Polyhedral Geometry of Phylogenetic Rogue Taxa

Bulletin of Mathematical Biology

Volumn 73, Issue 6, 2011, Pages 1202-1226

  Cueto, María Angélica ^a   Matsen, Frederick A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Distance based phylogenetic inference; Linear programming; Minimum evolution; Normal fan; Polytope

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; PHYLOGENY;

BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; MODELS, GENETIC; PHYLOGENY;

EID: 79955549582     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-010-9556-x     Document Type: Article

References (47)

1. Baurain, D., Brinkmann, H., and Philippe, H. (2007). Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors? Mol. Biol. Evol., 24(1), 6.
2. Berger, S. A., and Stamatakis, A. (2009). Evolutionary placement of short sequence reads. http://arxiv. org/abs/0911. 2852.
3. Bordewich, M., Gascuel, O., Huber, K. T., and Moulton, V. (2009). Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans. Comput. Biol. Bioinfo., 6(1), 110-117.
4. Brodal, G. S., Fagerberg, R., and Pedersen, C. N. S. (2004). Computing the quartet distance between evolutionary trees in time O(nlog n). Algorithmica, 38(2), 377-395.
5. Bryant, D., Tsang, J., Kearney, P., and Li, M. (2000). Computing the quartet distance between evolutionary trees. In Proceedings of the eleventh annual ACM-SIAM symposium on discrete algorithms (p. 286). Society for Industrial and Applied Mathematics, Philadelphia.
6. Chailloux, E., Manoury, P., and Pagano, B. (2000). Developing applications with objective caml. http://caml. inria. fr/ocaml/index. en. html.
7. DeBry, R. W. (2005). The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Syst. Biol., 54(3), 432.
8. Desper, R., and Gascuel, O. (2002a). Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. In Workshop on algorithms in bioinformatics (WABI) (pp. 357-374).
9. Desper, R., and Gascuel, O. (2002b). Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol., 9(5), 687-705.
10. Desper, R., and Gascuel, O. (2004). Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol., 21(3), 587-598.
11. Desper, R., and Gascuel, O. (2005). The minimum evolution distance-based approach to phylogenetic inference. In O. Gascuel (Ed.), Mathematics of evolution and phylogeny (pp. 1-32). Oxford: Oxford University Press.
12. Eickmeyer, K., Huggins, P., Pachter, L., and Yoshida, R. (2008). On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol., 3(5).
13. Ewald, G. (1996). Graduate texts in mathematics: Vol. 168. Combinatorial convexity and algebraic geometry. New York: Springer.
14. Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool., 27(4), 401-410.
15. Felsenstein, J. (1995). PHYLIP (phylogeny inference package), version 3. 57 c. Department of Genetics, University of Washington, Seattle.
16. Felsenstein, J. (2004). Inferring Phylogenies. Sunderland, MA: Sinauer Press.
17. Galassi, M., Davies, J., Theiler, J., Gough, B., Jungman, G., Alken, P., Booth, M., and Rossi, F. (2009). GNU scientific library reference manual (3rd ed.). Network Theory Ltd. http://www. gnu. org/software/gsl/.
18. Gawrilow, E., and Joswig, M. (2000). Polymake: A framework for analyzing convex polytopes. In G. Kalai, and G. M. Ziegler (Eds.), Polytopes-combinatorics and computation (pp. 43-74). Basel: Birkhäuser.
19. Graybeal, A. (1998). Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol., 47(1), 9.
20. Guillemot, S. and Pardi, F. (2009). Personal communication.
21. Heath, T. A., Hedtke, S. M., and Hillis, D. M. (2008a). Taxon sampling and the accuracy of phylogenetic analyses. J. Syst. Evol., 46(3), 239-257.
22. Heath, T. A., Zwickl, D. J., Kim, J., and Hillis, D. M. (2008b). Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol., 57(1), 160.
23. Hedtke, S. M., Townsend, T. M., and Hillis, D. M. (2006). Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol., 55(3), 522.
24. Hendy, M. D., and Penny, D. (1989). A framework for the quantitative study of evolutionary trees. Syst. Zool., 38(4), 297-309.
25. Hillis, D. M. (1996). Inferring complex phylogenies. Nature, 383(6596), 130.
26. Hillis, D. M., Pollock, D. D., McGuire, J. A., and Zwickl, D. J. (2003). Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol., 52(1), 124-126.
27. Jensen, A. N. (2009). Gfan-A software system for Gröbner fans. Available at http://www. math. tu-berlin. de/~jensen/software/gfan/gfan. html.
28. Kim, J. (1996). General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol., 45(3), 363.
29. Mailund, T., and Pedersen, C. N. S. (2004). QDist-Quartet distance between evolutionary trees. Bioinformatics, 971.
30. Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. (1994). fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Bioinformatics, 10(1), 41.
31. Pachter, L., and Sturmfels, B. (Eds.) (2005). Algebraic statistics for computational biology (p. 69). Cambridge: Cambridge University Press. Chap. II.
32. Padberg, M. W. and Grötschel, M. (1985). Polyhedral computations. In Wiley-intersci. ser. discrete math. The traveling salesman problem (pp. 307-360). Chichester: Wiley.
33. Poe, S. (1998). Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol., 47(1), 18.
34. Poe, S. (2003). Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol., 52(3), 423-428.
35. Pollock, D. D., Zwickl, D. J., McGuire, J. A., and Hillis, D. M. (2002). Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol., 51(4), 664-671.
36. Rannala, B., Huelsenbeck, J. P., Yang, Z., and Nielsen, R. (1998). Taxon sampling and the accuracy of large phylogenies. Syst. Biol., 47(4), 702-710.
37. Robinson, D. F., and Foulds, L. R. (1981). Comparison of phylogenetic trees. Math. Biosci, 53(1-2), 131-147.
38. Ronquist, F., Huelsenbeck, J. P., and van der Mark, P. (2005). MrBayes 3. 1 manual. http://mrbayes. csit. fsu. edu/mb3. 1_manual. pdf.
39. Rosenberg, M. S., and Kumar, S. (2001). Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci., 98(19), 10751.
40. Rosenberg, M. S., and Kumar, S. (2003). Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol., 52(1), 119-124.
41. Saitou, N., and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4(4), 406-425.
42. Steel, M. A., and Penny, D. (1993). Distributions of tree comparison metrics-Some new results. Syst. Biol., 42(2), 126.
43. Studier, J. A., and Keppler, K. J. (1988). A note on the neighbor-joining method of Saitou and Nei. Mol. Biol. Evol., 5(6), 729-731.
44. Sullivan, J., and Swofford, D. L. (1997). Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol., 4(2), 77-86.
45. Von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N., and Bork, P. (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315(5815), 1126.
46. Ziegler, G. M. (2006). Graduate texts in mathematics: Vol. 152. Lectures on polytopes. Berlin: Springer.
47. Zwickl, D. J. and Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol., 51(4), 588.