Missing entries and multiple trees: Instability, relationships, and support in parsimony analysis

Journal of Vertebrate Paleontology

Volumn 23, Issue 2, 2003, Pages 311-323

  Wilkinson, Mark ^a  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; DATA INTERPRETATION; DATA PROCESSING; DATA QUALITY; PHYLOGENETICS; TAXONOMY;

EID: 0043205924     PISSN: 02724634     EISSN: 19372809     Source Type: Journal    
DOI: 10.1671/0272-4634(2003)023[0311:MEAMTI]2.0.CO;2     Document Type: Article

References (44)

1. Anderson, J. S. 2001. The phylogenetic trunk: maximal inclusion oi taxa with missing data in an analysis of Lepospondyli (Vertebrata: Tetrápoda). Systematic Biology 50:170-193
2. Benton, M. J. 1990. The species of Rhynchosaurus, a rhynchosaur (Reptilia, Diapsida) from the Middle Triassic of England. Philosophical Transactions of the Royal Society of London, B, 328:213-306
3. Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803
4. Clack, J. A. 1998. A new early Carboniferous tetrapod with a mélange of crown-group characters. Nature 394:66-69
5. Donoghue, M. J., R. G. Olmstead, J. E Smith, and J. D. Palmer. 1992. Phylogenetic relationships of Dipsacales based on rbcE sequences. Annals of the Missouri Botanical Gardens 79:333-345
6. Dyke, G. J., and J. L. Thorley. 1998. Reduced cladistic consensus methods and the inter-relationships of Protoavis, Avimimus and Mesozoic birds. Archaeopteryx 16:123-129
7. Farris, J. S., V. A. Albert, M. Kallersjo, D. Lipscomb, and A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124
8. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
9. Fraser, N. C., and M. J. Benton. 1989. The Triassic reptiles Brachyrhinodon and Polysphenodon and the relationships of sphenodontids. Zoological Journal of the Linnean Society 96:413-445
10. Gauthier, J. A. 1986. Saurischian monophyly and the origin of birds. Memoires of the California Academy of Sciences 8:1-47
11. Gauthier, J. A., A. G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209
12. Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Systematic Biology 51:369-381
13. Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae: Serpentes). Systematic Zoology 38:7-25
14. Margush, T., and F. R. McMorris. 1981. Consensus n-trees. Bulletin of Mathematical Biology 43:239-244
15. Nixon, K. C., and J. M. Carpenter. 1996. On consensus, collapsability and clade concordance. Cladistics 12:305-201
16. Nixon, K. C., and Q. D. Wheeler. 1992. Extinction and the origin of species; pp. 119-143 in M. J. Novacek and Q. D. Wheeeler (eds.), Extinction and Phylogeny. Columbia University Press, New York
17. Page, R. D. M. 1992. Comments on the information content of classifications. Cladistics 8:87-95
18. Rowe, T. 1988. Definition, diagnosis and origin of Mammalia. Journal of Vertebrate Paleontology 8:241-264
19. Sokal, R. R., and E J. Rohlf. 1981. Taxonomic congruence in the Leptodomorpha re-examined. Systematic Zoology 30:309-325
20. Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent?; pp. 295-333 in M. M. Miyamoto and J. Cracraft (eds.), Phylogenetic Analysis of DNA Sequences. Oxford University Press, Oxford
21. Swofford, D. L. 1998. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts
22. Thorley, J. L. 2000. Cladistic information, leaf stability and supertree construction. Ph.D. thesis, Department of Biological Sciences, Faculty of Science, University of Bristol, U.K., pp
23. Thorley, J. L., and R. D. M. Page. 2000. RadCon: phylogenetic tree comparison and consensus. Bioinformatics 16:486-487
24. Thorley, J. L., and M. Wilkinson. 1999. Testing the phylogenetic stability of early tetrapods. Journal of Theoretical Biology 200:343-344
25. Thorley, J. L., M. Wilkinson, and M. A. Charleston. 1998. The information content of consensus trees; pp. 91-98 in A. Rizzi, M. Vichi, and H.-H. Bock (eds.), Advances in Data Science and Classification. Springer, Berlin
26. Upchurch, P. 1998. The phylogenetic relationships of sauropod dinosaurs. Zoological Journal of the Linnean Society 124:43-103
27. Wilkinson, M. 1992. Consensus, compatibility and missing data in phylogenetic inference. Ph.D. thesis, Department of Geology, Faculty of Science, University of Bristol, U.K., 367 pp
28. Wilkinson, M. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Systematic Biology 43:343-368
29. Wilkinson, M. 1995a. Coping with missing entries in phylogenetic inference using parsimony. Systematic Biology 44:501-514
30. Wilkinson, M. 1995b. More on reduced consensus methods. Systematic Biology 44:435-439
31. Wilkinson, M. 1996. Majority-rule reduced consensus methods and their use in bootstrapping. Molecular Biology and Evolution 13:437-444
32. Wilkinson, M. 1997. Characters, congruence and quality: a study of neuroan-atomical and traditional data in caecilian phylogeny. Biological Reviews 72:423-470
33. Wilkinson, M. 1999. Choosing and interpreting a tree for the oldest mammal. Journal of Vertebrate Paleontology 19:187-190
34. Wilkinson, M. 2001a. REDCON 3.0. Software and documentation. The Department of Zoology, Natural History Museum, London
35. Wilkinson, M. 2001b. TAXEQ3. Software and documentation. The Department of Zoology, Natural History Museum, London
36. Wilkinson, M., and M. J. Benton. 1995. Missing data and rhynchosaur phylogeny. Historical Biology 10:137-150
37. Wilkinson, M., and M. J. Benton. 1996. Sphenodontid phylogeny and the problems of multiple trees. Philosophical Transactions of the Royal Society of London, B, 351:1-16
38. Wilkinson, M., S. J. Suter, and V. L. Shires. 1996. The reduced cladistic consensus method and cassiduloid echinoid phytogeny. Historical Biology 12:63-73
39. Wilkinson, M., and J. L. Thorley. 2001a. No compromise on consensus. Taxon 50:181-184
40. Wilkinson, M., and J. L. Thorley. 2001b. The efficiency of strict consensus trees. Systematic Biology 50:610-613
41. Wilkinson, M., and J. L. Thorley. 2003. Reduced consensus; in M. Janowitz, F.-J. Lapointe, E R. McMorris, B. Mirkin, and F. S. Roberts (eds.), Bioconsensus. DIMACS series in discrete mathematics and theoretical computer science, American Mathematical Society, Providence. In press
42. Wilkinson, M., J. L. Thorley, and P. M. Upchurch. 2000. A chain is no stronger than its weakest link: double decay analyses of phylogenetic hypotheses. Systematic Biology 49:754-776
43. Wills, M. A., D. E. G. Briggs, R. A. Fortey, and M. Wilkinson. 1995. The significance of fossils in understanding arthropod evolution. Verhandlungen der Deutschen Zoologischen Gesellschaft 88:203-215
44. Wills, M. A., D. E. G. Briggs, R. A. Fortey, M. Wilkinson, and P. H. A. Sneath. 1998. An arthropod phylogeny based on fossil and recent taxa; pp. 33-105 in G. E. Edgecombe (ed.), Arthropod Fossils and Phylogeny. Columbia University Press, New York