PhySIC: A veto supertree method with desirable properties

Systematic Biology

Volumn 56, Issue 5, 2007, Pages 798-817

  Ranwez, Vincent ^a   Berry, Vincent ^b   Criscuolo, Alexis ^a,b   Fabre, Pierre Henri ^a   Guillemot, Sylvain ^b   Scornavacca, Celine ^a,b   Douzery, Emmanuel J P ^a  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b LIRMM   (France)

Author keywords

Formal properties; Phylogenetics; Polynomial time algorithms; Primates; Software; Supertrees; Triplets; Veto methods

Indexed keywords

PRIMATES;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; METHODOLOGY; PHYLOGENY; PRIMATE;

ALGORITHMS; ANIMALS; CLASSIFICATION; MODELS, BIOLOGICAL; PHYLOGENY; PRIMATES; SOFTWARE;

EID: 38449122640     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701639754     Document Type: Article

References (63)

1. Adams, E. 1972. Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21:390-397.
2. Aho, A. V., Y. Sagiv, T. G. Szymanski, and J. D. Ullman. 1981. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comp. 10:405-421.
3. Bandelt, H.-Jv and A. W. M. Dress. 1986. Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7:309-343.
4. Baum, B. R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
5. Baum, B. R. and M. A. Ragan. 2004. The MRP method. Pages 17-34 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. Bininda-Emonds, ed.). Kluwer, The Netherlands.
6. Berry, V., and O. Gascuel. 2000. Inferring evolutionary trees with strong combinatorial evidence. Theor. Comput. Sci. 240:217-298.
7. Berry, V., S. Guillemot, F. Nicolas, and C. Paul. 2005. On the approximation of computing evolutionary trees. In Proceedings of the 11th International Computing and Combinatorics Conference (COCOON' 05) (L. Wang, ed.). LNCS. Springer. 3595:115-125. (Pubitemid 41450192)
8. Berry, V., and F. Nicolas. 2004. Maximum agreement and compatible supertrees. Pages 205-219 in Proceedings of CPM (S. C. Sahinalp, S. Muthukrishnan, and U. Dogrusoz, eds.), volume 3109 of LNCS. (Pubitemid 39747424)
9. Berry, V., and C. Semple. 2006. Fast computation of supertrees for compatible phylogenies with nested taxa. Syst. Biol. 55:270-288.
10. Bininda-Emonds, O. R. P. 2003. Novel versus unsupported clades: Assessing the qualitative support for clades in MRP supertrees. Syst. Biol. 52:839-848. (Pubitemid 38106049)
11. Bininda-Emonds, O. R. P. 2004a. The evolution of supertrees. Trends Ecol. Evol. 19:315-322. (Pubitemid 38729833)
12. Bininda-Emonds, O. R. P. 2004b. Phylogenetic supertrees: Combining information to reveal the tree of life, volume 4 of Computational biology series. Kluwer, The Netherlands.
13. Bininda-Emonds, O. R. P., and H. N. Bryant. 1998. Properties of matrix representation with parsimony analyses. Syst. Biol. 47:497-508. (Pubitemid 128451088)
14. Bryant, D. 1997. Building trees, hunting for trees and comparing trees: Theory and method in phylogenetic analysis. PhD thesis, Department of Mathematics, University of Canterbury, UK.
15. Bryant, D., and V. Berry. 2001. A structured family of clustering and tree construction methods. Adv. Appl. Math. 27:705-732.
16. Bryant, D., C. Semple, and M. Steel. 2004. Supertree methods for ancestral divergence dates and other applications. Pages 129-150 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. Bininda-Emonds, ed.), volume 4 of Computational biology series. Kluwer, The Netherlands.
17. Chen, D., L. Diao, O. Eulenstein, D. Fern-ndez-Baca, and M. J. Sanderson. 2003. Flipping: A supertree construction method. Pages 135-160 in Bioconsensus, volume 61 of Series in discrete mathematics and theoretic computer science, DIMACS. American Mathematics Society, Providence, Rhode Island.
18. Cotton, J. A., C. S. C. Slater, and M. Wilkinson. 2006. Discriminating supported and unsupported relationships in supertrees using triplets. Syst. Biol. 55:345-350.
19. Criscuolo, A., V. Berry, E. J. P. Douzery, and O. Gascuel. 2006. SDM: A fast distance-based approach for (super)tree building in phylogenomics. Syst. Biol. 55:740-755.
20. Daniel, P. 2004. Supertree methods: Some new approaches. Master's thesis, University of Canterbury, UK.
21. Daniel, P., and C. Semple. 2004. Supertree algorithms for nested taxa. Pages 151-171 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. Bininda-Emonds, ed.), volume 4 of Computational biology series. Kluwer, The Netherlands.
22. Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res. 12:1080-1090. (Pubitemid 34785201)
23. Davies, T. J., T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen. 2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc. Natl. Acad. Sci. USA 101:1904- 1909. (Pubitemid 38232637)
24. Dekker, M. C. 1986. Reconstruction methods for derivation trees. Master's thesis, University of Amsterdam, The Netherlands.
25. Delsuc, E, H. Brinkmann, and H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-375. (Pubitemid 40577180)
26. Dutheil, J., S. Gaillard, E. Bazin, S. Glemin, V. Ranwez, N. Galtier, and K. Belkhir. 2006. Bio++: A set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 7:188.
27. Goloboff, P. A., 2005. Minority-rule supertrees? MRP, compatibility, and MinFlip may display the least frequent groups. Cladistics 21:282-294. (Pubitemid 41537317)
28. Goloboff, P. A., and D. Pol. 2002. Semi-strict supertrees. Cladistics 18:514-525. (Pubitemid 36374534)
29. Goodman, M., L. I. Grossman, and D. E. Wildman. 2005. Moving primate genomics beyond the chimpanzee genome. Trends Genet. 21:511-517. (Pubitemid 41132586)
30. Gordon, A. G. 1986. Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labelled leaves. J. Classif. 3:335- 348.
31. Grunewald, S., M. A. Steel, and M. S. Swenson. 2007. Closure operations in phylogenetics. Math Biosci. 208:521-537. (Pubitemid 47101858)
32. Guillemot, S., and V. Berry. 2007. Finding a largest subset of rooted triples identifying a tree is an NP-hard task. Technical report, LIRMM, University of Montpellier 2.
33. Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst. Biol. 52:696-704. (Pubitemid 37365050)
34. Huson, D. H., S. M. Nettles, and T. J. Warnow. 1999. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6:369-386.
35. Karanth, K. P., T. Delefosse, B. Rakotosamimanana, T. J. Parsons, and A. D. Yoder. 2005. Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. Proc. Natl. Acad. Sci. USA 102:5090-5095.
36. Lapointe, F.-J., and G. Cucumel. 1997. The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46:306-312. (Pubitemid 127092068)
37. Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the gammaproteobacteria. PLoS Biol. 1:101-109.
38. Margush, T, and F. McMorris. 1981. Consensus n-trees. Bull. Math. Biol. 43:239-244.
39. Neumann, D. A. 1983. Faithful consensus methods for rc-trees. Math. Biosci. 63:271-287.
40. Page, R. D. M. 2002. Modified mincut supertrees. Pages 537-552 in Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (WABI'02) (R. Guig6 and D. Gusfield, eds.). Springer, Rome, Italy.
41. Pisani, D., and M. Wilkinson. 2002. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 51:151- 155. (Pubitemid 35169412)
42. Poux, C, P. Chevret, D. Huchon, W. W. de Jong, and E. J. P. Douzery. 2006. Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. Syst. Biol. 55:228-244.
43. Poux, C, and E. J. P. Douzery. 2004. Primate phylogeny, evolutionary rate variations, and divergence times: A contribution from the nuclear gene IRBP. Am. J. Phys. Anthropol. 124:1-16. (Pubitemid 39030310)
44. Purvis, A. 1995a. A composite estimate of primate phylogeny. Philos. Trans. R. Soc. Lond. B Biol. Sci. 348:405-421.
45. Purvis, A. 1995b. A modification to Baum and Ragan's method for combining phylogenetic trees. Syst. Biol. 44:251-255.
46. Ragan, M. A. 1992. Matrix representation in reconstructing phylogenetic relationships among the eukaryots. Biosystems 28:47-55. (Pubitemid 23043822)
47. Roos, C, J. Schmitz, and H. Zischler. 2004. Primate jumping genes elucidate strepsirrhine phylogeny. Proc. Natl. Acad. Sci. USA 101:10650- 10654. (Pubitemid 38955797)
48. Ross, H. A., and A. G. Rodrigo. 2004. An assessment of matrix representation with compatibility in supertree construction, in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.), volume 4 of Computational biology series. Kluwer, The Netherlands.
49. Sanderson, M. J., A. Purvis, and C. Henze. 1998. Phylogenetic supertrees: Assembling the trees of life. Trends Ecol. Evol. 13:105-109. (Pubitemid 28136253)
50. Semple, C, and M. Steel. 2000. A supertree method for rooted trees. Discrete Appl. Math. 105:147-158.
51. Semple, C. and M. A. Steel. 2003. Phylogenetics, volume 24 of Oxford lecture series in mathematics and its applications. Oxford University Press, Oxford, UK.
52. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116. (Pubitemid 29368141)
53. Singer, S. S., J. Schmitz, C. Schwiegk, and H. Zischler. 2003. Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates). Mol. Phylogenet. Evol. 26:490-501. (Pubitemid 36386504)
54. Steel, M. A. 1992. The complexity of reconstructing trees from qualitative characters and subtree. J. Classif. 9:91-116.
55. Steel, M. A., A. W. M. Dress, and S. Bocker. 2000. Simple but fundamental limitations on supertree and consensus tree methods. Syst. Biol. 49:363-368.
56. Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4blO. Sinauer Associates, Sunderland, Massachusetts.
57. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The clustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882. (Pubitemid 28022245)
58. Thorley, J. L., and M. Wilkinson. 2003. A view of supertrees methods. Pages 185-194 in Bioconsensus (M. F. Janowitz, EJ. Lapointe, F. R. McMorris, and F. S. Roberts, eds.), volume 61 of Discrete mathematics and theoretical computer science, DIMACS American Mathematics Society, Providence, Rhode, Island.
59. Wilkinson, M. 1994. Common cladistic information and its consensus representation: Reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368. (Pubitemid 24976651)
60. Wilkinson, M., D. Pisani, J. A. Cotton, and I. Corfe. 2005. Measuring support and finding unsupported relationships in supertrees. Syst. Biol. 54:823-831. (Pubitemid 43142298)
61. Wilkinson, M., J. Thorley, D. Pisani, F.-J. Lapointe, and O. Mclnerney. 2004. Some desiderata for liberal supertree. Pages 227-246 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.), volume 4 of Computational biology series. Kluwer, The Netherlands.
62. Wilson, D. E., and D. M. Reeder. 2005. Mammal species of the world. Johns Hopkins University Press, Baltimore, Maryland.
63. Xing, J., H. Wang, K. Han, D. A. Ray, C. H. Huang, L. G. Chemnick, C.-B. Stewart, T. R. Disotell, O. A. Ryder, and M. A. Batzer. 2005. A mobile element based phylogeny of Old World monkeys. Mol. Phylogenet. Evol. 37:872-880. (Pubitemid 41597796)