Quantification of the success of phylogenetic inference in simulations

Cladistics

Volumn 22, Issue 3, 2006, Pages 249-255

  Simmons, Mark P ^a   Webb, Colleen T ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHYLOGENETICS; TOPOLOGY; TREE;

EID: 33745034045     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2006.00105.x     Document Type: Article

References (51)

1. Bremer K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795 803.
2. Conant G.C. Lewis P.O., 2001. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol. Biol. Evol. 18, 1024 1033.
3. Cummings M.P. Handley S.A. Myers D.S. Reed D.L. Rokas A. Winka K., 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52, 477 487.
4. Davis J.I., 1995. A phylogenetic structure for the monocotyledons, as inferred from chloroplast DNA restriction site variation, and a comparison of measures of clade support. Syst. Bot. 20, 503 527.
5. Day W.H.E., 1986. Analysis of quartet dissimilarity measures between undirected phylogenetic trees. Syst. Zool. 35, 325 333.
6. Efron B. Halloran E. Holmes S., 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl Acad. Sci. USA, 93, 13429 13434.
7. Faith D.P. Ballard J.W.O., 1994. Length differences and topology-dependent tests: a response to Källersjö et al. Cladistics 10, 57 64.
8. Farris J.S. Albert V.A. Källersjö M. Lipscomb D. Kluge A.G., 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99 124.
9. Felsenstein J., 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22, 240 249.
10. Felsenstein J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401 410.
11. Felsenstein J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783 791.
12. Gatesy J., 2000. Linked branch support and tree stability. Syst. Biol. 49, 800 807.
13. Goloboff P.A. Farris J.S., 2001. Methods for quick consensus estimation. Cladistics 17, S26 S34.
14. Goloboff P.A. Farris J.S. Källersjö M. Oxelman B. Ramírez M.J. Szumik C.A., 2003a. Improvements to resampling measures of group support. Cladistics 19, 324 332.
15. Goloboff P.A. Farris J.S. Nixon K.C., 2003b. T.N.T. Tree Analysis using New Technology). Program and documentation distributed by the authors, http://www.zmuc.dk/public/phylogeny
16. Graybeal A., 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47, 9 17.
17. Hedges S.B., 1992. The number of replications needed for accurate estimation of the bootstrap, p value in phylogenetic studies. Mol. Biol. Evol. 9, 366 369.
18. Hillis D.M., 1996. Inferring complex phylogenies. Nature 383, 130 131.
19. Hillis D.M. Huelsenbeck J.P. Cunningham C.W., 1994. Application and accuracy of molecular phylogenies. Science 264, 671 677.
20. Huelsenbeck J.P., 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44, 17 48.
21. Huelsenbeck J.P. Hillis D.M., 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42, 247 264.
22. Jukes T.H. Cantor C.R., 1969. Evolution of protein molecules. In : Munro H.N. (Ed.), Mammalian Protein Metabolism, Vol. 3. Academic Press, New York, pp. 21 132.
23. Källersjö M. Farris J.S. Kluge A.G. Bult C., 1992. Skewness and permutation. Cladistics, 8, 275 287.
24. Kolaczkowski B. Thornton J.W., 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431, 980 984.
25. Lassmann T. Sonnhammer E.L.L., 2002. Quality assessment of multiple alignment programs. FEBS Lett. 529, 126 130.
26. Lee M.S.Y., 2000. Tree robustness and clade significance. Syst. Biol. 49, 829 836.
27. Müller K., 2004. PRAP - computation of Bremer support for large data sets. Mol. Phylogenet. Evol. 31, 780 782.
28. Oxelman B. Backlund M. Bremer B., 1999. Relationships of the Buddlejaceae s.1. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data. Syst. Bot. 24, 164 182.
29. Penny D. Hendy M.D., 1985. The use of tree comparison metrices. Syst. Zool. 34, 75 82.
30. Pons J. Vogler A.P., 2006. Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. Cladistics 22, 144 156.
31. Rannala B. Yang Z., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304 311.
32. Robinson D.F. Foulds L.R., 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131 147.
33. Salamin N. Hodkinson T.R. Savolainen V., 2005. Towards building the tree of life: a simulation study for all angiosperm genera. Syst. Biol. 54, 183 196.
34. Siddall M.E., 1998. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone. Cladistics. 14, 209 220.
35. Simmons M.P. Miya M., 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. Mol. Phylogenet. Evol. 31, 351 362.
36. Simmons M.P. Pickett K.M. Miya M., 2004a. How meaningful are Bayesian posterior probabilities? Mol. Biol. Evol. 21, 188 199.
37. Simmons M.P. Reeves A. Davis J.I., 2004b. Character-state space versus rate of evolution for phylogenetic inference. Cladistics 20, 191 204.
38. Simmons M.P. Zhang L.-B. Webb C.T. Reeves A., 2006. How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Syst. Biol 55, 245 258.
39. Simmons M.P. Zhang L.-B. Webb C.T. Reeves A. Miller J.A., 2006. The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters. Cladistics 22, 175 185.
40. Subramanian A.R. Weyer-Menkhoff J. Kaufmann M. Morgenstern B., 2005. DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 6, 66.
41. Suzuki Y. Glazko G.V. Nei M., 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl Acad. Sci. USA, 99, 16138 16143.
42. Swofford D.L., 1991. When are phylogeny estimates from molecular and morphological data incongruent?. In : Miyamoto M.M. Cracraft J. (Eds Phylogenetic Analysis of DNA Sequences. Oxford University Press, New York, pp. 295 333.
43. Swofford D.L., 2001. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer, Sunderland, MA.
44. Wenzel J.W. Siddall M.E., 1999. Noise. Cladistics 15, 51 64.
45. Wiens J.J., 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47, 625 640.
46. Wiens J.J., 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. 54, 731 742.
47. Winer B.J. Brown D.R. Michels K.M., 1991. Statistical Principles in Experimental Design. McGraw-Hill, New York.
48. Yang Z., 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555 556.
49. Yang Z., 1998. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47, 125 133.
50. Yang Z.B. Rannala B., 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54, 455 470.
51. Zujko-Miller C. Miller J.A., 2003. PEST: Precision estimated by sampling traits. http://www.gwu.edu/∼clade/spiders/pestDocs.htm, program distributed by the authors.