Reciprocal illumination in the gene content tree of life

Systematic Biology

Volumn 55, Issue 3, 2006, Pages 441-453

  Lienau, E Kurt ^a,b   DeSalle, Rob ^a   Rosenfeld, Jeffrey A ^a,b   Planet, Paul J ^a,c  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

CCM; Consistency; Corroboration; Gene content; Homology; ILD; Phylogeny; Presence absence; Tree of life

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMPUTER SIMULATION; GENETIC DATABASE; METHODOLOGY; PHYLOGENY; SEQUENCE HOMOLOGY;

ALGORITHMS; CLASSIFICATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, GENETIC; MODELS, GENETIC; PHYLOGENY; SEQUENCE HOMOLOGY;

EID: 33747341087     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150600697416     Document Type: Article

References (89)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
2. Apweiler, R., A. Bairoch, and C. H. Wu. 2004. Protein sequence databases. Curr. Opin. Chem. Biol. 8:76-80. (Pubitemid 38201481)
3. Bansal, A. K., and T. E. Meyer. 2002. Evolutionary analysis by whole-genome comparisons. J. Bacteriol. 184:2260-2272. (Pubitemid 34259676)
4. Bowers, P. M., S. J. Cokus, D. Eisenberg, and T. O. Yeates. 2004. Use of logic relationships to decipher protein network organization. Science 306:2246-2249. (Pubitemid 40024459)
5. Brochier, C, E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5. (Pubitemid 34031845)
6. Brochier, C, P. Forterre, and S. Gribaldo. 2005a. An emerging phylogenetic core of Archaea: Phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5:36.
7. Brochier, C, S. Gribaldo, Y. Zivanovic, F. Confalonieri, and P. Forterre. 2005b. Nanoarchaea: Representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6:R42.
8. Brochier, C, and H. Philippe. 2002. Phylogeny: A non-hyperthermophilic ancestor for bacteria. Nature 417:244. (Pubitemid 34534699)
9. Brower, A. 1996. Three steps of homology assesment. Cladistics 12:265-272.
10. Brown, J. R., C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281-285. (Pubitemid 32626033)
11. Clarke, G. D., R. G. Beiko, M. A. Ragan, and R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:2072-2080. (Pubitemid 34259655)
12. Colless, D. 1980. Congruence between morphometric and allozyme data for Menidia species - A reappraisal. Sys. Zool. 29:289-299.
13. Curgy, J., J. Vavra, and C. Vivares. 1980. Presence of ribosomal RNAs with prokaryotic properties in Microsporidia. Biol. Cell 38:49-52.
14. Darlu, P., and G. Lecointre. 2002. When does the incongruence length difference test fail? Mol. Biol. Evol. 19:432-437. (Pubitemid 34289418)
15. DePinna, M. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7:367-394.
16. Di Giulio, M. 2003a. The ancestor of the Bacteria domain was a hyperthermophile. J. Theor. Biol. 224:277-283. (Pubitemid 37297424)
17. Di Giulio, M. 2003b. The universal ancestor and the ancestor of bacteria were hyperthermophiles. J. Mol. Evol. 57:721-730. (Pubitemid 37543986)
18. Dolphin, K., R. Belshaw, C. D. Orme, and D. L. Quicke. 2000. Noise and incongruence: Interpreting results of the incongruence length difference test. Mol. Phylogenet. Evol. 17:401-406. (Pubitemid 32065244)
19. Dowton, M., and A. D. Austin. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy - The behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51:19-31. (Pubitemid 35169405)
20. Dutilh, B. E., M. A. Huynen, W. J. Bruno, and B. Snel. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol. 58:527-539. (Pubitemid 38609888)
21. Edlund, T, J. Li, G. Visvesvara, M. Vodkin, G. McLaughlin, and S. Katiyar. 1996. Phylogenetic analysis of beta-tubulin sequences from amitochondrial protozoa. Mol. Phylogenet. Evol. 5:359-367. (Pubitemid 126321176)
22. Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41:1105-1123. (Pubitemid 26020088)
23. Farris, J. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
24. Farris, J. 1994. Testing the Significance of Incongruence. Cladistics 10:315-319.
25. Farris, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18:374-385.
26. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
27. Fitz-Gibbon, S. T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-4222. (Pubitemid 29500255)
28. Germot, A., H. Philippe, and H. Le Guyader. 1997. Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol. Biochem. Parasitol. 87:159-168. (Pubitemid 27283278)
29. Goloboff, P. 1993. Estimating character weights during tree search. Cladistics 9:83-91.
30. Goloboff, P. 1997. Self-weighted optimization: Tree searches and character state reconstructions under implied transformation costs. Cladistics 13:225-245. (Pubitemid 127435640)
31. Gophna, U., W. F. Doolittle, and R. L. Charlebois. 2005. Weighted genome trees: Refinements and applications. J. Bacteriol. 187:1305-1316. (Pubitemid 40299455)
32. Grant, T., and A. Kluge. 2003. Data exploration in phylogenetic inference: Scientific, heuristic, or neither. Cladistics 19:379-418. (Pubitemid 37316981)
33. Gu, X., and H. Zhang. 2004. Genome phylogenetic analysis based on extended gene contents. Mol. Biol. Evol. 21:1401-1408. (Pubitemid 38823742)
34. Harlow, T. J., J. P. Gogarten, and M. A. Ragan. 2004. A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics 5:45.
35. Hennig, W. 1966. Phylogenetic systematics. Translated by D. Dwight Davis and Rainer Zangerl. Urbana, University of Illinois Press.
36. Hipp, A. L., J. C. Hall, and K. J. Sytsma. 2004. Congruence versus phylogenetic accuracy: Revisiting the incongruence length difference test. Syst. Biol. 53:81-89. (Pubitemid 38370422)
37. Hirt, R. P., B. Healy, C. R. Vossbrinck, E. U. Canning, and T. M. Embley. 1997. A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: Molecular evidence that microsporidia once contained mitochondria. Curr. Biol. 7:995-998. (Pubitemid 28017078)
38. Hirt, R. P., J. M. Logsdon, Jr., B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci. USA 96:580-585. (Pubitemid 29061251)
39. House, C. H., and S. T. Fitz-Gibbon. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: An update. J. Mol. Evol. 54:539-547. (Pubitemid 34271134)
40. Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer, and K. O. Stetter. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67. (Pubitemid 34498815)
41. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755. (Pubitemid 32851390)
42. Hughes, A., V. Ekollu, R. Friedman, and J. Rose. 2005. Gene family content-based phylogeny of prokaryotes: The effect of criteria for inferring homology. Syst. Biol. 54:268-276. (Pubitemid 40707807)
43. Huson, D. H., and M. Steel. 2004. Phylogenetic trees based on gene content. Bioinformatics 20:2044-2049. (Pubitemid 39236556)
44. Ishihara, R., and Y. Hayashi. 1968. Some properties of ribosomes from the sporoplasm of Nosema bombycis. J. Invert. Pathol. 11:377-385.
45. Kamaishi, T., T. Hashimoto, Y. Nakamura, Y. Masuda, F. Nakamura, K. Okamoto, M. Shimizu, and M. Hasegawa. 1996a. Complete nucleotide sequences of the genes encoding translation elongation factors 1 alpha and 2 from a microsporidian parasite, Glugea plecoglossi: Implications for the deepest branching of eukaryotes. J. Biochem. (Tokyo) 120:1095-1103.
46. Kamaishi, T., T. Hashimoto, Y. Nakamura, F. Nakamura, S. Murata, N. Okada, K. Okamoto, M. Shimizu, and M. Hasegawa. 1996b. Protein phylogeny of translation elongation factor EF-1 alpha suggests microsporidians are extremely ancient eukaryotes. J. Mol. Evol. 42:257-263. (Pubitemid 26102493)
47. Katinka, M. D., S. Duprat, E. Cornillot, G. Metenier, F. Thomarat, G. Prensier, V. Barbe, E. Peyretaillade, P. Brottier, P. Wincker, F. Delbac, H. El Alaoui, P. Peyret, W. Saurin, M. Gouy, J. Weissenbach, and C. P. Vivares. 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450-453. (Pubitemid 34173726)
48. Keeling, P. J. 2003. Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of Microsporidia. Fungal Genet. Biol. 38:298-309. (Pubitemid 36398176)
49. Keeling, P. J., and W. F. Doolittle. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13:1297-1305. (Pubitemid 26408935)
50. Kluge, A. 1969. Quantitative phyletics and the evolution of Anurans. Syst. Zool. 18:1-32.
51. Kluge, A. 2003. The repugnant and the mature in phylogenetic inference: A temporal similarity and historical identity. Cladistics 19:356-368. (Pubitemid 37084230)
52. Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984. (Pubitemid 39434418)
53. Krause, A., J. Stoye, and M. Vingron. 2005. Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 6:15.
54. Lake, J. A., E. Henderson, M. Oakes, and M. W. Clark. 1984. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl. Acad. Sci. USA 81:3786-3790. (Pubitemid 14087803)
55. Lake, J. A., and M. C. Rivera. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: Conditioned reconstruction. Mol. Biol. Evol. 21:681-690. (Pubitemid 38452101)
56. Lee, M. S. 2001. Uninformative characters and apparent conflict between molecules and morphology. Mol. Biol. Evol. 18:676-680. (Pubitemid 32268021)
57. Leipe, D. D., J. H. Gunderson, T. A. Nerad, and M. L. Sogin. 1993. Small subunit ribosomal RNA+ of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol. Biochem. Parasitol. 59:41-48.
58. Lin, J., and M. Gerstein. 2000. Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels. Genome Res. 10:808-818. (Pubitemid 30433354)
59. Marcotte, E. M., M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
60. Nixon, K. C. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414. (Pubitemid 30203167)
61. Overbeek, R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96:2896-2901. (Pubitemid 29148815)
62. Park, J., and S. A. Teichmann. 1998. DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics 14:144-150. (Pubitemid 28395873)
63. Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. 1999. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96:4285-4288. (Pubitemid 29190328)
64. Peyretaillade, E., V. Broussolle, P. Peyret, G. Metenier, M. Gouy, and C. P. Vivares. 1998. Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin. Mol. Biol. Evol. 15:683-689. (Pubitemid 28240673)
65. Popper, K. R. 1968. The logic of scientific discovery, 3d edition. Hutchinson, London.
66. Randau, L., R. Munch, M. J. Hohn, D. Jahn, and D. Soil. 2005. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433:537-541. (Pubitemid 40204312)
67. Rieppel, O., and M. Kearney. 2002. Similarity. Biol. J. Linn. Soc. 75:59-82.
68. Rivera, M. C, and J. A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74-76.
69. Rivera, M. C, and J. A. Lake. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155. (Pubitemid 39243461)
70. Rohlf, F. 1982. Consensus indices for comparing classifications. Math. Biosci. 59:131-144.
71. Siddall, M. E., and A. G. Kluge. 1999. Letter to the editor. Cladistics 15:429-440.
72. Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110. (Pubitemid 29036294)
73. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637. (Pubitemid 27464953)
74. Tatusov, R. L., D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram, B. S. Rao, B. Kiryutin, M. Y. Galperin, N. D. Fedorova, and E. V. Koonin. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28. (Pubitemid 32054398)
75. Tekaia, R, A. Lazcano, and B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550-557. (Pubitemid 29361271)
76. Thomarat, F, C. P. Vivares, and M. Gouy. 2004. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes. J. Mol. Evol. 59:780-791. (Pubitemid 40100874)
77. Vossbrinck, C. R., J. V. Maddox, S. Friedman, B. A. Debrunner-Vossbrinck, and C. R. Woese. 1987. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326:411-414. (Pubitemid 17053774)
78. Vossbrinck, C. R., and C. R. Woese. 1986. Eukaryotic ribosomes that lack a 5.8S RNA. Nature 320:287-288. (Pubitemid 16040248)
79. Waters, E., M. J. Hohn, I. Ahel, D. E. Graham, M. D. Adams, M. Barnstead, K. Y. Beeson, L. Bibbs, R. Bolanos, M. Keller, K. Kretz, X. Lin, E. Mathur, J. Ni, M. Podar, T. Richardson, G. G. Sutton, M. Simon, D. Soil, K. O. Stetter, J. M. Short, and M. Noordewier. 2003. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 100:12984-12988. (Pubitemid 37340012)
80. Wheeler, W. 1995. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44:321-341.
81. Wheeler, W. 2001. Homology and the optimization of DNA sequence data. Cladistics 17:S3-S11. (Pubitemid 32430561)
82. Wheeler, W. C, J. Gatesy, and R. DeSalle. 1995. Elision: A method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites. Mol. Phylogenet. Evol. 4:1-9.
83. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
84. Wolf, M., T. Muller, T. Dandekar, and J. D. Pollack. 2004. Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int. J. Syst. Evol. Microbiol. 54:871-875. (Pubitemid 38771793)
85. Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet 18:472-479.
86. Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tacusov, and E. V. Koonin. 2001a. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8.
87. Wolf, Y. I., I. B. Rogozin, A. S. Kondrashov, and E. V. Koonin. 2001b. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:356-372. (Pubitemid 32243846)
88. Yang, S., R. F. Doolittle, and P. E. Bourne. 2005. Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. USA 102:373-378. (Pubitemid 40116774)
89. Yoder, A. D., J. A. Irwin, and B. A. Payseur. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50:408-424.