A simulation test bed for hypotheses of genome evolution

Bioinformatics

Volumn 23, Issue 7, 2007, Pages 825-831

  Beiko, Robert G ^a,b   Charlebois, Robert L ^c,d  

^a DALHOUSIE UNIVERSITY   (Canada)

^b Australian Government Australian Research Council   (Australia)

^c DALHOUSIE UNIVERSITY   (Canada)

^d Sanofi Pasteur   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; GENE SEQUENCE; GENE TRANSFER; GENOME; HYPOTHESIS; MICROORGANISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; SIMULATION; SPECIES DIFFERENTIATION; SPECIES EXTINCTION; STATISTICAL ANALYSIS; VALIDATION PROCESS; BACTERIAL GENOME; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; GENETICS; METHODOLOGY;

PROTEOME;

CHROMOSOME MAPPING; COMPUTER SIMULATION; EVOLUTION; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MODELS, GENETIC; PROTEOME; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 34248572619     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm024     Document Type: Article

References (68)

1. Ababneh,F. et al. (2006) Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22, 1225-1231.
2. Addario-Berry,L. et al. (2003) Ancestral maximum likelihood of evolutionary trees is hard. Lect. N. Bioinformatics, 2812, 202-215.
3. Azad,R.K. and Lawrence,J.G. (2005) Use of artificial genomes in assessing methods for atypical gene detection. PLoS Comput. Biol., 1, e56.
4. Beiko,R.G. et al. (2005) Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA, 102, 14332-14337.
5. Bentley,S.D. and Parkhill,J. (2004) Comparative genomic structure of prokaryotes. Annu. Rev. Genet., 38, 771-792.
6. Blouin,C. et al. (2005) Impact of taxon sampling on the estimation of rates of evolution at sites. Mol. Biol. Evol., 22, 784-791.
7. Cambillau,C. and Claverie,J.M. (2000) Structural and genomic correlates of hyperthermostability. J. Biol. Chem., 275, 32383-32386.
8. Colless,D.H. (1995) Relative symmetry of cladograms and phenograms - an experimental-study. Syst. Biol., 44, 102-108.
9. Doolittle,R.F. and Handy,J. (1998) Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr. Opin. Genet. Dev., 8, 630-636.
10. Echols,N. et al. (2002) Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res., 30, 2515-2523.
11. 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.
12. Foerstner,K.U. et al. (2005) Environments shape the nucleotide composition of genomes. EMBO Rep., 6, 1208-1213.
13. Futuyma,D.J. and Moreno,G. (1988) The evolution of ecological specialization. Annu. Rev. Ecol. Syst., 19, 207-233.
14. Gogarten,J.P. and Townsend,J.P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol., 3, 679-687.
15. Gogarten,J.P. et al. (2002) Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol., 19, 2226-2238.
16. Gould,S.J. et al. (1977) The shape of evolution: A comparison of real and random clades. Paleobiology, 3, 23-40.
17. Heard,S.B. (1992) Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution, 46, 1818-1826.
18. Hendrickson,H. and Lawrence,J.G. (2006) Selection for chromosome architecture in bacteria. J. Mol. Evol., 62, 615-629.
19. Hickey,D.A. and Singer,G.A. (2004) Genomic and proteomic adaptations to growth at high temperature. Genome Biol., 5, 117.
20. Itoh,T. et al. (2002) Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc. Natl. Acad. Sci. USA, 99, 12944-12948.
21. Jain,R. et al. (1999) Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. USA, 96, 3801-3806.
22. Jain,R. et al. (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol., 20, 1598-1602.
23. Jermiin,L.S. et al. (2003) Hetero: A program to simulate the evolution of DNA on a four-taxon tree. Appl. Bioinformatics, 2 159-163.
24. Jordan,I.K. et al. (2001) Lineage-specific gene expansions in bacterial and archaeal genomes. Genome. Res., 11, 555-565.
25. Karev,G.P. et al. (2002) Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol. Biol., 2, 18.
26. Karev,G.P. et al. (2003) Simple stochastic birth and death models of genome evolution: Was there enough time for us to evolve? Bioinformatics, 19, 1889-1900.
27. Karev,G.P. et al. (2004) Gene family evolution: An in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol. Biol., 4, 32.
28. Kassen,R. (2002) The experimental evolution of specialists, generalists, and the maintenance of diversity. J. Evol. Biol., 15, 173-190.
29. Kendall,D.G. (1948) On the generalized birth-and-death process. Ann. Math. Stat., 19, 1-15.
30. Kunin,V. and Ouzounis,C.A. (2003) The balance of driving forces during genome evolution in prokaryotes. Genome. Res., 13, 1589-1594.
31. Lawrence,J.G. and Ochman,H. (1997) Amelioration of bacterial genomes: rates of change and exchange. Mol. Evol., 44, 383-397.
32. Lawrence,J.G. and Ochman,H. (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA, 95, 9413-9417.
33. Lawrence,J.G. and Roth,J.R. (1999) Genomic flux: Genome evolution by gene loss and acquisition. In: Charlebois,R.L. (ed.) Organization of the Prokaryotic Genome. ASM Press, Washington, D.C.
34. Lio,P. and Goldman,N. (1998) Models of molecular evolution and phylogeny. Genome. Res., 8, 1233-1244.
35. Lockhart,P.J. et al. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol., 11, 605-612.
36. Merkl,R. (2003) A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J. Mol. Evol. 57, 453-466.
37. Milkman,R. and Bridges,M.M. (1990) Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics, 126 505-517.
38. Mooers,A.O. and Heard,S.B. (1997) Evolutionary process from phylogenetic tree shape. Q. Rev. Biol., 72, 31-54.
39. Moran,N.A. (1996) Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA, 93, 2873-2878.
40. Nakamura,Y. et al. (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36, 760-766.
41. Pang,A. et al. (2005) SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics, 6, 236.
42. Pybus,O.G. and Harvey,P.H. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. Biol. Sci., 267 2267-2272.
43. Rabosky,D.L. (2006) Likelihood methods for detecting temporal shifts in diversification rates. Evolution, 60, 1152-1164.
44. Ragan,M.A. (2001) Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev., 11, 620-626.
45. Ragan,M.A. et al. (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol., 14, 4-8.
46. Rambaut,A. and Grassly,N.C. (1997) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13, 235-238.
47. Rambaut,A. et al. (1996) Bi-De: An application for simulating phylogenetic processes. Comput. Appl. Biosci., 12, 469-471.
48. Raup,D.M. et al. (1973) Stochastic models of phylogeny and the evolution of diversity. J. Geol., 81, 525-542.
49. Ree,R.H. (2005) Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution, 59, 257-265.
50. Rispe,C. et al. (2004) Mutational and selective pressures on codon and amino acid Usage in Buchnera, endosymbiotic bacteria of aphids. Genome. Res., 14, 44-53.
51. Sharp,P.M. et al. (2005) Variation in the strength of selected codon USAge bias among bacteria. Nucleic Acids Res., 33, 1141-1153.
52. Singer,G.A. and Hickey,D.A. (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol., 17, 1581-1588.
53. Sinha,N. and Nussinov,R. (2001) Point mutations and sequence variability in proteins: Redistributions of preexisting populations. Proc. Natl. Acad. Sci. USA, 98, 3139-3144.
54. Stiller,J.W. and Hall,B.D. (1999) Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol., 16, 1270-1279.
55. Stoye,J. et al. (1998) Rose: Generating sequence families. Bioinformatics, 14, 157-163.
56. Sullivan,J. and Swofford,D.L. (1997) Are guinea pigs rodents? the importance of adequate models in molecular phylogenetics. J. Mammal. Evol., 4, 77-86.
57. Tavaré, S. (1986) Some probabilistic and statistical problems on the analysis of DNA sequences. In: Lectures in Mathematics in the Life Sciences; American Mathematical Society, New York City, USA, pp. 57-86.
58. Thorne,J.L. et al. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. Mol. Evol., 33, 114-124.
59. Wang,H.C. et al. (2001) Analysis of codon USAge patterns of bacterial genomes using the self-organizing map. Mol. Biol. Evol., 18, 792-800.
60. Whelan,S. and Goldman,N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
61. Yampolsky,L.Y. and Stoltzfus,A. (2005) The exchangeability of amino acids in proteins. Genetics, 170, 1459-1472.
62. Yang,Z. (1993) Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10, 1396-1401.
63. Yang,Z. (1995) A space-time process model for the evolution of DNA sequences. Genetics, 139, 993-1005.
64. Yang,Z. (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci., 13, 555-556.
65. Yang,Z. et al. (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol., 11, 316-324.
66. Yule,G.U. (1924) A mathematical theory of evolution, based on the conclusions of Dr J.C. Willis. Phil. Trans. R. Soc. Lond., B, 213, 21-87.
67. Zhang,J. (2003) Evolution by gene duplication: An update. Trends. Ecol. Evol., 18, 292-298.
68. Zhaxybayeva,O. et al. (2006) Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res., 16, 1099-110