434-448.
67. WIENS, J. J., AND B. D, HOLLINGSWORTH. 2000. War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Systematic Biology 49:143-159.
68. ZAMUDIO, K. R., K. B. JONES, AND R. H. WARD. 1997. Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex. Systematic Biology 46:284-305.
69. ZUG, G. R., L. J. VITT, AND J. P. CALDWELL. 2001. Herpetology: An Introductory Biology of Amphibians and Reptiles. Academic Press, San Diego, California, U.S.A.