Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny

Gene

Volumn 390, Issue 1-2, 2007, Pages 75-83

  Arndt, Peter F ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Ancient DNA reconstruction; CpG effect; Nucleotide substitution; Phylogeny

Indexed keywords

ALGORITHM; ARTICLE; CPG ISLAND; DEAMINATION; HUMAN; METHYLATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLESIOMORPHY; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; BASE COMPOSITION; CPG ISLANDS; DNA; DOGS; EVOLUTION, MOLECULAR; HUMANS; LIKELIHOOD FUNCTIONS; MICE; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; SEQUENCE ALIGNMENT;

CANIS FAMILIARIS;

EID: 33846905201     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.11.022     Document Type: Article

References (40)

1. Arndt P.F., and Hwa T. Identification and measurement of neighbor dependent nucleotide substitution processes. Bioinformatics 21 (2005) 2322-2328
2. Arndt P.F., Burge C.B., and Hwa T. DNA sequence evolution with neighbor-dependent mutation. J Comput. Biol. 10 (2003) 313-322
3. Arndt P.F., Petrov D.A., and Hwa T. Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Mol. Biol. Evol. 20 11 (2003) 1887-1896
4. Arndt P.F., Hwa T., and Petrov D.A. Substantial regional variations in the substitution rates in the human genome: importance of the GC-content, gene density and telomere-specific effects. J. Mol. Evol. 60 (2005) 748-763
5. Barry D., and Hartigan J.A. Statistical analysis of hominoid molecular evolution. Stat. Sci. 2 2 (1987) 191-210
6. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene 241 1 (2000) 3-17
7. Bollback J.P. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19 7 (2002) 1171-1180
8. Box M.J. A comparison of several current optimization methods and use of transformations in constrained problems. Comput. J. 9 1 (1966) 67-77
9. Chang J.T. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci. 137 1 (1996) 51-73
10. Collins T.M., Wimberger P.H., and Naylor G.J.P. Compositional bias, character state bias and character state reconstruction using parsimony. Syst. Biol. 43 4 (1994) 482-496
11. Coulondre C., et al. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274 5673 (1978) 775-780
12. Duret L., et al. Vanishing GC-rich isochores in mammalian genomes. Genetics 162 4 (2002) 1837-1847
13. Easteal S. Molecular evidence for the early divergence of placental mammals. Bioessays 21 12 (1999) 1052-1058 (discussion 1059)
14. Eyre-Walker A. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47 6 (1998) 686-690
15. Eyre-Walker A., and Hurst L.D. The evolution of isochores. Nat. Rev., Genet. 2 7 (2001) 549-555
16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 6 (1981) 368-376
17. Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 5 (1994) 725-736
18. Hedges S.B., Parker P.H., Sibley C.G., and Kumar S. Continental breakup and the ordinal diversification of birds and mammals. Nature 381 6579 (1996) 226-229
19. Holder M., and Lewis P.O. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev., Genet. 4 4 (2003) 275-284
20. Huelsenbeck J.P., and Bollback J.P. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50 3 (2001) 351-366
21. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 8 (2001) 754-755
22. Huelsenbeck J.P., Ronquist F., Nielsen R., and Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 5550 (2001) 2310-2314
23. Hwang D.G., and Green P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl. Acad. Sci. U. S. A. 101 39 (2004) 13994-14001
24. Krishnan N.M., et al. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference. Mol. Biol. Evol. 21 10 (2004) 1871-1883
25. Lio P., and Goldman N. Models of molecular evolution and phylogeny. Genome Res. 8 (1998) 1233-1244
26. Lunter G., and Hein J. A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics 20 Suppl. 1 (2004) I216-I223
27. McLachlan G.J., and Krishnan T. The EM Algorithm and Extensions (1997), John Wiley & Sons, Inc, New York
28. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 5 (1986) 418-426
29. Pedersen A.-M.K., and Jensen J.L. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol. 18 (2001) 763-776
30. Perna N., and Kocher T. Unequal base frequencies and the estimation of substitution rates. Mol. Biol. Evol. 12 2 (1995) 359-361
31. Press W.H., et al. Numerical Recipes in C. The Art of Scientific Computing (1992), Cambridge University Press, Cambridge
32. Siepel A., and Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol. 11 2-3 (2004) 413-428
33. Siepel A., and Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21 3 (2004) 468-488
34. Uzzell T., and Corbin K.W. Fitting discrete probability distributions to evolutionary events. Science 172 988 (1971) 1089-1096
35. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 6915 (2002) 520-562
36. Whelan S., and Goldman N. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167 4 (2004) 2027-2043
37. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 3 (1994) 306-314
38. Yang Z. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39 1 (1994) 105-111
39. Yang Z., Goldman N., and Friday A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11 2 (1994) 316-324
40. Zuckerkandl E., and Pauling L. Molecules as documents of evolutionary history. J. Theor. Biol. 8 2 (1965) 357-366