The future of phylogeny reconstruction

Zoologica Scripta

Volumn 26, Issue 4, 1997, Pages 303-311

  Farris, James S ^a  

^a SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; PHYLOGENY; TAXONOMY; ZOOLOGY;

EID: 0031421547     PISSN: 03003256     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1463-6409.1997.tb00420.x     Document Type: Article

References (27)

1. Ballard, J. W. O., Olsen, G. J., Faith, D. P., Odgers, W. A., Rowell, D. M. & Atkinson, P. W. 1992. Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods. - Science 258: 1345-1348.
2. Bremer, K. 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. - Evolution 42: 795-803.
3. Carpenter, J. M. 1996. Uninformative bootstrapping. - Cladistics 12: 177-181.
4. Carpenter, J. M., Goloboff, P. & Farris, J. S. 1997. PTP is meaningless, T-PTP is contradictory: A reply to Trueman. - Cladistics 13 (in press).
5. Chase, M., Soltis, D., Olmstead, R., Morgan, D., Les, D., Mishler, B., Duvall, M., Price, R., Hills, H., Qui, Y., Kron, K., Rettig, J., Conti, E., Palmer, J., Manhert, J., Sytsma, K., Michaels, H., Kress, W., Karol, K., Clark, W., Herden, M., Gaut, B., Jansen, R., Kim, K., Wimpee, C., Smith, J., Furnier, G., Strauss, S., Xiang, Q., Plunkett, G., Soltis, P., Swench, S., Williams, S., Gadek, P., Quinn, C., Eguiarte, L., Golenberg, E., Learn, G., Graham, S., Barett, S., Dayanandan, S. & Albert, V. A. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. - Ann. M. bot. Gdn. 80: 528-580.
6. Colless, D. H. 1995. Relative symmetry of cladograms and phenograms: an experimental study. - Syst. Biol. 44: 102-108.
7. Faith, D. P. 1991. Cladistic permutation tests for monophyly and non-monophyly. - Syst. Zool. 40: 366-375.
8. Farris, J. S. 1970. Methods for computing Wagner trees. - Syst. Zool. 19: 83-92.
9. Farris, J. S. 1983. The logical basis of phylogenetic analysis. In N. I. Platnick & V. A. Funk (eds.), Advances in cladistics, Vol. 2 (pp. 7-36). New York: Columbia University Press.
10. Farris, J. S., Albert, V. A., Källersjö, M., Lipscomb, D. L. & Kluge, A. G. 1996. Parsimony jackknifing outperforms neighbor-joining. -Cladistics 12: 99-124.
11. Farris, J. S. & Källersjö, M. 1994. Pro bono publico. Cladistics 10: 85-95.
12. Farris, J. S., Källersjö, M., Kluge, A. G. & Bult, C. 1994. Permutations. -Cladistics 10: 65-76.
13. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. - Evolution 39: 783-791.
14. Felsenstein, J. 1993. PHYLIP. Ver. 3.5c. [Computer software and manual]. Seattle, Washington: Department of Genetics, University of Washington.
15. Gustafsson, M. H. G. & Bremer, K. 1995. Morphology and phylogenetic relationships of the Asteraceae, Calyceraceae, Campanulaceae, Goodeniaceae, and related families (Asterales). - Am. J. of Bot. 82: 250-265.
16. Heard, S. B. & Mooers, A. 1996. Imperfect information and the balance of cladograms and phenograms. - Syst. Biol. 45: 115-118.
17. Harshman, J. 1994. The effect of irrelevant characters on bootstrap values. - Syst. Biol. 43: 419-424.
18. Hedges, S. B. & Sibley, C. G. 1994. Molecules vs. morphology in evolution: the case of the "pelecaniform" birds. Proceedings of the National Academy of Sciences, USA 91: 9861-9865.
19. Kumar, S., Tamura, K. & Nei, M. 1993. MEGA: Molecular evolutionary genetics analysis. Ver. 1.01. [Computer software and manual]. University Park, Pennsylvania: Pennsylvania State University.
20. Olmstead, R. G., Bremer, B., Scott, K. M. & Palmer, J. D. 1993. A parsimony analysis of the Asteridae sensu lato based on rbcL sequences. - Ann. M. bot. Gdn. 80: 700-722.
21. Rice, K. A., Donoghue, M. J. & Olmstead, R. G. 1997. Analyzing large data sets: rbcL 500 revisited. - Syst. Biol. 46: 554-563.
22. Rzhetsky, A. & Nei, M. 1992. A simple method for estimating and testing minimum-evolution trees. - Molec. Biol. Evol. 9: 945-967.
23. Saitou, N. & Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. - Molec. Biol. Evol. 6: 514-525.
24. Stoneking, M., Sherry, S. & Vigilant, L. 1992. Geographic origin of human mitochondrial DNA revisited. - Syst. Biol. 41: 384-391.
25. Sitnikova, T., Rzhetsky, A. & Nei, M. 1995. Interior-branch and bootstrap tests of phylogenetic trees. - Molec. Biol. Evol. 12: 319-333.
26. Swofford, D. L., Thorne, J. L., Felsenstein, J. & Wiegmann, B. M. 1996. The topology-dependent permutation test for monophyly does not test for monophyly. - Syst. Biol. 45: 575-579.
27. Wheeler, W. C., Cartwright, P. & Hayashi, C. Y. 1993. Arthropod phylogeny: A combined approach. - Cladistics 9: 1-39.