Do phylogenetic methods produce trees with biased shapes?

Evolution

Volumn 50, Issue 4, 1996, Pages 1418-1424

  Huelsenbeck, John P ^a,b   Kirkpatrick, Mark ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cladogenesis; extinction; maximum likelihood; neighbor joining; parsimony; phylogenetic tree; speciation; tree balance; tree shape; tree symmetry; UPGMA

Indexed keywords

EID: 0029821511     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1558-5646.1996.tb03915.x     Document Type: Article

References (31)

1. CAVALLI-SFORZA, L., AND A. W. F. EDWARDS. 1967. Phylogenetic analysis: Models and estimation procedures. Am. J. Hum. Genet. 19:233-257.
2. COLLESS, D. H. 1982. Phylogenetics: The theory and practice of phylogenetic systematics II. Book review. Syst. Zool. 31:100-104.
3. _. 1995. Relative symmetry of cladograms and phenograms: An experimental study. Syst. Biol. 44:102-108.
4. EDWARDS, A. W. F. 1970. Estimation of branching points of a branching diffusion process. J. R. Stat. Soc B 32:155-174.
5. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
6. _. 1991. Phylogenetic inference package (PHYLIP), vers. 3.4. Univ. of Washington, Seattle.
7. FITCH, W. M. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
8. FURNAS, G. W. 1984. The generation of random, binary, unordered trees. J. Class. 1:187-233.
9. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J Mol. Evol. 36:182-198.
10. GUYER, C., AND J. B. SLOWINSKI. 1991. Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages. Evolution 45:340-350.
11. _. 1993. Adaptive radiation and the topology of large phylogenies. Evolution 47:253-263.
12. HARDING, E. F. 1971. The probabilities of rooted tree shapes generated by random bifurcation. Adv. Appl. Prob. 3:44-77.
13. HEARD, S. B. 1992. Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46: 1818-1826.
14. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
15. KENDALL, D. G. 1948. On the generalized "birth-death" process. Annu. Rev. Math. Stat. 19:1-15.
16. KIDD, K. K., AND L. A. SGARAMELLA-ZONTA. 1971. Phylogenetic analysis: Concepts and methods. Am. J. Hum. Genet. 23:235-252.
17. KIRKPATRICK, M., AND M. SLATKIN. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47:1171-1181.
18. MOOERS, A. Ø. In press. Tree balance and tree completeness. Evolution.
19. MOOERS, A. Ø., R. D. M. PAGE, A. PURVIS, AND P. H. HARVEY. In press. Phylogenetic noise leads to unbalanced cladistic tree reconstructions. Syst. Biol.
20. RZHETSKY, A., AND M. NEI. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
21. SACKIN, M. J. 1972. "Good" and "bad" phenograms. Syst. Zool. 21:225-226.
22. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
23. SANDERSON, M. J., AND G. BHARATHAN. 1993. Does cladistic information affect inferences about branching rates? Syst. Biol. 42:1-17.
24. SAVAGE, H. M. 1983. The shape of evolution: Systematic tree topology. Biol. J. Linn. Soc. 20:225-244.
25. SHAO, K.-T., AND R. R. SOKAL. 1990. Tree balance. Syst. Zool. 39: 266-276.
26. SOKAL, R. R., AND C. D. MICHENER. 1958. A statistical method for evaluating systematic relationships. Univ. of Kansas Sci. Bull. 28:1409-1438.
27. STEEL, M. A., AND D. PENNY. 1993. Distributions of tree comparison metrics - Some new results. Syst. Biol. 42:126-141.
28. SWOFFORD, D. L. 1996. PAUP*: Phylogenetic analysis using parsimony, vers. 4.0. Sinauer, Sunderland, MA.
29. SWOFFORD, D. L., AND G. J. OLSEN. 1990. Phylogeny reconstruction. Pp. 411-501 in D. M. Hillis and C. Moritz, eds. Molecular systematics. Sinauer, Sunderland, MA.
30. TAYLOR, H. M., AND S. KARLIN. 1984. An introduction to stochastic modeling. Academic Press, Orlando, FL.
31. YULE, G. U. 1924. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S. Phil. Trans. R. Soc. Lond. A 213:21-87.