Phylogeny of snakes (Serpentes): Combining morphological and molecular data in likelihood, Bayesian and parsimony analyses

Systematics and Biodiversity

Volumn 5, Issue 4, 2007, Pages 371-389

  Lee, Michael S Y ^a,b   Hugall, Andrew F ^a,b   Lawson, Robin ^c   Scanlon, John D ^d  

^a SOUTH AUSTRALIAN MUSEUM   (Australia)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c CALIFORNIA ACADEMY OF SCIENCES   (United States)

^d Riversleigh Fossil Centre   (Australia)

Author keywords

Character weighting; Maximum likelihood; Morphology; Partitioned branch support; Partitioned likelihood support; Serpentes

Indexed keywords

ALETHINOPHIDIA; ANILIUS; LOXOCEMUS; PACHYOPHIIDAE; SERPENTES; TROPIDOPHIS; UNGALIOPHIS; WONAMBI; XENOPELTIS;

EID: 35948935045     PISSN: 14772000     EISSN: 14780933     Source Type: Journal    
DOI: 10.1017/S1477200007002290     Document Type: Article

References (85)

1. BAKER, R.H. & DESALLE, R. 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Systematic Biology 46, 654-673.
2. BARKER, F.K. & LUTZONI, F.M. 2002. The utility of the incongruence length difference test. Systematic Biology 51, 625-657.
3. BARRETT, M., DONOGHUE, M.J. & SOBER, E. 1991. Against consensus. Systematic Biology 40, 486-493.
4. BELLAIRS, A.D'A. & UNDERWOOD, G. 1951. The origin of snakes. Biological Reviews 26, 193-237.
5. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
6. BROMHAM, L., WOOLFIT, M., LEE, M.S.Y. & RAMBAUT, A. 2002. Testing the relationship between morphological and molecular rates of change among phylogenies. Evolution 56, 1921-1930.
7. BRYANT, H.N. 1997. Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names. Biological Journal of the Linnean Society 62, 497-503.
8. BULL, J.J., HUELSENBECK, J.P., CUNNINGHAM, C.W., SWOFFORD, D.L. & WADDELL, P.J. 1993. Partitioning and combining data in phylogenetic analysis. Systematic Biology 42, 384-397.
9. CALDWELL, M.W. 1999. Squamate phylogeny and the relationships of snakes and mosasauroids. Zoological Journal of the Linnean Society 125, 115-147.
10. CAMP, C.L. 1923. Classification of the lizards. Bulletin of the American Museum of Natural History 48, 289-481.
11. CANTINO, P.D. & DE QUEIROZ, K. 2000. Phylocode: A Phylogenetic Code of Biological Nomenclature. http://www.ohiou.edu/ phylocode.
12. COPE, E.D. 1864. On the characters of the higher groups of Reptilia Squamata - and especially of the Diploglossa. Proceedings of the Academy of Natural Sciences, Philadelphia 1864, 224-231.
13. CUNDALL, D. & GREENE, H.W. 1982. Evolution of the feeding apparatus in alethinophidian snakes. American Zoologist 22, 924.
14. CUNDALL, D., & GREENE, H.W. 2000. Feeding in snakes. In: SCHWENK, K., Ed., Feeding: Form, Function, and Evolution in Tetrapod Vertebrates. Academic Press, San Diego, pp. 293-333.
15. CUNDALL, D., WALLACH, V. & ROSSMAN, D.A. 1993. The systematic relationships of the snake genus Anomochilus. Zoological Journal of the Linnean Society 109, 275-299.
16. DOWLING, H.G. & DUELLMAN, W.E. 1978. Systematic Herpetology: A Synopsis of Families and Higher Categories. HISS Publications in Herpetology No. 7. HISS Publications, New York.
17. DUḾERIL, A.-M.-C. & BIBRON, G. 1844. Erpetologie ǵeńerale ou histoire naturelle complète des reptiles. Vol. 6. Librarie Encycloṕedique de Roret, Paris.
18. EDWARDS, A.F.W. 1992. Likelihood. Expanded edition. Johns Hopkins University Press.
19. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17, 368-376.
20. FELSENSTEIN, J. 1992. Phylogenies from restriction sites: a maximum-likelihood approach. Evolution 46, 159-173.
21. FELSENSTEIN, J. 2004. Inferring phylogenies. Sinauer, Sunderland, MA.
22. GATESY, J., O'GRADY, P. & BAKER, R.H. 1999. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher-level artiodactyl taxa. Cladistics 15, 271-313.
23. GATESY, J., AMATO, G., NORELL, M., DESALLE, R. & HAYASHI, C. 2003. Combined support for wholesale taxonomic atavism in gavialine crocodylians. Systematic Biology 52, 403-422.
24. GOLDMAN, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of DNA substitution and to parsimony analyses. Systematic Biology 39, 345-361.
25. GREENE, H.W. 1983. Dietary correlates of the origin and radiation of snakes. American Zoologist 23, 431-441.
26. GREENE, H.W. 1997. Snakes - The Evolution of Mystery in Nature. University of California Press, Berkeley.
27. HASEGAWA, M., KISHINO, H. & YANO, T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160-174.
28. HEISE, P.J., MAXSON, L.R., DOWLING, H.G. & HEDGES, S.B. 1995. Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes. Molecular Biology and Evolution 12, 259-265.
29. HILLIS, D.M. 1996. Inferring complex phylogenies. Nature 383, 130-131.
30. HOFFSTETTER, R. 1939. Contribution a l'étude des Elapidae actuels et fossiles et de l'ostéologie des ophidiens. Archives du Museum D'Histoire Naturelle de Lyon 15, 1-78.
31. HUELSENBECK, J.P. & RONQUIST, F.R. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
32. JAMIESON, B.G.M., TILLIER, S., TILLIER, A., JUSTINE, J.-L., LING, E., JAMES, S., MCDONALD, K. & HUGALL, A.F. 2002. Phylogeny of the Megascolecidae and Crassiclitellata (Oligochaeta, Annelida): Combined versus partitioned analysis using nuclear (28S) and mitochondrial (12S, 16S) rDNA. Zoosystema 24, 707-734.
33. JERMIIN, L.S., OLSEN, G., MENGERSEN, K.L. & EASTEAL, S. 1997. Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis. Molecular Biology and Evolution 14, 1296-1302.
34. JUKES, T.H. & CANTOR, C.R. 1969. Evolution of protein molecules. In: MUNRO, H.N., Ed., Mammalian Protein Metabolism. Academic Press, New York, pp. 21-132.
35. KELLY, C.M., BARKER, N.P. & VILLET, M.H. 2003. Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes. Systematic Biology 52, 439-459.
36. KLUGE, A.G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38, 7-25.
37. KLUGE, A.G. 1991. Boine snake phylogeny and research cycles. Miscellaneous Publications of the Museum of Zoology, University of Michigan 178, 1-58.
38. KLUGE, A.G. 1993. Calabaria and the phylogeny of erycine snakes. Zoological Journal of the Linnean Society 107, 293-351.
39. KLUGE, A.G. 1998. Sophisticated falsificationism and research cycles: consequences for differential character weighting in phylogenetic systematics. Zoologica Scripta 26, 349-360.
40. KRAUS, F. & BROWN, W.M. 1998. Phylogenetic relationships of colubroid snakes based on mitochondrial DNA sequences. Zoological Journal of the Linnean Society 122, 455-487.
41. LAWSON, R., SLOWINSKI, J.B. & BURBRINK, F.T. 2004. A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia. Journal of Zoology, London 263, 1-10.
42. LEE, M.S.Y. 1997. The phylogeny of varanoid lizards and the affinities of snakes. Philosphical Transactions of the Royal Society of London, Series B 352, 53-91.
43. LEE, M.S.Y. 1998. Convergent evolution and character correlation in burrowing reptiles: towards a resolution of squamate phylogeny. Biological Journal of the Linnean Society 65, 369-453.
44. LEE, M.S.Y. 2005a. Squamate phylogeny revisited: taxon sampling, character analysis, and data congruence. Organisms, Diversity and Evolution 5, 25-45.
45. LEE, M.S.Y. 2005b. Molecular evidence and snake origins. Biology Letters 1, 227-230.
46. LEE, M.S.Y. & CALDWELL, M.W. 2000. Adriosaurus and the affinities of mosasaurs, dolichosaurs, and snakes. Journal of Paleontology 74, 915-937.
47. LEE, M.S.Y. & HUGALL, A.F. 2003. Partitioned likelihood support and the evaluation of dataset conflict. Systematic Biology 52, 15-22.
48. LEE, M.S.Y. & SCANLON, J.D. 2002. Snake phylogeny based on osteology, soft anatomy, and behaviour. Biological Reviews 77, 333-401.
49. LEWIS, P.O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50, 913-925.
50. MCDIARMID, R.W., CAMPBELL, J.A. & TOURÉ, T.A. 1999. Snake Species of the World: A Taxonomic and Geographic Reference. Volume 1. The Herpetologist's League, Washington, DC.
51. MCDOWELL, S.B. 1975. A catalogue of the snakes of New Guinea and the Solomons, with special reference to those in the Bernice P. Bishop Museum. Part II. Anilioidea and Pythoninae. Journal of Herpetology 9, 1-80.
52. MCDOWELL, S.B. 1987. Systematics. In: SEIGEL, R.A., COLLINS, J.T.C. & NOVAK, S.S., Eds., Snakes: Ecology and Evolutionary Biology. MacMillan, New York, pp. 1-50.
53. NIXON, K.C. & CARPENTER, J.M. 1996. On simultaneous analysis. Cladistics 12, 221-241.
54. NOPCSA, F. 1923. Eidolosaurus und Pachyophis. Zwei neue Neocom-Reptilien. Palaeontographica 65, 99-154.
55. POSADA, D. & CRANDALL, K. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
56. RAGE, J.-C. & ESCUILLIÉ, F. 2002. Eupodophis, new name for the genus Podophis Rage and Escuillié, 2000, an extinct bipedal snake, preoccupied by Podophis Wiegmann, 1834 (Lacertilia, Scincidae). Amphibia-Reptilia 23, 232-233.
57. RAGE, J.-C. & ESCUILLIÉ, F. 2003. The Cenomanian: stage of hindlimbed snakes. Carnets de Géologie/Notebooks on Geology, Maintenon, Article 2003/01 (Reference number: CG2003_A01_JCR-FE). 11 pp. http://paleopolis.rediris.es/cg/ukindex. html
58. RIEPPEL, O. 1988. A review of the origin of snakes. Evolutionary Biology 22, 37-130.
59. RIEPPEL, O., ZAHER, H., TCHERNOV, E. & POLCYN, M.J. 2003. The anatomy and relationships of Haasiophis terrasanctus, a fossil snake with well-developed hind limbs from the mid-Cretaceous of the Middle East. Journal of Paleontology 77, 536-558.
60. RONQUIST, F. & HUELSENBECK, J.P. 2003. MrBayes 3: Bayesian Phylogenetic Inference Under Mixed Models. Computer program and documentation. www.morphbank.ebc.uu.se/mrbayes.
61. SAVITZKY, A.H. 1983. Coadapted character complexes among snakes: fossoriality, piscivory, and durophagy. American Zoologist 23, 397-409.
62. SCANLON, J.D. 1996. Studies in the palaeontology and systematics of Australian snakes. Ph.D. dissertation, University of New South Wales, Sydney.
63. SCOTLAND, R.W., OLMSTEAD, R.G. & BENNET, J.R. 2003. Phylogeny reconstruction: The role of morphology. Systematic Biology 52, 539-548.
64. SCHWENK, K. 1988. Comparative morphology of the lepidosaur tongue and its relevance to squamate phylogeny. In: ESTES, R. and PREGILL, G., Eds., Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford Univ. Press, Stanford, California, pp. 569-598.
65. SEO, T-K., KISHINO, H. & THORNE, J.L. 2005. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proc. Natl. Acad. Sci. USA 102, 4436-4441.
66. SLOWINSKI, J.B. & LAWSON, R. 2002. Snake phylogeny based on mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 24, 194-202.
67. SORENSON, M. 1999. TreeRot Version 2. Computer program and documentation. Distributed by the author, Boston University.
68. STEEL, M. & PENNY, D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Molecular Biology and Evolution 17, 839-850.
69. STRIMMER, K. & RAMBAUT, A. 2002. Inferring confidence sets of possibly misspecified gene trees. Proceedings of the Royal Society of London, Series B 269, 137-142.
70. SWOFFORD, D.L. 2002. PAUP* - Phylogenetic Analysis Using Parsimony (*and other methods). Version 4, beta versions 8-10. Sinauer, Sunderland MA.
71. TCHERNOV, E., RIEPPEL, O., ZAHER, H., POLCYN, M.J. & JACOBS, L.L. 2000. A fossil snake with limbs. Science 287, 2010-2012.
72. THOMAS, R.A. 1989. The relationships of Antillean Typhlops (Serpentes: Typhlopidae) and the description of three new Hispaniolan species. In: WOODS, C.A., Ed., Biogeography of the West Indies: Past, Present, and Future. Sandhill Crane Press, Gainesville, Florida, pp. 409-432.
73. THOMPSON, J., GIBSON, T. & HIGGINS, D. 1997. Clustal W version 1.7. Program and documentation. www.es.embnet.org/Doc/clustalw/
74. TOWNSEND, T.M., LARSON, A., LOUIS, E. & MACEY, R.J. 2004. Molecular phylogenetics of Squamata: the position of snakes, Amphisbaenians, and Dibamids, and the root of the squamate tree. Systematic Biology 53, 735-757.
75. TUFFLEY, C. & STEEL, M. 1997. Links between maximum likelihood andmaximum parsimony under a simple model of site substitution. Bulletin of Mathemtical Biology 59, 581-607.
76. UNDERWOOD, G. 1967. A Contribution to the Classification of Snakes. Publication No. 653. British Museum (Natural History), London.
77. VIDAL, N. & HEDGES, S.B. 2002. Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes. Comptes Rendes, Biologies 325, 977-985.
78. VIDAL, N. & HEDGES, S.B. 2004. Molecular evidence for a terrestrial origin of snakes. Biology Letters 271, 226-229.
79. WAHLBERG, N., BRABY, M.F., BROWER, A.V.Z., DE JONG, R., LEE, M.-M., NYLIN, S., PIERCE, N., SPERLING, F.A.H., VILA, R., WARREN, A.D. & ZAKHAROV, E. 2005. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proceedings: Biological Sciences 272, 1577-1586.
80. WALLACH, V. 1998. The visceral anatomy of blindsnakes and wormsnakes and its systematic implications (Serpentes: Anomalepididae, Typhlopidae, Leptotyphlopidae). Ph.D. dissertation, Northeastern University, Boston, MA.
81. WALLS, G.L. 1940. Ophthalmological implications for the early history of snakes. Copeia 1940, 1-8.
82. WILCOX, T.P., ZWICKL, D.J., HEATH, T.A. & HILLIS, D.M. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25, 361-371.
83. YEATES, D. 1992. Why remove autapomorphies? Cladistics 8, 387-389.
84. ZAHER, H. 1994. Les Tropidopheoidea (Serpentes: Alethinophidia) sont-ils réellement monophyletique? Arguments en faveur de leur polyphyletisme. Comptes Rendus de l'Académie des Sciences, Sciences de la Vie 317, 471-478.
85. ZAHER, H. & RIEPPEL, O. 1999. The phylogenetic relationships of Pachyrhachis problematicus, and the evolution of limblessness in snakes (Lepidosauria, Squamata). Comptes Rendus de l'Académie des Sciences, Sciences de la terre et des planètes 329, 831-837.