Strengths and limitations of the minimum evolution principle

Systematic Biology

Volumn 50, Issue 5, 2001, Pages 621-627

  Gascuel, Olivier ^a   Bryant, David ^a   Denis, François ^a  

^a LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; BIOLOGICAL MODEL; EVOLUTION; PHYLOGENY; REGRESSION ANALYSIS; SPECIES DIFFERENCE;

ALGORITHMS; ANALYSIS OF VARIANCE; EVOLUTION; LEAST-SQUARES ANALYSIS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 0035527361     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351501753328767     Document Type: Review

References (26)

1. ATTESON, K. 1997. The performance of the NJ method of phylogeny reconstruction. Pages 133-148 in Mathematical hierarchies and biology (B. Mirkin, F. R. McMorris, F. S. Roberts, and A. Rzhetsky, eds.). American Mathematical Society, Providence, Rhode Island.
2. BRUNO, W. J., N. D. SOCCI, AND A. L. HALPERN. 2000. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17:189-197.
3. BRYANT, D., AND P. WADDELL. 1998. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Mol. Biol. Evol. 7:1346-1359.
4. BULMER, M. 1991. Use of the method of generalized least squares in reconstructing phytogenies from sequence data. Mol. Biol. Evol. 8:868-883.
5. CAVALLI-SFORZA, L. L., AND A. W. F. EDWARDS. 1967. Phylogenetic analysis: Models and estimation procedures. Am. J. Hum. Genet. 19:223-257.
6. DENIS, F., AND O. GASCUEL. 2000. On the consistency of the minimum-evolution principle of phylogenetic inference. LIRMM Research Report 2000-219, available on request from the authors.
7. DE SOETE, G. 1983. A least-squares algorithm for fitting additive trees to proximity data. Psychometrika 48:621-626.
8. FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
9. FELSENSTEIN, J. 1997. An alternating least-squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46:101-111.
10. FITCH, W. M., AND E. MARGOLIASH. 1967. Construction of phylogenetic trees. Science 155:279-284.
11. GASCUEL, O. 1997a. Concerning the NJ algorithm and its unweighted version, UNJ. Pages 149-170 in Mathematical hierarchies and biology (B. Mirkin, F. R. McMorris, F. S. Roberts, and A. Rzhetsky, eds.). American Mathematical Society, Providence, Rhode Island.
12. GASCUEL, O. 1997b. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695.
13. GASCUEL, O. 2000a. On the optimization principle in phylogenetic analysis and the minimum evolution criterion. Mol. Biol. Evol. 17:401-405.
14. GASCUEL, O. 2000b. Data model and classification by trees: The minimum variance reduction (MVR) method. J. Classif. 17:67-99.
15. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
16. KIDD, K. K., AND L. A. SGARAMELLA-ZONTA. 1971. Phylogenetic analysis: Concepts and methods. Am. J. Hum. Genet. 23:235-252.
17. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
18. KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
19. LAWSON, C. M., AND R. J. HANSON. 1974. Solving least squares problems. Prentice Hall, Englewood Cliffs, New Jersey.
20. MAKARENKOV, V., AND B. LECLERC. 1999. An algorithm for the fitting of a tree metric according to a weighted least-squares criterion. J. Classif. 16:3-26.
21. NEI, M., AND L. JIN. 1989. Variances of the average numbers of nucleotide substitutions within and between populations. Mol. Biol. Evol. 6:290-300.
22. RZHETSKY, A., AND M. NEI. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073-1095.
23. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: A new method for reconstruction of phylogenetic trees. Mol. Biol. Evol. 4:406-425.
24. SEARL, S. R. 1971. Linear models. Wiley, New York.
25. SWOFFORD, D. L., G. L. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular sytematics (D. M. Hillis, C. Motitz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
26. ZARESTKII, K. 1965. Reconstructing a tree from the distances between its leaves. Usp. Math. Nauk 20:90-92 (in Russian).