On consensus, collapsibility, and clade concordance

Cladistics

Volumn 12, Issue 4, 1996, Pages 305-321

  Nixon, Kevin C ^a   Carpenter, James M ^b  

^a Department of Obstetrics Gynecology   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLADE CONCORDANCE; CLADISTICS; CONSENSUS TREE;

EID: 0030378088     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1006/clad.1996.0023     Document Type: Article

References (48)

1. ADAMS, E. N. 1972. Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390-397.
2. BREMER, K. 1990. Combinable component consensus. Cladistics 6: 369-372.
3. CARPENTER, J. M. 1987. Phylogenetic relationships and classification of the Vespinae (Hymenoptera: Vespidae). Syst. Entomol. 12: 413-431.
4. CARPENTER, J. M. 1992. Random cladistics. Cladistics 8: 147-153.
5. CARPENTER, J. M., P. A. GOLOBOFF, AND J. S. FARRIS. 1996. Randomization and confusion: A reply to Trueman. Cladistics (submitted).
6. CODDINGTON, J. A. AND N. SCHARFF. 1994. Problems with zero-length branches. Cladistics 10: 415-423.
7. 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.
8. FARRIS, J. S. 1970. Methods for computing Wagner trees. Syst. Zool. 19: 83-92.
9. FARRIS, J. S. 1988. Hennig86, ver. 1.5. Program and documentation. Port Jefferson Station, New York.
10. FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417-419.
11. FELSENSTEIN, J. 1980. PHYLIP. Program and documentation. University of Washington, Seattle.
12. FITCH, W. M. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20: 406-416.
13. GOLOBOFF, P. A. 1993a. Pee-Wee, ver. 1.96. Program and documentation. Ithaca, New York.
14. GOLOBOFF, P. A. 1993b. Nona, ver. 0.96. Program and documentation. Ithaca, New York.
15. GORDON, A. D. 1980. On the assessment and comparison of classifications. In: Tomassone, R. (ed.), Analyse de donnees et informatique. INRIA, LeChesnay: 149-160.
16. KALLERSJO, M., J. S. FARRIS, A. G. KLUGE, AND C. BULT. 1992. Skewness and permutation. Cladistics 8: 275-287.
17. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38: 1-25.
18. LORENZEN, S. AND J. SIEG. 1991. PHYLIP, PAUP and HENNIG86. How reliable are computer parsimony programs used in systematics? Zeitschrift fur Zoologishe Systematik und Evolutionsforschung 30: 239-255.
19. MADDISON, W. P. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5: 365-377.
20. MADDISON, W. P. AND D. R. MADDISON. 1992. MacClade, version 3. Program and documentation. Sinauer Associates, Sunderland, MA.
21. MARGUSH, T. AND F. R. MCMORRIS. 1981. Consensus n-trees. Bull. Math. Biosci. 43: 239-244.
22. MICHENER, C. D. 1977. Discordant evolution and the classification of allodapine bees. Syst. Zool. 26: 32-56.
23. MICKEVICH, M. F. 1978. Taxonomic congruence. Syst. Zool. 27: 143-158.
24. MICKEVICH, M. F. AND J. S. FARRIS. 1980. PHYSYS (Phylogenetic analysis system). Program and documentation.
25. MICKEVICH, M. F. AND J. S. FARRIS. 1984. PHYSYS (Phylogenetic analysis system). Documentation for VAX/ VMS installation at Harvard University, Cambridge.
26. MICKEVICH, M. F. AND N. I. PLATNICK. 1989. On the information content of classifications. Cladistics 5: 33-47.
27. MIYAMOTO, M. M. 1985. Consensus cladograms and general classifications. Cladistics 1: 186-189.
28. NELSON, G. 1979. Cladistic analysis and synthesis: Principles and definitions, with a historical note on Adanson's Familles des Plan tes (1763-1764). Syst. Zool. 28: 1-21.
29. NELSON, G. AND N. I. PLATNICK. 1991. Three-taxon statements: A more precise use of parsimony? Cladistics 7: 351-366.
30. NIXON, K. C. 1995. Clados, ver. 1.49. Program and documentation. Trumansburg, New York.
31. NIXON, K. C. AND J. M. CARPENTER. 1996. On simultaneous analysis. Cladistics 12 (in press).
32. NIXON, K. C. AND Q. D. WHEELER. 1992. Extinction and the origin of species. In: Wheeler, Q. D. and M. Novacek (eds), Extinction and Phylogeny. Columbia University Press, New York: 119-143.
33. PAGE, R. D. M. 1988. Quantitative cladistic biogeography: Constructing and comparing area cladograms. Syst. Zool. 37: 254-270.
34. PAGE, R. D. M. 1989. Comments on component-compatibility in historical biogeography. Cladistics 5: 167-182.
35. PATTERSON, C., D. M. WILLIAMS, AND C. J. HUMPHRIES. 1993. Congruence between molecular and morphological phylogenies. Ann. Rev. Ecol. Syst. 24: 153-188.
36. PLATNICK, N. I. 1987. An empirical comparison of microcomputer parsimony programs. Cladistics 3: 121-144.
37. PLATNICK, N. I., C. E. GRISWOLD, AND J. A. CODDINGTON. 1991. On missing entries in cladistic analysis. Cladistics 7: 337-343.
38. POGUE, M. G. AND M. F. MICKEVICH. 1990. Character definitions and character state delineation: The bete noire of phylogenetic inference. Cladistics 6: 319-361.
39. ROHLF, F. J. 1982. Consensus indices for comparing classifications. Math. Biosci. 59: 131-144.
40. SCHUH, R. T. AND J. S. FARRIS. 1981. Methods for investigating taxonomic congruence and their application to the Leptopodomorpha. Syst. Zool. 30: 331-351.
41. SCHUH, R. T. AND J. T. POLHEMUS. 1980. Analysis of taxonomic congruence among morphological ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera). Syst. Zool. 29: 1-26.
42. SOKAL, R. R. AND F. J. ROHLF. 1981. Taxonomic congruence in the Leptopodomorpha reexamined. Syst. Zool. 30: 309-325.
43. SWOFFORD, D. L. 1985. PAUP, ver. 2.4. Program and documentation. Illinois Natural History Survey, Champaign.
44. SWOFFORD, D. L. 1989. PAUP, ver. 3.0. Program and documentation. Illinois Natural History Survey, Champaign.
45. SWOFFORD, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? In: Miyamoto, M. M. and J. Cracraft (eds), Advances in DNA Systematics. Oxford University Press, Oxford: 295-333.
46. THOMPSON, H. S. 1990. Songs of the Doomed. Summit Books, New York.
47. WILKINSON, M. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43: 343-368.
48. WILKINSON, M. 1995. Arbitrary resolutions, missing entries, and the problem of zero-length branches in parsimony analysis. Syst. Biol. 44: 108-111.