Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of crocodylia

Systematic Biology

Volumn 53, Issue 2, 2004, Pages 342-355

  Gatesy, John ^a   Baker, Richard H ^b   Hayashi, Cheryl ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLIGATOR; ANIMAL; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; HISTOLOGY; META ANALYSIS; METHODOLOGY; PHYLOGENY; REVIEW; STATISTICAL ANALYSIS;

ALLIGATORS AND CROCODILES; ANIMALS; CLASSIFICATION; DATA INTERPRETATION, STATISTICAL; META-ANALYSIS; PHYLOGENY; RESEARCH DESIGN;

ALLIGATOR; ANIMALIA; CROCODYLIDAE (ALL CROCODILES);

EID: 2442449251     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490423971     Document Type: Review

References (83)

1. Baker, R., and R. DeSalle. 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46:654-673.
2. Barrett, M., M. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486-493.
3. Baum, B. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
4. Bininda-Emonds, O., and H. Bryant. 1998. Properties of matrix representation with parsimony analyses. Syst. Biol. 47:497-508.
5. Bininda-Emonds, O., J. Gittleman, and A. Purvis. 1999. Building large trees by combining phylogenetic information: A complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74:143-175.
6. Bininda-Emonds, O., J. Gittleman, and M. Steel. 2002. The (super)tree of life: Procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33:265-289.
7. Bininda-Emonds, O., K. Jones, S. Price, R. Grenyer, M. Cardillo, M. Habib, A. Purvis, and J. Gittleman. 2003. Supertrees are a necessary not-so-evil: A comment on Gatesy et al. Syst. Biol. 52:724-729.
8. Bininda-Emonds, O., K. Jones, S. Price, R. Grenyer, M. Cardillo, and A. Purvis. In press. Garbage in, garbage out: Some practical issues in supertree construction. In Phylogenetic supertrees: Combining information to reveal the tree of life (O. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht, The Netherlands.
9. Bininda-Emonds, O., and M. Sanderson. 2001. Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst. Biol. 50:565-579.
10. Bremer, K. 1994. Branch support and tree stability. Cladistics 10:295-304.
11. Brochu, C. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Syst. Biol. 46:479-522.
12. Brochu, C. 2002. Thecachampsoides minor and early gavialoid history: Coastal Atlantic origins of longirostrine crocodylians. J. Vertebr. Paleontol. 22:39A.
13. Brochu, C. 2003. Phylogenetic approaches toward crocodylian history. Annu. Rev. Earth Planet. Sci. 31:357-397.
14. Brochu, C., and L. Densmore. 2001. Crocodile phylogenetics: A summary of current progress. Pages 3-8 in Crocodilian biology and evolution (G. Grigg, F. Seebacher, and C. Franklin, eds.). Surrey Beatty and Sons, Chipping Norton, New South Wales.
15. Brochu, C., and P. Gingerich. 2000. New tomistomine crocodylian from the middle Eocene (Bartonian) of Wadi Hitan, Fayum Province, Egypt. Contrib. Mus. Paleontol. Univ. Mich. 30:251-268.
16. Brooks, D., and D. McLennan. 1993. Parascript: Parasites and the language of evolution. Smithsonian Institution Press, Washington, D.C.
17. Bryant, H. In press. The cladistics of matrix representation with parsimony analysis. In Phylogenetic supertrees: Combining information to reveal the tree of life (O. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht, The Netherlands.
18. Buscalioni, A., F. Ortega, D. Weishampel, and C. Jianu. 2001. A revision of the crocodyliform Allodaposuchus precedens from the Upper Cretaceous of the Hateg Basin, Romania. Its relevance in the phylogeny of Eusuchia. J. Vertebr. Paleontol. 21:74-86.
19. Caccone, A., J. Gibbs, V. Ketmaier, E. Suatoni, and J. Powell. 1999. Origin and evolutionary relationships of giant Galapagos tortoises. Proc. Natl. Acad. Sci. USA 96:13223-13228.
20. Campbell, H. 1972. Ecological or phylogenetic interpretations of crocodilian nesting habits. Nature 238:404-405.
21. Cohen, M., and C. Gans. 1970. The chromosomes of the order Crocodilia. Cytogenetics 9:81-105.
22. Daubin, V., M. Gouy, and G. Perriere. 2001. Bacterial molecular phylogeny using supertree approach. Genome Inf. 12:155-164.
23. Densmore, L. 1983. Biochemical and immunological systematics of the order Crocodilia. Pages 397-465 in Evolutionary biology, Volume 16 (M. K. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum Press, New York.
24. Densmore, L., and P. White. 1991. The systematics and evolution of the Crocodilia as suggested by restriction endonuclease analysis of mitochondrial and nuclear ribosomal DNA. Copeia 1991:602-615.
25. De Queiroz, K., and S. Poe. 2001. Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Syst. Biol. 50:305-321.
26. Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J. Mol. Biol. 212:599-635.
27. Farris, J. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume 2 (N. Platnick and V. Funk, eds.). Columbia Univ. Press, New York.
28. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
29. Gatesy, J., and G. Amato. 1992. Sequence similarity of 12S ribosomal segment of mitochondrial DNAs of gharial and false gharial. Copeia 1992:241-244.
30. Gatesy, J., G. Amato, M. Norell, R. DeSalle, and C. Hayashi. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 52:403-422.
31. Gatesy, J., and P. Arctander. 2000. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: A combined analysis of gross anatomical evidence and DNA sequences from five genes. Syst. Biol. 49:515-538.
32. Gatesy, J., R. DeSalle, and W. Wheeler. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2:152-157.
33. Gatesy, J., C. Hayashi, R. DeSalle, and E. Vrba. 1994. Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes. Evolution 48:188-196.
34. Gatesy, J., C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:652-664.
35. Gatesy, J., P. O'Grady, and R. Baker. 1999. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15:271-313.
36. Gatesy, J., and M. Springer. In press. A critique of matrix representation with parsimony super trees. In Phylogenetic supertrees: Combining information to reveal the tree of life (O. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht, The Netherlands.
37. Goloboff, P., and D. Pol. 2002. Semi-strict supertrees. Cladistics 18:514-525.
38. Gladstein, D., and W. Wheeler. 1997. POY: Phylogeny reconstruction via direct optimization of DNA data, version 2.0 American Museum of Natural History, New York.
39. Greer, A. 1970. Evolutionary and systematic significance of crocodilian nesting habits. Nature 227:523-524.
40. Groth, J., and G. Barrowclough. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12:115-123.
41. Harlid, A., A. Janke, and U. Arnason. 1997. The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds. Mol. Biol. Evol. 14:754-761.
42. Harshman, J., C. Huddleston, J. Bollback, T. Parsons, and M. Braun. 2003. True and false gharials: A nuclear gene phylogeny of Crocodylia. Syst. Biol. 52:386-402.
43. Janke, A., and U. Arnason. 1997. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent Archosauria (birds and crocodiles). Mol. Biol. Evol. 14:1266-1272.
44. Janke, A., D. Erpenbeck, M. Nilsson, and U. Arnason. 2001. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): Implications for amniote phylogeny. Proc. R. Soc. Lond. B 268:623-631.
45. Jones, K., A. Purvis, A. MacLarnon, O. Bininda-Emonds, and N. Simmons. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biol. Rev. 77:223-259.
46. Kennedy, M., and R. D. M. Page. 2002. Seabird supertrees: Combining partial estimates of procellariiform phylogeny. Auk 119:88-108.
47. Kluge, A. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
48. Kluge, A. 1997. Testability and the refutation and corroboration of cladistics hypotheses. Cladistics 13:81-96.
49. Kraus, F., L. Jarecki, M. Miyamoto, S. Tanhauser, and P. Laipis. 1992. Mispairing and compensational changes during the evolution of mitochondrial ribosomal DNA. Mol. Biol. Evol. 9:770-774.
50. Lee, M., and A. Hugall. 2003. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 52:15-22.
51. Liu, F., M. Miyamoto, N. Freire, P. Ong, M. Tennant, T. Young, and K. Gugel. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789.
52. Maddison, W. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
53. Marks, J., C. Schmid, and V. Sarich. 1988. DNA hybridization as a guide to phylogeny: Relations of the Hominoidea. J. Hum. Evol. 17:769-786.
54. Matthee, C., J. Burzlaff, J. Taylor, and S. Davis. 2001. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50:367-390.
55. Mindell, D., M. Sorenson, D. Dimcheff, M. Hasegawa, J. Ast, and T. Yuri. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138-152.
56. Miyamoto, M., and W. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
57. Murphy, W., E. Eizrik, W. Johnson, Y. Zhang, O. Ryder, and S. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
58. Norell, M. 1989. The higher level relationships of the extant Crocodylia. J. Herpetol. 23:325-335.
59. O'Keefe, F., and P. Wagner. 2001. Inferring and testing hypotheses of cladistic character dependence by using character compatibility. Syst. Biol. 50:657-675.
60. Patterson, C. 1982. Morphological characters and homology. Pages 21-74 in Problems of phylogenetic reconstruction (A. Joysey and A. Friday, eds.). Academic Press, London.
61. Pisani, D., and M. Wilkinson. 2002. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 51:151-155.
62. Pisani, D., A. Yates, M. Langer, and M. Benton. 2002. A genus-level supertree of the Dinosauria. Proc. R. Soc. Lond. B 269:915-921.
63. Poe, S. 1996. Data set incongruence and the phylogeny of crocodilians. Syst. Biol. 45:393-414.
64. Purvis, A. 1995. A composite estimate of primate phylogeny. Philos. Trans. R. Soc. Lond. B 348:405-421.
65. Ragan, M. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:53-58.
66. Ray, D., and L. Densmore. 2002. The crocodilian mitochondrial control region: General structure, conserved sequences, and evolutionary implications. J. Exp. Zool. 294:334-345.
67. Rodrigo, A. 1993. A comment on Baum's method for combining phylogenetic trees. Taxon 42:631-636.
68. Rodrigo, A. 1996. On combining cladograms. Taxon 45:267-274.
69. Roman, J., and B. W. Bowen. 2000. The mock turtle syndrome: Genetic identification of turtle meat purchased in the south-eastern United States of America. Anim. Conserv. 3:61-65.
70. Salamin, N., T. Hodkinson, and V. Savolainen. 2002. Building supertrees: An empirical assessment using the grass family (Poaceae). Syst. Biol. 51:136-150.
71. Sanderson, M., A. Purvis, and C. Henze. 1998. Phylogenetic supertrees: Assembling the trees of life. Trends Ecol. Evol. 13:105-109.
72. Siddall, M. 1997. Prior agreement: Arbitration or arbitrary. Syst. Biol. 46:766-770.
73. Slowinski, J. B., and R. D. M. Page. 1999. How should species phylogenies be inferred from sequence data. Syst. Biol. 48:814-825.
74. Soltis, P., D. Soltis, and M. Chase. 1999. Angiosperm phylogeny inferred from mutiple genes as a tool for comparative biology. Nature 402:402-404.
75. Springer, M., and W. DeJong. 2001. Which mammalian supertree to bark up? Science 291:1709-1711.
76. Swofford, D. 1998. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b8. Sinauer, Sunderland, Massachusetts.
77. Swofford, D., and G. Olsen. 1990. Phylogeny reconstruction. Pages 411-501 in Molecular systematics, 1st edition (D. Hillis and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts.
78. Templeton, A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
79. White, P., and L. Densmore. 2001. DNA sequence alignments and data analysis methods: Their effect on the recovery of crocodylian relationships. Pages 29-37 in Crocodilian biology and evolution (G. Grigg, F. Seebacher, and C. Franklin). Surrey Beatty and Sons, Chipping Norton, New South Wales.
80. Wilkinson, M., J. L. Thorley, D. T. J. Littlewood, and R. A. Bray. 2001. Towards a phylogenetic supertree of Platyhelminthes? Pages 292-301 in Interrelationships of the Platyhelminthes (D. T. J. Littlewood and R. A. Bray, eds.). Taylor and Francis, London.
81. Wollenberg, K., and W. Atchley. 2000. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. USA 97:3288-3291.
82. Wu, X., D. Brinkman, and A. Russell. 1996. A new alligator from the Upper Cretaceous of Canada and the relationships of early eusuchians. Palaeontology 39:351-375.
83. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.