The akaike information criterion will not choose the no common mechanism model

Systematic Biology

Volumn 59, Issue 4, 2010, Pages 477-485

  Holder, Mark T ^a   Lewis, Paul O ^b   Swofford, David L ^c,d  

^a UNIVERSITY OF KANSAS   (United States)

^b UNIVERSITY OF CONNECTICUT   (United States)

^c DUKE UNIVERSITY   (United States)

^d NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; EVOLUTION; STATISTICAL MODEL;

EVOLUTION; MODELS, GENETIC; MODELS, STATISTICAL; BIOLOGICAL EVOLUTION;

EID: 77953795613     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq028     Document Type: Article

References (30)

1. Akaike H. 1973. Information theory as an extension of the maximum likelihood principle. In: Petrov B.N., Csaki F., editors. Second International Symposium on Information Theory. Akademiai Kiado. New York: Academic Press. p. 267-281.
2. Alon N., Chor B., Pardi F., Rapoport A. 2010. Approximate maximum parsimony and ancestral maximum likelihood. IEEE/ACM Trans. Comput. Biol. Bioinform. 7:183-187.
3. Cavender J.A. 1978. Taxonomy with confdence. Math. Biosci. 40: 271-280.
4. Farris J.S. 1973. A probability model for inferring evolutionary trees. Syst. Zool. 22:250-256.
5. Farris J.S. 2008. Parsimony and explanatory power. Cladistics. 24: 825-847.
6. Felsenstein J.1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22:240-249.
7. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
8. Gaucher E., Miyamoto M. 2005. A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol. Phylogent. Evol. 37:928-931.
9. Goldman N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst. Zool. 39:345-361.
10. Goloboff P.A. 2003. Parsimony, likelihood, and simplicity. Cladistics. 19:91-103.
11. Hendy M.D., Penny D., Steel M.A. 1994. A discrete Fourier analysis for evolutionary trees. Proc. Natl. Acad. Sci. USA. 91:3339-3343.
12. Huelsenbeck J.P., Ane C., Larget B., Ronquist F. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst. Biol. 57:406-419.
13. Huelsenbeck J.P., Lander K. 2003. Frequent inconsistency of parsimony under a simple model of Cladogenesis. Syst. Biol. 52: 641-648.
14. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. Maryland Heights (MO): Academic Press. p. 21-132.
15. Kass R.E., Raftery A.E. 1995. Bayes factors. J. Am. Stat. Assoc. 90: 773-795.
16. Katz R. 1981. On some criteria for estimating the order of a Markov chain. Technometrics. 23:243-249.
17. Kim J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing number of taxa. Syst. Biol. 45:363-374.
18. Kim J., Sanderson M.J. 2008. Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap. Syst. Biol. 57: 665-674.
19. Kolaczkowski B., Thornton J.W. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature. 431:980-984.
20. Mossel E. 2003. On the impossibility of reconstructing ancestral data and phylogenies. J. Comput. Biol. 10:2003.
21. Neyman J. 1971. Molecular studies of evolution: a source of novel statistical problems. In: Gupta S.S, Yackel J., editors. Statistical decision theory and related topics. New York: Academic Press. p. 1-27.
22. Sanderson M., Kim J. 2000. Parametric phylogenetics? Syst. Biol. 49:817-829.
23. Schwarz G. 1978. Estimating the dimension of a model. Ann. Stat. 6:461-464.
24. Sober E. 2004. The contest between parsimony and likelihood. Syst. Biol. 53:644-653.
25. Spencer M., Susko E., Roger A. 2005. Likelihood, parsimony, and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164.
26. Steel M. 1989. Distributions on bicoloured evolutionary trees [dissertation]. [Palmerston North (New Zealand)]: Massey University.
27. Steel M. 2000. Suffcient conditions for two tree reconstruction techniques to succeed on suffciently long sequences. SIAM J. Dis. Math. 14:36-48.
28. Steel M. 2005. Should phylogenetic models be trying to 'ft an elephant'. Trends Genet. 21:307-309.
29. Steel M., Penny D. 2004. Two further links between MP and ML under the Poisson model. Appl. Math. Lett. 17:785-790.
30. Tuffey C., Steel M. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581-607.