Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

Systematic Biology

Volumn 55, Issue 3, 2006, Pages 426-440

  Burleigh, J Gordon ^a   Driskell, Amy C ^a   Sanderson, Michael J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Nonparametric bootstrapping; Phylogenetics; Supermatrix; Supertree; Supertree bootstrapping

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; PHYLOGENY; PLANT; YEAST;

ALGORITHMS; ANIMALS; GENOME; GENOMICS; MODELS, BIOLOGICAL; PHYLOGENY; PLANTS; VARIATION (GENETICS); YEASTS;

EID: 33747375683     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150500541722     Document Type: Article

References (64)

1. Baker, R. H., and R. DeSalle. 1997. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst. Biol. 46:654-673. (Pubitemid 127366000)
2. Bapteste, E., H. Brinkmann, J. A. Lee, D. V. Moore, C. W. Sensen, P. Gordon, L. Durufl6, T. Gaasterland, P. Lopez, M. Miiller, and H. Philippe. 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-1419. (Pubitemid 34136507)
3. Barrett, M., M. J. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486-493.
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 42:637-640.
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. R. P. Bininda-Emonds, ed.) Kluwer Academic, Dordrecht, the Netherlands.
6. 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)
7. Bininda-Emonds, O. R. P. 2004. The evolution of supertrees. Trends Ecol. Evol. 19:315-322. (Pubitemid 38729833)
8. Bininda-Emonds, O. R. P., J. L. Gittleman, and M. A. Steel. 2002. The (super)tree of life: Procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33:265-289.
9. Bininda-Emonds, O. R. P., K. E. Jones, S. A. Price, M. Cardillo, R. Grenyer, and A. Purvis. 2004. Garbage in, garbage out: Data issues in supertree construction. Pages 267-280 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.) Kluwer Academic, Dordrecht, the Netherlands.
10. Bininda-Emonds, O. R. P., and M. J. Sanderson. 2001. Assessment of the accuracy of matrix representation with parsimony supertree construction. Syst. Biol. 50:565-579.
11. Blair, J. E., K. Ikeo, T. Gojobori, and S. B. Hedges. 2002. The evolutionary position of nematodes. BMC Evol. Biol. 2:7.
12. Blair, J. E., P. Shah, and S. B. Hedges. 2005. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bionformatics 6:53.
13. Bremer, K. 1988. The limits of amino-scid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
14. Bull, J. J., J. P. Huelsenbeck, C. W. Huelsenbeck, D. L. Swofford, and P. J. Waddell. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
15. Cotton, J. A., and R. D. M. Page. 2002. Going nuclear: Vertebrate phylogeny and gene family evolution reconciled. P. Roy. Soc. Lond. B Bio. 269:1555-1561.
16. Creevey, C. J., D. A. Fitzpatrick, G. K. Philip, R. J. Kinsella, M. J. O'Connell, M. M. Pentony, S. A. Travers, M. Wilkinson, and J. O. Mclnerney. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? P. Roy. Soc. Lond. B Bio. 271:2551-2558.
17. Creevey, C. J., and J. O. Mclnerney. 2004. Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21:390-392. (Pubitemid 40246612)
18. Cunningham, C. W. 1997. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46:464-478. (Pubitemid 127386647)
19. Daubin, V., M. Gouy, and G. Perriére. 2001. Bacterial molecular phylogeny using supertree approach. Genome Informatics 12:155-164.
20. DeBry, R. W., and R. G. Olmstead. 2000. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Syst. Biol. 49:171-179.
21. de Queiroz, A., M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
22. Dopazo, H., and J. Dopazo. 2005. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 6:R41.
23. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.
24. Driskell, A. C., C. Ané, J. G. Burleigh, M. M. McMahon, B. C. O'Meara, and M. J. Sanderson. 2004. Prospects for building the tree of life from large sequence databases. Science 306:1172-1174. (Pubitemid 39488993)
25. Efron, B. 1994. Missing data, imputation, and the bootstrap. J. Am. Stat. Assoc. 89:463-475.
26. Escobar-Páramo, A. Sabbagh, P. Darlu, O. Pradillon, C. Vaury, E. Denamur, and G. Lecointre. 2004. Decreasing the effects of horizontal gene transfer on bacterial phylogeny: The Escherichia coli case study. Mol. Phylogent. Evol. 30:243-250.
27. Farris, J. S., V. A. Albert, M. Källersjö, D. Lipscomb, and A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
28. Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1994. Testing significance of incongruence. Cladistics 10:315-319.
29. Farris, J. S., A. G. Kluge, and M. J. Eckhardt. 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19:172-191.
30. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
31. Gatesy, J., and R. H. Baker. 2005. Hidden likelihood support in genomic data: Can forty-five wrongs make a right? Syst. Biol. 54:483-492. (Pubitemid 41040446)
32. Gatesy, J., R. H. Baker, and C. Hayashi. 2004. Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:342-355. (Pubitemid 38611188)
33. Gatesy, J., C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:652-664. (Pubitemid 35180694)
34. Gatesy, J., P. O'Grady, and R. H. Baker. 1999. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyls taxa. Cladistics 15:271-313.
35. Gatesy, J., and M. S. Springer. 2004. A critque of matrix representation with parsimony supertrees. Pages 369-388 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.) Kluwer Academic, Dordrecht, the Netherlands.
36. Hendy, M. D., and D. Penny. 1982. Branch and bound algorithms for determining minimal evolutionary trees. Math. Biosci. 59:277-290. (Pubitemid 13136172)
37. Huelsenbeck, J. P., J. J. Bull, and C. W. Cunningham. 1996. Combining data in phylogenetic analyses. Trends Ecol. Evol. 11:152-158.
38. Hughes, J., and A. P. Vogler. 2004. The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: The problem of incomplete data. Mol. Phylogenet. Evol. 32:601-615. (Pubitemid 38836858)
39. Kennedy, M., and R. D. M. Page. 2002. Seabird supertrees: Combining partial estimates of procellariiform phylogeny. Auk 119:88-108. (Pubitemid 34231482)
40. Lee, Y, R. Sultana, G. Pertea, J. Cho, S. Karamycheva, J. Tsai, B. Parvizi, F. Cheung, V. Antonescu, J. White, I. Holt, F. Liang, and J. Quackenbush. 2002. Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA). Genome Res. 12:493-502. (Pubitemid 34233026)
41. Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the γ-proteobacteria. PLoS 1:101-109.
42. Liu, F.-G. R., M. M. Miyamoto, N. P. Freire, P. Q. Ong, M. R. Tennant, T. S. Young, and K. F. Gugel. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789. (Pubitemid 32198983)
43. Mort, M. E., P. S. Soltis, D. E. Soltis, and M. L. Mabry. 2000. Comparison of three methods for estimating internal support on phylogenetic trees. Syst. Biol. 49:160-171.
44. Novacek, M. J. 2001. Mammalian phylogeny: Genes and supertrees. Current Biology 11:R573-R575. (Pubitemid 32675757)
45. Page, R. D. M. 2004. Taxonomy, supertrees, and the tree of life. Pages 247-266 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.) Kluwer Academic, Dordrecht, the Netherlands.
46. Philip, G. K., C. J. Creevey, and J. O. Mclnerney. 2005. The Opisthokonta and Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol. Biol. Evol. 22:1175-1184.
47. Philippe, H., N. Lartillot, and H. Brinkman. 2005. Multigene analysis of bilaterians corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-1253. (Pubitemid 40577762)
48. Philippe, H., E. A. Snell, E. Bapteste, P. Lopez, P. W. H. Holland, and D. Casane. 2004. Phylogenomics of eukaryotes: Impact of missing data on large alignments. Mol. Biol. Evol. 21:1740-1752. (Pubitemid 39096890)
49. Pisani, D., and M. Wilkinson. 2002. MRP, taxonomic congruence and total evidence. Syst. Biol. 51:151-155.
50. Purvis, A. 1995. A modification to Baum and Ragan's method for combining phylogenetic trees. Syst. Biol. 44:251-255.
51. Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:53-58.
52. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804. (Pubitemid 37355944)
53. Ronquist, F. 1996. Matrix representation of trees, redundancy, and weighting. Syst. Biol. 45:247-253.
54. Ronquist, F., J. Juelsenbeck, and T. Britton. 2004. Bayesian supertrees. Pages 193-224 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.) Kluwer Academic, Dordrecht, the Netherlands.
55. Sanderson, M. J. 2003. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302. (Pubitemid 36181923)
56. Sanderson, M. J., A. Purvis, and C. Henze. 1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecol. Evol. 13:105-109. (Pubitemid 28136253)
57. Sanderson, M. J., and M. F. Wojciechowski. 2000. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49:671-685. (Pubitemid 33213084)
58. Seo, T.-K., H. Kishino, and J. L. Thorne. 2005. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proc. Natl. Acad. Sci. USA 102:4436-4441. (Pubitemid 40397130)
59. Springer, M. S., and W. W. de Jong. 2001. Which mammalian supertree to bark up? Science 291:1709-1711. (Pubitemid 32198958)
60. Swofford, D. L., 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0bl0. Sinauer Associates, Sunderland, Massachusetts.
61. Wilkinson, M., J. A. Cotton, C. Creevey, O. Eulenstein, S. R. Harris, F.-J. Lapointe, C. Levasseur, J. O. Mclnerney, D. Pisani, and J. L. Thorley. 2005. The shape of supertrees to come: Tree shape related properties of fourteen supertree methods. Syst. Biol. 54:419-431. (Pubitemid 41040441)
62. Wilkinson, M., J. L. Thorley, D. T. J. Littlewood, and R. Bray. 2001. Towards a phylogenetic supertree of Platyhelminthes? Pages 292-301 in Interrelationships of the Platyhelminthes (D. Littlewood and R. Bray, eds.) Chapman Hall, London.
63. Wolf, Y. I., I. B. Rogozin, and E. V. Koonin. 2004. Coelomata and not ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36. (Pubitemid 38088522)
64. Yan, C, J. G. Burleigh, and O. Eulenstein. 2005. Identifying optimal incomplete phylogenetic data sets from sequence databases. Mol. Phylogent. Evol. 35:528-535. (Pubitemid 40607947)