Supertree construction in the genomic age

Methods in Enzymology

Volumn 395, Issue , 2005, Pages 745-757

  Bininda Emonds, Olaf R P ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; CONSERVATION BIOLOGY; GENE SEQUENCE; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; THEORETICAL MODEL;

EID: 19944417239     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)95038-6     Document Type: Article

References (47)

1. Aho A.V., Sagiv Y., Szymanski T.G., Ullman J.D. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10:1981;405-421
2. Baum B.R. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon. 41:1992;3-10
3. Baum B.R., Ragan M.A. Reply to A.G. Rodrigo's "A comment on Baum's method for combining phylogenetic trees." Taxon. 42:1993;637-640
4. Bininda-Emonds O.R.P., Gittleman J.L., Purvis A. Building large trees by combining phylogenetic information: A complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74:1999;143-175
5. Bininda-Emonds O.R.P., Sanderson M.J. Assessment of the accuracy of matrix representation with parsimony supertree construction. Syst. Biol. 50:2001;565-579
6. Bininda-Emonds O.R.P., Gittleman J.L., Steel M.A. The (super)tree of life: Procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33:2002;265-289
7. Bininda-Emonds O.R.P., Jones K.E., Price S.A., Grenyer R., Cardillo M., Habib M., Purvis A., Gittleman J.L. Supertrees are a necessary not-so-evil: A comment on Gatesy et al. Syst. Biol. 52:2003;724-729
8. Bininda-Emonds O.R.P. The evolution of supertrees. Trends Ecol. Evol. 6:2004;315-322
9. Bryant D., Semple C., Steel M. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;129-150 Kluwer Academic, Dordrecht, The Netherlands
10. Burleigh J.G., Eulenstein O., Fernández-Baca D., Sanderson M.J. Supertree methods for ancestral divergence dates and other applications. MRF Supertrees. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;65-85 Kluwer Academic, Dordrecht, The Netherlands
11. Chen D., Diao L., Eulenstein O., Fernández-Baca D., Sanderson M.J. Flipping: A supertree construction method. Janowitz M.F., Lapointe F.-J., McMorris F.R., Mirkin B., Roberts F.S. "Bioconsensus" Vol. 61:2003;135-160 American Mathematical Society, Providence, RI
12. Daubin V., Gouy M., Perrière G. Bacterial molecular phylogeny using supertree approach. Genome Inform. 12:2001;155-164
13. Daubin V., Gouy M., Perrière G. A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res. 12:2002;1080-1090
14. Davies T.J., Barraclough T.G., Chase M.W., Soltis P.S., Soltis D.E., Savolainen V. Darwin's abominable mystery: Insights from a supertree of angiosperms. Proc. Natl. Acad. Sci. USA. 101:2004;1904-1909
15. Felsenstein J. The number of evolutionary trees. Syst. Zool. 27:1978;27-33
16. Gatesy J., Matthee C., DeSalle R., Hayashi C. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:2002;652-664
17. Gatesy J., Springer M.S. A critique of matrix representation with parsimony supertrees. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;369-388 Kluwer Academic, Dordrecht, The Netherlands
18. Gatesy J., Baker R.H., Hayashi C. Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:2004;342-355
19. Gittleman J.L., Jones K.E., Price S.A. Supertrees: Using complete phylogenies in comparative biology. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;439-460 Kluwer Academic, Dordrecht, the Netherlands
20. Goloboff P.A., Pol D. Semi-strict supertrees. Cladistics. 18:2002;514-525
21. Gordon A.D. Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves. J. Classif. 3:1986;31-39
22. Huson D.H., Nettles S.M., Warnow T.J. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6:1999a;369-386
23. Huson D.H., Vawter L., Warnow T.J. Solving large scale phylogenetic problems using DCM2. Lengauer T., Schneider R., Bork P., Brutlag D., Glasgow J., Mewes H.-W., Zimmer R. "Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology" Vol. 7:1999b;118-129 AAAI Press, Menlo Park, CA
24. Jones K.E., Purvis A., MacLarnon A., Bininda-Emonds O.R.P., Simmons N.B. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biol. Rev. 77:2002;223-259
25. Källersjö M., Farris J.S., Chase M.L., Bremer B., Fay M.F., Humphries C.J., Petersen G., Seberg O., Bremer K. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants. Pl. Syst. Evol. 213:1998;259-287
26. Kluge A.G. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:1989;7-25
27. Lanyon S.M. Phylogenetic frameworks: Towards a firmer foundation for the comparative approach. Biol. J. Linn. Soc. 49:1993;45-61
28. Lapointe F.-J., Cucumel G. The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46:1997;306-312
29. Lapointe F.-J., Kirsch J.A.W., Hutcheon J.M. Total evidence, consensus, and bat phylogeny: A distance based approach. Mol. Phylogenet. Evol. 11:1999;55-66
30. Levasseur C., Lapointe F.-J. Increasing phylogenetic accuracy with global congruence. Janowitz M.F., Lapointe F.-J., McMorris F.R., Mirkin B., Roberts F.S. "Bioconsensus" Vol. 61:2003;221-230 American Mathematical Society, Providence, RI
31. Page R.D.M. Modified minifut supertrees. Guigó R., Gusfield D. "Algorithms in Bioinformatics, Second International Workshop, WABI, 2002, Rome, Italy, September 17-21, 2002, Proceedings" Vol. 2452:2002;537-552 Springer, Berlin
32. Peterson J.D., Umayam L.A., Dickinson T., Hickey E.K., White O. The comprehensive microbial resource. Nucleic Acids Res. 29:2001;123-125
33. Piaggio-Talice R., Burleigh J.G., Eulenstein O. Quartet supertrees. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;173-191 Kluwer Academic, Dordrecht, the Netherlands
34. Pisani D., Yates A.M., Langer M.C., Benton M.J. A genus-level supertree of the Dinosauria. Proc. R. Soc. Lond. B. 269:2002;915-921
35. Purvis A. A composite estimate of primate phylogeny. Philos. Trans. R. Soc. Lond. B. 348:1995;405-421
36. Ragan M.A. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:1992;53-58
37. Ronquist F. Matrix representation of trees, redundancy, and weighting. Syst. Biol. 45:1996;247-253
38. Ronquist F., Huelsenbeck J.P., Britton T. Bayesian supertrees. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;193-224 Kluwer Academic, Dordrecht, the Netherlands
39. Roshan U., Moret B.M.E., Williams T.L., Warnow T. Performance of supertree mathods on various data set decompositions. Bininda-Emonds O.R.P. "Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life" Vol. 3:2004;301-328 Kluwer Academic, Dordrecht, the Netherlands
40. Salamin N., Hodkinson T.R., Savolainen V. Building supertrees: An empirical assessment using the grass family (Poaceae). Syst. Biol. 51:2002;136-150
41. Sanderson M.J., Purvis A., Henze C. Phylogenetic supertrees: Assembling the trees of life. Trends Ecol. Evol. 13:1998;105-109
42. Sanderson M.J., Driskell A.C., Ree R.H., Eulenstein O., Langley S. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20:2003;1036-1042
43. Semple C., Steel M. A supertree method for rooted trees. Discrete Appl. Math. 105:2000;147-158
44. Slowinski J.B., Page R.D.M. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:1999;814-825
45. Steel M. The complexity of reconstructing trees from qualitative characters and subtrees. J. Classif. 9:1992;91-116
46. Wilkinson M. Coping with abundant missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:1995;501-514
47. Zimmer E.A., White T.J., Cann R.L., Wilson A.C. "Molecular Evolution: Producing the Biochemical Data." Methods Enzymol. 224:1993;3-725