More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy

Molecular Biology and Evolution

Volumn 22, Issue 5, 2005, Pages 1337-1344

  Rokas, Antonis ^a   Carroll, Sean B ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Gene number; Genomics; Phylogenetic accuracy; Phylogenetics; Taxon number; Tree of life

Indexed keywords

ACCURACY; ANGIOSPERM; ARTICLE; CLADISTICS; CONTROLLED STUDY; GENE NUMBER; MAMMAL; NONHUMAN; PHYLOGENY; TAXON; YEAST;

EVOLUTION, MOLECULAR; FUNGAL PROTEINS; MODELS, GENETIC; PHYLOGENY; SACCHAROMYCES;

EID: 17744398025     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi121     Document Type: Article

References (59)

1. Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
2. Bapteste, E., H. Brinkmann, J. A. Lee et al. (11 co-authors). 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.
3. Bininda-Emonds, O. R., S. G. Brady, J. Kim, and M. J. Sanderson. 2001. Scaling of accuracy in extremely large phylogenetic trees. Pac. Symp. Biocomput. 547-558.
4. Blair, J. E., K. Ikeo, T. Gojobori, and S. B. Hedges. 2002. The evolutionary position of nematodes. BMC Evol. Biol. 2:7.
5. Carmean, D., and B. J. Crespi. 1995. Do long branches attract flies? Nature 373:666.
6. Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76.
7. Cummings, M. P., S. P. Otto, and J. Wakeley. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
8. Dietrich, F. S., S. Voegeli, S. Brachat et al. (17 co-authors). 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307.
9. Dujon, B., D. Sherman, G. Fischer et al. (67 co-authors). 2004. Genome evolution in yeasts. Nature 430:35-44.
10. Erdos, P. L., M. A. Steel, L. A. Szekely, and T. J. Warnow. 1999a. A few logs suffice to build (almost) all trees (I). Random Struct. Algorithms 14:153-184.
11. _. 1999b. A few logs suffice to build (almost) all trees: Part II. Theor. Comput. Sci. 221:77-118.
12. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
13. _. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
14. Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
15. Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
16. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
17. Hendy, M. D., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
18. Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
19. _. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
20. Hittinger, C. T., A. Rokas, and S. B. Carroll. 2004. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc. Natl. Acad. Sci. USA 101:14144-14149.
21. Jones, T., N. A. Federspiel, H. Chibana et al. (12 co-authors). 2004. The diploid genome sequence of Candida albicans. Proc. Natl. Acad. Sci. USA 101:7329-7334.
22. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
23. Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
24. Kim, J. 1998. Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47:43-60.
25. Kopp, A., and J. R. True. 2002. Phylogeny of the oriental Drosophila melanogaster species group: a multilocus reconstruction. Syst. Biol. 51:786-805.
26. Kurtzman, C. P., and C. J. Robnett. 2003. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res. 3:417-432.
27. Lockhart, P. J., D. Huson, U. Maier, M. J. Fraunholz, Y. Van de Peer, A. C. Barbrook, C. J. Howe, and M. A. Steel. 2000. How molecules evolve in eubacteria. Mol. Biol. Evol. 17:835-838.
28. Lutzoni, F., F. Kauff, C. J. Cox et al. (47 co-authors). 2004. Assembling the fungal tree of life: progress, classification and evolution of subcellular traits. Am. J. Bot. 91:1446-1480.
29. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
30. Moncalvo, J. M., R. Vilgalys, S. A. Redhead et al. (14 co-authors). 2002. One hundred and seventeen clades of euagarics. Mol. Phylogenet. Evol. 23:357-400.
31. Mossel, E. 2001. Reconstruction on trees: beating the second eigenvalue. Ann. Appl. Probab. 11:285-300.
32. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
33. Peterson, K. J., and D. J. Eernisse. 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3:170-205.
34. Philippe, H. 2000. Long branch attraction and protist phylogeny. Protist 151:307-316.
35. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
36. Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
37. Rannala, B., J. P. Huelsenbeck, Z. H. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
38. Robinson, D. R., and L. R. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
39. Rodrigo, A. G., P. R. Bergquist, P. L. Bergquist, and P. R. Reeves. 1994. Are sponges animals? An investigation into the vagaries of phylogenetic inference. Pp. 47-54 in R. W. M. van Soest, T. M. G. van Kempen, and J. C. Braekman, eds. Sponges in time and space. Balkema, Rotterdam, The Netherlands.
40. Rokas, A., N. King, J. Finnerty, and S. B. Carroll. 2003a. Conflicting phylogenetic signals at the base of the metazoan tree. Evol. Dev. 5:346-359.
41. Rokas, A., J. A. A. Nylander, F. Ronquist, and G. N. Stone. 2002. A maximum likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae); implications for insect phylogenetic studies. Mol. Phylogenet. Evol. 22:206-219.
42. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003b. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
43. Rosenberg, M. S., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98:10751-10756.
44. Sanderson, M. J., and H. B. Shaffer. 2002. Troubleshooting molecular phylogenetic analyses. Annu. Rev. Ecol. Syst. 33:49-72.
45. Satta, Y., J. Klein, and N. Takahata. 2000. DNA archives and our nearest relative: the trichotomy problem revisited. Mol. Phylogenet. Evol. 14:259-275.
46. Sober, E., and M. Steel. 2002. Testing the hypothesis of common ancestry. J. Theor. Biol. 218:395-408.
47. Sokal, R. R., and F. J. Rohlf. 1995. Biometry: the principles and practice of statistics in biological research. Freeman, New York.
48. Soltis, D. E., V. A. Albert, V. Savolainen et al. (11 co-authors). 2004. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 9:477-483.
49. Soltis, D. E., and P. S. Soltis. 2004. Amborella not a "basal angiosperm"? Not so fast. Am. J. Bot. 91:997-1001.
50. Soltis, P. S., D. E. Soltis, and M. W. Chase. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-404.
51. Souciet, J., M. Aigle, F. Artiguenave et al. (24 co-authors). 2000. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 487:3-12.
52. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
53. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. Sinauer Associates, Sunderland, Mass.
54. Tautz, D., P. Arctander, A. Minelli, R. H. Thomas, and A. P. Vogler. 2003. A plea for DNA taxonomy. Trends Ecol. Evol. 18:70-74.
55. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
56. Thorley, J. L., and M. Wilkinson. 1999. Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200:343-344.
57. 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.
58. Zanis, M. J., D. E. Soltis, P. S. Soltis, S. Mathews, and M. J. Donoghue. 2002. The root of the angiosperms revisited. Proc. Natl. Acad. Sci. USA 99:6848-6853.
59. Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.