Spatial and temporal heterogeneity in nucleotide sequence evolution

Molecular Biology and Evolution

Volumn 25, Issue 8, 2008, Pages 1683-1694

  Whelan, Simon ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Covarion; Heterogeneity; Heterotachy; Maximum likelihood; Phylogenetics; Temporal hidden Markov models

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; GENE SEQUENCE; GENETIC HETEROGENEITY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC HETEROGENEITY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 47649095950     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn119     Document Type: Article

References (40)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
2. Ané C, Burleigh JG, McMahon MM, Sanderson MJ. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol. 22:914-924.
3. Barry D, Hartigan JA. 1987. Asynchronous distances between homologous DNA sequences. Biometrics. 43:261-276.
4. Chang BS, Jönsson K, Kazmi MA, Donoghue MJ, Sakmar TP. 2002. Recreating a functional ancestral archosaur visual pigment. Mol Biol Evol. 19:1483-1489.
5. Fares MA, Travers SAA. 2006. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraint analyses. Genetics. 173:9-23.
6. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
7. Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol. 17:368-376.
8. Galtier N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol. 18:866-873.
9. Galtier N, Gouy M. 1998. Inferring pattern and process: maximum likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 15:871-879.
10. Gruenheit N, Lockhart PJ, Steel M, Martin W. 2008. Difficulties in Testing for Covarion-Like Properties of Sequences Under the Confounding Influence of Changing Proportions of Variable Sites. Mol Biol Evol. doi:10.1093/molbev/msn098.
11. Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc Natl Acad Sci USA. 101:12957-12962.
12. Hasegawa M, Hashimoto T. 1993. Ribosomal RNA trees misleading? Nature. 361:23.
13. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
14. Herbeck JT, Degnan PH, Wernegreen JJ. 2005. Nonhomogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts Within the Enterobacteriales (γ-Proteobacteria). Mol Biol Evol. 22:520-532.
15. Huelsenbeck JP. 2002. Testing a covariotide model of DNA substitution. Mol Biol Evol. 19:698-707.
16. Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature. 431:980-984.
17. Kosiol C, Bofkin L, Whelan S. 2006. Phylogenetics by likelihood: evolutionary modelling as a tool for understanding the genome. J Biomed Inform. 39:51-61.
18. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109.
19. Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7.
20. Matsen FA, Steel M. 2007. Phylogenetic mixtures on a single tree can mimic a tree of another topology. Syst Biol. 56:767-775.
21. Pagel M, Meade A. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol. 53:571-581.
22. Rodrigue N, Philippe H, Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol. 23:1762-1775.
23. Self SG, Liang K-L. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Am Stat Assoc. 82:605-610.
24. Siepel A, Bejerano G, Pedersen JS, et al. (16 co-authors). 2005. Evolutionarily conserved elements in vertebrate insect, worm, and yeast genomes. Genome Res. 15:1034-1050.
25. Soyer OS, Goldstein RA. 2004. Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. J Mol Biol. 339:227-242.
26. Thorne JL, Goldman N, Jones DT. 1996. Combining protein evolution and secondary structure. Mol Biol Evol. 13:666-673.
27. Tuffley C, Steel M. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math Biosci. 147:63-91.
28. Wang HC, Spencer M, Susko E, Roger AJ. 2007. Testing for covarion-like evolution in protein sequences. Mol Biol Evol. 24:294-305.
29. Whelan S. 2007. New approaches to phylogenetic tree search and their application to large numbers of protein alignments. Syst Biol. 56:727-740.
30. Whelan S, de Bakker PIW, Quevillon E, Rodriguez N, Goldman N. 2006. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 34:D327-D331.
31. Whelan S, Goldman N. 1999. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics. Mol Biol Evol. 16:1292-1299.
32. Whelan S, 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.
33. Whelan S, Lió P, Goldman N. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17:262-272.
34. Yang Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401.
35. Yang Z. 1994. Estimating the pattern of nucleotide substitution. J Mol Evol. 39:105-111.
36. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 11:367-372.
37. Yang Z. 1995. A space-time process model for the evolution of DNA sequences. Genetics. 139:993-1005.
38. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS. 13:555-556.
39. Yang Z, Bielawski J. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15:496-503.
40. Yang Z, Roberts D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol Biol Evol. 12:451-458.