Can we avoid "sIN" in the house of "no common mechanism"?

Systematic Biology

Volumn 60, Issue 1, 2011, Pages 96-109

  Steel, Mike ^a  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; CLASSIFICATION; EVOLUTION; METHODOLOGY; PHYLOGENY; SHORT SURVEY; STATISTICAL MODEL;

BIOLOGICAL EVOLUTION; CLASSIFICATION; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY;

EID: 79952174584     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq069     Document Type: Short Survey

References (56)

1. Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. In: Petrov B., Csaki F., editors. Information theory. Budapest: Akademiai Kiado. p. 267-281.
2. Allman E. S., Ané C., Rhodes J. A. 2008. Identifiability of a Markovian model of molecular evolution with gamma-distributed rates. Adv. Appl. Probab. 40:228-249.
3. Allman E. S., Rhodes J. A. 2006. The identifiability of tree topology for phylogenetic models, including covarion and mixture models. J. Comput. Biol. 13:1101-1113. (Pubitemid 43993453)
4. Allman E. S., Rhodes J. A. 2008. Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites. Math. Biosci. 211:18-33. (Pubitemid 350298117)
5. Atteson K. 1999. The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica. 25:251-278. (Pubitemid 129674400)
6. Billera L., Holmes S., Vogtmann K. 2001. Geometry of the space of phylogenetic trees. Adv. Appl. Math. 27:733-767.
7. Cavender J. A. 1978. Taxonomy with confidence. Math. Biosci. 40:271-280. (Pubitemid 9045615)
8. Cavender J. A. 1981. Tests of phylogenetic hypotheses under generalized models. Math. Biosci. 54:217-229.
9. Chai J., Housworth E. 2011. On Rogers's proof of identifiability for the GTR + Γ + I model. Syst. Biol. in press.
10. Chang J. T. 1996. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci. 137:51-73. (Pubitemid 26307662)
11. Daskalakis C., Mossel E., Roch S. 2009. Evolutionary trees and the Ising model on the Bethe lattice: a proof of Steel's conjecture. Probab. Theor. Related Fields. in press. doi:10.1007/s00440-009-0246-2.
12. Farris J. S. 2008. Parsimony and explanatory power. Cladistics. 24:825-847.
13. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
14. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
15. Fischer M., Thatte B. 2010. Revisiting an equivalence between maximum parsimony and maximum likelihood methods in phylogenetics. Bull. Math. Biol. 72:208-220.
16. Fitch W. 1971. Rate of change of concomitantly variable codons. J. Mol. Evol. 1:84-96.
17. Gaucher E., Miyamoto M. 2005. A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol. Phylogenet. Evol. 37:928-931. (Pubitemid 41597800)
18. Grimmett G., Stirzaker D. 2001. Probability and random processes. 3rd ed. Oxford: Oxford University Press.
19. Gronau I., Moran S., Snir S. 2008. Fast and reliable reconstruction of phylogenetic trees with very short edges. In: Shang-Hua Teng, editor. SODA: ACM-SIAM Symposium on Discrete Algorithms. Philadelphia (PA): Society for Industrial and Applied Mathematics. p. 379-388.
20. Hillis D. M. 1996. Inferring complex phylogenies. Nature. 383:130-131.
21. Hillis D. M., Huelsenbeck J. P., Swofford D. L. 1994. Hobgoblin of phylogenetics? Nature. 369:363-364.
22. Holder M., Lewis P. O., Swofford D. 2010. The Akaike information criterion will not chose the no common mechanism model. Syst. Biol. 59:477-485.
23. Huelsenbeck J., Alfaro M., Suchard M. 2011. Biologically-inspired phylogenetic models strongly outperform the no-common-mechanism model. Syst. Biol. in press.
24. Huelsenbeck J., Ané C., Larget B., Ronquist F. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst. Biol. 57:406-419. (Pubitemid 351882204)
25. Kim J. 2000. Slicing hyperdimensional oranges: the geometry of phylogenetic estimation. Mol. Phyl. Evol. 17:58-75.
26. Kimura M., Crow J. 1964. The number of alleles that can be maintained in a finite population. Genetics. 49:725.
27. Kolackzkowski B., Thornton J. W. 2009. Long-branch attraction bias and inconsistency in Bayesian phylogenetics. PLos One. 4: e7891.
28. Lake J. 1987. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol. Biol. Evol. 4:167-191. (Pubitemid 17054810)
29. Lemey P., Salemi M., Vandamme A.-M. 2009. The Phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. New York: Cambridge University Press.
30. Lewis P. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
31. Matsen F. A., Mossel E., Steel M. 2008. Mixed-up trees: the structure of phylogenetic mixtures. B. Math. Biol. 70:1115-1139.
32. Matsen F. A., Steel M. 2007. Phylogenetic mixtures on a single tree can mimic a tree of another topology. Syst. Biol. 56:767-775.
33. Mossel E., Roch S., Steel M. 2009. Shrinkage effect in ancestral maximum likelihood. IEEE/ACM Trans. Comput. Biol. Bioinform. 6:126-133.
34. Mossel E., Steel M. 2004. A phase transition for a random cluster model on phylogenetic trees. Math. Biosci. 187:189-203. (Pubitemid 38096340)
35. Moulton V., Steel M. 2004. Peeling phylogenetic 'oranges'. Adv. Appl. Math. 33:710-727.
36. Neyman J. 1971. Molecular studies of evolution: a source of novel statistical problems. In: Gupta S., Yackel J., editors. Statistical decision theory and related topics. New York: Academic Press. p. 1-27.
37. Phillipé H., Zhou Y., Brinkmann H., Rodrigue N., Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 5:50.
38. Schulmeister S. 2004. Inconsistency of maximum parsimony revisited. Syst. Biol. 53:521-528. (Pubitemid 39290197)
39. Semple C., Steel M. 2003. Phylogenetics. Oxford: Oxford University Press.
40. Sober E. 2004. The contest between likelihood and parsimony. Syst. Zool. 53:6-16.
41. Sober E. 2008. Evidence and evolution: the logic behind the science. Cambridge: Cambridge University Press.
42. Steel M. 2010. Consistency of Bayesian inference of resolved phylogenetic trees. arXiv:1001.2864.
43. Steel M., Penny D. 2004. Two further links between MP and ML under the poisson model. Appl. Math. Lett. 17:785-790.
44. Steel M., Penny D. 2005. Parsimony, phylogeny and genomics. In: Albert V., editor. Maximum parsimony and the phylogenetic information in multi-state characters. Oxford: Oxford University Press. p. 163-178.
45. Steel M., Székely L. A. 2002. Inverting random functions (ii): explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math. 15:562-575. (Pubitemid 35355426)
46. Steel M., Székely L., Mossel E. 2009. Phylogenetic information complexity: is testing a tree easier than finding it? J. Theor. Biol. 258:95-102.
47. Steel M. A., Fu Y. X. 1995. Classifying and counting linear phylogenetic invariants for the Jukes-Cantor model. J. Comput. Biol. 2:39-47.
48. Steel M. A., Székely L. 2009. Inverting random functions (iii): discrete MLE revisited. Ann. Comb. 13:373-390.
49. Steel M. A., Székely L., Hendy M. 1994. Reconstructing trees when sequence sites evolve at variable rates. J. Comput. Biol. 1:153-163.
50. Stefankovic D., Vigoda E. 2007. Phylogeny of mixture models: robustness of maximum likelihood and non-identifiable distributions. J. Comput. Biol. 14:156-189. (Pubitemid 46709353)
51. Swofford D. L., Olsen G. J., Waddell P. J., Hillis D. M. 1996. Phylogenetic inference. Chapter 11. In: Hillis D. M., Moritz C., Marble B. K., editors. Molecular systematics. 2nd ed. Sunderland (MA): Sinauer Associates.
52. Tuffley C., Steel M. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. B. Math. Biol. 59:581-607. (Pubitemid 27208833)
53. Wald A. 1949. A note on the consistency of the maximum likelihood estimate. Ann. Math. Stat. 20:595-600.
54. Warnow T., Evans S. N., Ringe D., Nakhleh L. 2006. A stochastic model of language evolution that incorporates homoplasy and borrowing. Chapter. 7. In: Forster P., Renfrew C., editors. Phylogenetic methods and the prehistory of languages. Cambridge: McDonald Institute for Archaeological Research. p. 75.
55. Wu J., Susko E. 2010. Rate variation need not defeat phylogenetic inference through pairwise comparisons. J. Theor. Biol. 263:587-589.
56. Wu J., Susko E., Roger A. J. 2008. An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol. Phylogenet. Evol. 46:801-806. (Pubitemid 351215914)