Tree robustness and clade significance

Systematic Biology

Volumn 49, Issue 4, 2000, Pages 829-836

  Lee, Michael S Y ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; DECISION TREE; GENETICS; LIZARD; MOLECULAR EVOLUTION; PHYLOGENY; REPRODUCIBILITY;

ANIMALS; DECISION TREES; EVOLUTION, MOLECULAR; LIZARDS; PHYLOGENY; REPRODUCIBILITY OF RESULTS;

EID: 0034351399     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351500750049879     Document Type: Article

References (34)

1. BAUM, D. A., R. L. SMALL, AND J. F. WENDEL. 1998. Biogeography and floral evolution of Baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Syst. Biol. 47:181-207.
2. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
3. BRYANT, H. N. 1995. Why autapomorphies should be removed: a reply to Yeates. Cladistics 11:381-384.
4. CARPENTER, J. M. 1996. Uninformative bootstrapping. Cladistics 12:177-181.
5. CUNNINGHAM, C. W. 1997. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
6. DONOGHUE, M. J., R. G. OLMSTEAD, J. F. SMITH, AND J. D. PALMER. 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Mo. Bot. Gard. 70:333-345.
7. EERNISSE, D. J., AND A. G. KLUGE. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules and morphology. Mol. Biol. Evol. 10:1170-1195.
8. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:366-375.
9. FARRIS, J. S., V. A. ALBERT, M. KÄLLERSJÖ, D. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing out-performs neighbour-joining. Cladistics 12:99-124.
10. FELSENSTEIN, J. 1985a. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. FELSENSTEIN, J. 1985b. Confidence limits on phylogenies with a molecular clock. Syst. Zool. 34:152-161.
12. FELSENSTEIN, J., AND H. KISHINO. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42:193-200.
13. GATESY, J., P. O'GRADY, AND R. H. BAKER. 1999. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15:271-313.
14. GRAHAM, S. W., J. R. KOHN, B. R. MORTON, J. E. ECKENWALDER, AND S. C. H. BARRETT. 1999. Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae. Syst. Biol. 47:545-567.
15. HARSHMAN, J. 1994. The effect of irrelevant characters on bootstrap values. Syst. Biol. 43:419-424.
16. HILLIS, D. M., AND J. J. BULL. 1993. An empirical test of bootstrapping as a method for assessing confidence in a phylogenetic analysis. Syst. Biol. 42:182-192.
17. HUELSENBECK, J. P., D. M. HILLIS, AND R. NIELSEN. 1996. A likelihood-ratio test of monophyly. Syst. Biol. 45:546-558.
18. KÄLLERSJÖ, M., J. S. FARRIS, A. G. KLUGE, AND C. BULT. 1992. Skewness and permutation. Cladistics 8:275-287.
19. KEOGH, J. S. 1998. Molecular phylogeny of elapid snakes and a consideration of their biogeographic history. Biol. J. Linn. Soc. 63:177-203.
20. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea. J. Mol. Evol. 29:170-179.
21. LANG, M. 1991. Generic relationships within Cordyliforms (Reptilia: Squamata). Bull. Inst. R. Sci. Nat. Belg. Biol. 61:121-188.
22. LARSON, A. R. 1994. The comparison of morphological and molecular data in phylogenetic systematics. Pages 371-390 in Molecular ecology and evolution: approaches and applications (B. Schierwater, B. Steit, G. P. Wagner, and R. deSalle, eds.). Birkhäuser Verlag, Basel, Switzerland.
23. LEE, M. S. Y., M. W. CALDWELL, AND J. D. SCANLON. 1999. A second primitive marine snake: Pachyophis woodwardi from the Cretaceous of Bosnia-Herzegovina. J. Zool. 248:509-520.
24. MACEY, J. R., J. A. SCHULTE, II, A. LARSON, B. S. TUNIYEV, N. ORLOV, AND T. J. PAPENFUSS. 1999. Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families. Mol. Phylogenet. Evol. 12:250-272.
25. RICE, W. R. 1989. Analysing tables of statistical tests. Evolution 43:223-225.
26. SANDERSON, M. J. 1995. Objections to bootstrapping: a critique. Syst. Biol. 44:299-320.
27. SANDERSON, M. J., AND M. J. DONOGHUE. 1996. The relationship between homoplasy and confidence in a phylogenetic tree. Pages 67-89 in Homoplasy: the recurrence of similarity in evolution (M. J. Sanderson and L. Hufford, eds.). Academic Press, San Diego.
28. SCHULTE, J. A., II, J. R. MACEY, A. LARSON, AND T. J. PAPENFUSS. 1998. Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae. Mol. Phylogenet. Evol. 10:367-376.
29. SWOFFORD, D. L. 1999. PAUP*. Phylogenetic analysis using parsimony (*and other methods). ver. 4. Computer Program. Sinauer Associates, Sunderland, Massachusetts.
30. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction site endonuclease cleavage site maps with particular reference to the humans and apes. Evolution 37:221-244.
31. URSING, B. M., AND U. ARNASON. 1998. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc. R. Soc. London B 265:2251-2255.
32. WILKINSON, M. 1997. Characters, congruence and quality: a study of neuroanatomical and traditional data in caecilian phylogeny. Biol. Rev. 72:423-470.
33. YEATES, D. 1992. Why remove autapomorphies? Cladistics 8:387-389.
34. ZARDOYA, R., AND A. MEYER. 1998. Complete mitochondrial genome indicates diapsid affinities of turtles. Proc. Natl. Acad. Sci. USA 95:14226-14231.