Inferring the phylogenetic position of Boa constrictor among the Boinae

Molecular Phylogenetics and Evolution

Volumn 34, Issue 1, 2005, Pages 167-180

  Burbrink, Frank T ^a  

^a Department of Biology   (United States)

Author keywords

Bayesian inference; Boa constrictor; Boinae; Cytochrome b; Maximum likelihood; Morphology; Parametric bootstraps; Partitioned; Priors; Snakes

Indexed keywords

CYTOCHROME B;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; GENETICS; GEOGRAPHY; HISTOLOGY; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; SNAKE;

ANIMALS; BAYES THEOREM; BOIDAE; CYTOCHROMES B; EVOLUTION, MOLECULAR; GEOGRAPHY; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY;

BOA; BOA CONSTRICTOR; BOINAE; SERPENTES;

EID: 9744267544     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.08.017     Document Type: Article

References (45)

1. C. Austin Molecular phylogeny and historical biogeography of Pacific island boas (Candoia) Copeia 2000 2000 341 352
2. W.R. Branch Hemipenes of the Madagascan Boas Acrantophis and Sanzinia, with a review of hemipeneal morphology in the Boinae J. Herpetol. 15 1981 91 99
3. R.E. Buskirk Zoogeographic patterns and tectonic history of Jamaica and the northern Carribbean J. Biogeography 12 1985 445 461
4. J.E. Cadle Geographic distributions: problems in phylogeny and zoogeography R.A. Seigel J.T. Collins S.S. Novak Snakes Ecology and Evolutionary Biology 1987 McGraw Hill New York 77 105
5. M.P. Cummings, S.A. Handley, D.S. Myers, D.L. Reed, A. Rokas, and K. Winka Comparing bootstrap and posterior probability values in the four-taxon case Syst. Biol. 52 2003 477 487
6. P. Erixon, B. Svenblad, T. Britton, and B. Oxelman The reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics Syst. Biol. 52 2003 665 673
7. D.R. Frost, and R. Etheridge A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata) Misc. Pub. Mus. Nat. Hist. Univ. Kans. 81 1989 1 65
8. Genecodes, 2000. Sequencher 4.1. Genecodes Corporation, Ann Arbor, Michigan
9. J.R.H. Gibbons The biogeography and evolution of pacific island reptiles and amphibians G. Grigg R. Shine H. Ehman Biology of Australian Frogs and Reptiles 1981 Royal Zoological Society of New South Wales Sydney, Australia 125 142
10. A. Graybeal Is it better to add taxa or characters to difficult phylogenetic problems? Syst. Biol. 47 1998 9 17
11. P. Harlow, and R. Shine Food habits and reproductive biology of the pacific island boas (Candoia) J. Herpetol. 26 1992 60 66
12. M.D. Hendy, and D. Penny A framework for the quantitative study of evolutionary trees Syst. Zool. 38 1989 297 309
13. D.H. Hillis, B.K. Mable, and C. Moritz Applications of molecular systematics: the state of the field and a look at the future D. Hillis C. Moritz B.K. Mable Molecular Systematics second ed. 1996 Sinauer Associates Massachusetts 515 543
14. J.P. Huelsenbeck, and F. Ronquist MrBayes: a program for the Bayesian 1989. Inference of phylogeny Bioinformatics 17 2001 754 755
15. R. Kass, and A. Raftery Bayes factors and model uncertainty Journal of the American Statistical Association 90 1995 773 795
16. A.G. Kluge Parsimony in vicariance biogeography: a quantitative method and a greater Antillean example Syst. Zool. 37 1988 315 328
17. A.G. Kluge A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes) Syst. Zool. 38 1989 7 25
18. A.G. Kluge Boine snake phylogeny and research cycles Misc. Publ. Mus. Zool. Univ. Mich. 178 1991 1 58
19. A.G. Kluge Calabaria and the phylogeny of erycine snakes Zool. J. Linn. Soc. 107 1993 293 351
20. B. Larget, and D. Simon Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees Mol. Bio. Evo. 16 1999 750 759
21. R. Lawson, J.B. Slowinski, and F.T. Burbrink A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia J. Zool. Lond. 263 2004 285 294
22. P. Lewis A likelihood approach to estimating phylogeny from discrete morphological character data Syst. Biol. 51 2001 913 925
23. J.R. Macey, A. Larson, N.B. Ananjeva, and T.J. Papenfuss Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards J. Mol. Evol. 44 1997 660 674
24. Maddison, D.R., Maddison, W.P., 2003. MacClade, Version 4.02. Sinauer Sunderland, Massachusetts
25. M. McCoy Reptiles of the Solomon Islands 1980 Wau Ecology Institute Handbook Wau, Papua New Guinea
26. McDiarmid, R.W., Campbell, J.A., Touré, T.A., 1999. Snakes Species of the World. A Taxonomic and Geographic Reference, vol. 1, Herpetol., League, Washington
27. S.B. McDowell A catalogue of the snakes of New Guinea and the Solomons, with special reference to those in Bernice P. Bishop Museum. III J. Hereptol. 13 1979 1 92
28. S.B. McDowell Systematics R.A. Seigel J.T. Collins S.S. Novak Snakes Ecology and Evolutionary Biology 1987 MacMillan Publ. Co New York 3 50
29. M.A. Newton, and A.E. Raftery Approximate Bayesian inference by the weighted likelihood bootstrap (with discussion) J.R. Stat. Soc. B Met. 56 1994 3 48
30. J. Nylander, F. Ronquist, J.P. Huelsenbeck, and J.L. Nieves-Aldrey Bayesian phylogenetic analysis of combined data Syst. Biol. 53 2004 47 67
31. K. Petren, and T.J. Case A phylogenetic analysis of body size evolution and biogeography in Chuckwallas (Sauromaulus) and other iguanines Evolution 51 1997 206 219
32. D.D. Pollock, D.J. Zwickle, J.A. McGuire, and D.M. Hillis Increased taxon sampling is advantageous for phylogenetic inference Syst. Biol. 51 2002 664 671
33. D. Posada, and K.A. Crandall MODELTEST: testing the model of DNA substitution Bioinformatics 14 1998 817 818
34. A. Rambaut, and N.C. Grassly Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Comput. Appl. Biosci. 13 1997 235 238
35. A. Schwartz, and R.W. Henderson Amphibians and reptiles of the West Indies: descriptions, distributions, and natural history 1991 Univ. FL Press Gainesville
36. H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
37. J.B. Slowinski, and R. Lawson Snake phylogeny: evidence from nuclear and mitochondrial genes Mol. Phylogenet. Evol. 24 2002 194 202
38. A.G. Smith, D.G. Smith, and B.M. Funnell Atlas of Mesozoic and Cenozoic Coastlines 1994 Cambridge University Press Cambridge
39. Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony*(and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts
40. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 24 1997 4876 4882
41. P.J. Tolson Phylogenetics of the boid snake genus Epicrates and Caribbean vicariance theory Occ. Papers Mus. Zool., Univ. Michigan 715 1987 1 68
42. G. Underwood A systematic analysis of boid snakes A. d'ABeallairs C.B. Cox Morphology and Biology of Reptiles Linn. Soc. Symp. Ser. vol. 3 1976 Academic Press London 151 175
43. G. Underwood, and A.F. Stimson A classification of pythons (Serpentes, Pythoninae) J. Zool., Lond. 221 1990 565 603
44. T.P. Wilcox, D.J. Zwickl, T.A. Heath, and D.M. Hillis Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Mol. Phylogenet. Evol. 25 2002 361 371
45. Z. Yang Maximum likelihood models for combined analyses of multiple sequence data J. Mol. Evol. 42 1996 587 596