PTP is Meaningless, T-PTP is Contradictory: A Reply to Trueman

Cladistics

Volumn 14, Issue 1, 1998, Pages 105-116

  Carpenter, James M ^a   Goloboff, Pablo A ^b   Farris, James S ^c  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b UNIVERSIDAD NACIONAL DE TUCUMÁN   (Argentina)

^c SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000443251     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.1998.tb00206.x     Document Type: Review

References (32)

1. Archie, J. W. (1989). A randomization test for phylogenetic information in systematic data. Syst. Zool. 38, 219-252.
2. Ballard, J. W. O., Olsen, G. J., Faith, D. P., Odgers, W. A., Rowell, D. M., and Atkinson, P. W. (1992). Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods. Science 258, 1345-1348.
3. Bremer, K. (1988). The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
4. Bremer, K. (1994). Branch support and tree stability. Cladistics 8, 295-304.
5. Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L., and Waddell, P. J. (1993). Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42, 384-397.
6. Carpenter, J. M. (1992). Random cladistics. Cladistics 8, 147-153.
7. Faith, D. P. (1990). Chauce marsupial relationships. Nature 345, 393-394.
8. Faith, D. P. (1991). Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40, 366-375.
9. Faith, D. P. (1992). On corroboration: A reply to Carpenter. Cladistics 8, 265-273.
10. Faith, D. P., and Ballard, J. W. (1994). Length differences and topology-dependent tests: a response to Källersjö et al. Cladistics 10, 57-64.
11. Faith, D. P., and Cranston, P. S. (1991). Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics. 7, 1-28.
12. Faith, D. P., and Trueman, J. W. H. (1996). When the topology-dependent permutation test (T-PTP) for monophyly returns significant support for monophyly, should that be equated with (a) rejecting a null hypothesis of nonmonophyly, (b) rejecting a null hypothesis of "no structure," (c) failing to falsify a hypothesis of monophyly, or (d) none of the above? Syst. Biol. 45, 580-586.
13. Farris, J. S. (1983). The logical basis of phylogenetic analysis. In "Advances in Cladistics 2" (N. I. Platnick, and V. A. Funk, Eds), pp. 7-36. Columbia University Press, New York.
14. Farris, J. S. (1995). Conjectures and refutations. Cladistics. 11, 105-118.
15. Farris, J. S., Albert, V., Källersjö, M., Lipscomb, D., and Kluge, A. G. (1996). Parsimony jackknifing outperforms neighbor-joining. Cladistics. 12, 99-124.
16. Farris, J. S., Källersjö, M., Kluge, A. G., and Bult, C. (1994). Permutations. Cladistics 10, 65-76.
17. Farris, J. S., Källersjö, M., Kluge, A. G., and Bult, C. (1995). Constructing a significance test for incongruence. Syst. Biol. 44, 570-572.
18. Felsenstein, J. (1986). Distance methods: A reply to Farris. Cladistics 2, 130-144.
19. Felsenstein, J. (1993). "PHYLIP, Version 3.5c". Department of Genetics, University of Washington, Seattle.
20. Goloboff, P. A. (1991a). Homoplasy and the choice among cladograms. Cladistics 7, 215-232.
21. Goloboff, P. A. (1991b). Random data, homoplasy and information. Cladistics 7, 395-106.
22. Goloboff, P. A. (1993). "NONA, Version 0.98". Program and documentation. New York, NY.
23. Källersjö, M., Farris, J. S., Kluge, A. G., and Bult, C. (1992). Skewness and permutation. Cladistics 8, 275-287.
24. Nixon, K. C. (1993). "Dada, Version 0.87". Program and documentation. Trumansburg, New York.
25. Popper, K. R. (1968). "The Logic of Scientific Discovery". Harper & Row, New York.
26. Popper, K. R. (1972). "Conjectures and Refutations: The Growth of Scientific Knowledge". Routledge & Keegan Paul, London.
27. Swofford, D. L., Thorne, J. L., Felsenstein, J., and Wiegmann, B. M. (1996). The topology-dependent permutation test for monophyly does not test for monophyly. Syst. Biol. 45, 575-579.
28. Thomas, R. H., Schaffner, W., Wilson, A. C., and Pääbo, S. (1989). DNA phylogeny of the extinct marsupial wolf. Nature 340, 465-467.
29. Tiegs, O. W., and Manton, S. M. (1958). The evolution of the Arthropoda. Biol. Rev. Cambridge Phil. Soc. 33, 255-337.
30. Trueman, J. W. H. (1993). Randomization confounded: A response to Carpenter. Cladistics 9, 101-109.
31. Trueman, J. W. H. (1996). Permutation tests and outgroups. Cladistics 12, 253-261.
32. Wheeler, W. C., Cartwright, P., and Hayashi, C. Y. (1993). Arthropod phylogeny: A combined approach. Cladistics 9, 1-39.