Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

Genome Research

Volumn 17, Issue 12, 2007, Pages 1932-1942

  Rasmussen, Matthew D ^a   Kellis, Manolis ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; DROSOPHILA; FUNGAL GENETICS; GENETIC ANALYSIS; INSECT GENETICS; NONHUMAN; ORTHOLOGY; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SPECIES DIVERSITY; SYNTENY; ANIMAL; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; FUNGAL GENE; GENE; GENETICS; GENOME; GENOMICS; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

ANIMALS; ARTIFICIAL INTELLIGENCE; DROSOPHILA; EVOLUTION, MOLECULAR; GENES, FUNGAL; GENES, INSECT; GENOME; GENOMICS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY; SYNTENY;

EID: 38849160068     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.7105007     Document Type: Article

References (81)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Ané, C., Larget, B., Baum, D.A., Smith, S.D., and Rokas, A. 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24: 412-426.
3. Arvestad, L., Berglund, A., Lagergren, J., and Sennblad, B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, pp. 326-335.
4. Avise, J.C., Shapira, J., Daniel, S.W., Aquadro, C.F., and Lansman, R.A. 1983. Mitochondrial DNA differentiation during the speciation process in Peromyscus. Mol. Biol. Evol. 1: 38-56.
5. Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., and Doolittle, W.F. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.
6. Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21: 163-193.
7. Bromham, L. and Penny, D. 2003. The modern molecular clock. Nat. Rev. Genet. 4: 216-224.
8. Bryant, D. and Waddell, P. 1998. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Mol. Biol. Evol. 15: 1346-1359.
9. Bull, J.J., Badgett, M.R., Wichman, H.A., Huelsenbeck, J.P., Hillis, D.M., Gulati, A., Ho, C., and Molineux, I.J. 1997. Exceptional convergent evolution in a virus. Genetics 147: 1497-1507.
10. Byrne, K.P. and Wolfe, K.H. 2005. The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15: 1456-1461.
11. Cannarozzi, G.M., Schneider, A., and Gonnet, G. 2006. A phylogenomic study of human, dog and mouse. PLoS Computat. Biol. e2.eor. doi: http://dx.doi.org/10.1371/journal.pcbi.0030002.eor.
12. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
13. Ciccarelli, F.D., Doerks, T., v. Mering, C., Creevey, C.J., Snel, B., and Bork, P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
14. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
15. Cooper, G.M., Brudno, M., Program, N.I.S.C.C.S., Green, E.D., Batzoglou, S., and Sidow, A. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13: 813-820.
16. Dehal, P. and Boore, J.L. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3: e314. doi: 10.1371/journal.pbio.0030314.
17. Dickerson, R.E. 1971. The structures of cytochrome c and the rates of molecular evolution. J. Mol. Evol. 1: 26-45.
18. Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pöhlmann, R., Luedi, P., Choi, S., et al. 2004. Comparison of the sequence of laboratory yeast to that of a distant relative, a small filamentous fungus, reveals that yeast evolved via genome duplication and separate evolution of homologous genes. Science 9: 304-307.
19. Drosophila 12 Genomes Consortium. 2007. Genomics on phylogeny: Evolution of genes and genomes in the genus Drosophila. Nature (in press). doi: 10.1038/nature06341.
20. Dufayard, J.-F., Duret, L., Penel, S., Gouy, M., Rechenmann, F., and Perriere, G. 2005. Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 21: 2596-2603.
21. Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., de Montigny, J., Marck, C., Neuvéglise, C., Talla, E., et al. 2004. Genome evolution in yeasts. Nature 430: 35-44.
22. Durand, D., Halldorsson, B.V., and Vernot, B. 2006. A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13: 320-335.
23. Edgar, R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
24. Edwards, S.V., Liu, L., and Pearl, D.K. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. 104: 5936-5941.
25. Eisen, J.A. 1998. Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8: 163-167.
26. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
27. Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington,
28. Felsenstein, J. and Churchill, G.A. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13: 93-104.
29. Fitch, W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99-113.
30. Gadagkar, S.R., Rosenberg, M.S., and Kumar, S. 2005. Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. J. Exp. Zoolog. B Mol. Dev. Evol. 304: 64-74.
31. Gascuel, O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14: 685-695.
32. Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., and Matsuda, G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28: 132-163.
33. Guindon, S. and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704.
34. Hahn, M. 2007. Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution. Genome Biol. 8: R141. doi: 10.1186/gb-2007-8-7-r141.
35. Hahn, M.W., Han, M.V., and Han, S.-G. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3: e197.
36. Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
37. Hillis, D.M., Huelsenbeck, J.P., and Cunningham, C.W. 1994. Application and accuracy of molecular phylogenies. Science 264: 671-677.
38. Hittinger, C.T., Rokas, A., and Carroll, S.B. 2004. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc. Natl. Acad. Sci. 101: 14144-14149.
39. Huelsenbeck, J. 1995. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12: 843-849.
40. Huelsenbeck, J.P. and Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
41. Huerta-Cepas, J., Dopazo, H., Dopazo, J., and Gabaldon, T. 2007. The human phylome. Genome Biol. 8: R109. doi: 10.1186/gb-2007-8-6- r109.
42. Jaillon, O., Aury, J.M., Brunet, F., Petit, J.L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
43. Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
44. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
45. Kellis, M., Birren, B.W., and Lander, E.S. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
46. Kim, S.Y. and Pritchard, J.K. 2007. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet. 3: e147. doi: 10.1371/journal.pgen.0030147.
47. Koonin, E.V., Makarova, K.S., and Aravind, L. 2001. Horizontal gene transfer in prokaryotes: Quantification and classification. Annu. Rev. Microbiol. 55: 709-742.
48. Kriegs, J.O., Churakov, G., Kiefmann, M., Jordan, U., Brosius, J., and Schmitz, J. 2006. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4: e91. doi: 10.1371/journal. pbio.0040091.
49. Kuhner, M.K. and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11: 459-468.
50. Li, H., Coghlan, A., Ruan, J., Coin, L.J., Heriche, J.-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., et al. 2006. TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34: D572-D580. doi: 10.1093/nar/gkj118.
51. Lynch, M. and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
52. Ma, B., Kowloon, H., Li, M., Waterloo, O., Zhang, L., and Center, B. 2000. From gene trees to species trees. SIAM J. Comput. 30: 729-752.
53. Miller, W., Makova, K.D., Nekrutenko, A., and Hardison, R.C. 2004. Comparative genomics. Annu. Rev. Genomics Hum. Genet. 5: 15-56.
54. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
55. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., and O'Brien, S.J. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.
56. Ohta, T. and Kimura, M. 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1: 18-25.
57. Page, R. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43: 58-77.
58. Page, R.D. and Charleston, M.A. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7: 231-240.
59. Philippe, H., Zhou, Y., Brinkmann, H., Rodrigue, N., and Delsuc, F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 5: 50. doi: 10.1186/1471-2148-5-50.
60. Pollard, D.A., Iyer, V.N., Moses, A.M., and Eisen, M.B. 2006. Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. PLoS Genet. 2: e173. doi: 10.1371/journal.pgen.0020173.
61. Richards, S., Liu, Y., Bettencourt, B.R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M.J., Chen, R., Meisel, R.P., et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18.
62. Robinson, D.F. and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53: 131-147.
63. Rokas, A., Williams, B.L., King, N., and Carroll, S.B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
64. Ronquist, F. and Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
65. Saitou, N. and Imanishi, T. 1989. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6: 514-525.
66. Schmidt, H.A., Strimmer, K., Vingron, M., and v. Haeseler, A. 2002. TREE-PUZZLE: Maximum-likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
67. Shimodaira, H. and Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16: 1114-1116.
68. Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-1050.
69. Stark, A., Lin, M.F., Kheradpour, P., Pedersen, J.S., Parts, L., Carlson, J.W., Crosby, M.A., Rasmussen, M.D., Roy, S., Deoras, A.N., et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (in press). doi: 10.1038/nature06340.
70. Storm, C.E.V. and Sonnhammer, E.L.L. 2003. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res. 13: 2353-2362.
71. Stoye, J., Evers, D., and Meyer, F. 1998. Rose: Generating sequence families. Bioinformatics 14: 157-163.
72. Tateno, Y., Takezaki, N., and Nei, M. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11: 261-277.
73. Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4: 251-262.
74. Uzzell, T. and Corbin, K.W. 1971. Fitting discrete probability distributions to evolutionary events. Science 172: 1089-1096.
75. Woese, C.R., Kandler, O., and Wheelis, M.L. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. 87: 4576-4579.
76. Wolfe, K.H. and Shields, D.C. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
77. Wong, A., Jensen, J.D., Pool, J.E., and Aquadro, C.F. 2007. Phylogenetic incongruence in the Drosophila melanogaster species group. Mol. Phylogenet. Evol. 43: 1138-1150.
78. Woods, R., Schneider, D., Winkworth, C.L., Riley, M.A., and Lenski, R.E. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. 103: 9107-9112.
79. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39: 306-314.
80. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
81. Zmasek, C.M. and Eddy, S.R. 2002. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3: 14. doi: 10.1186/1471-2105-3-14.