RY-coding and non-homogeneous models can ameliorate the maximum-likelihood inferences from nucleotide sequence data with parallel compositional heterogeneity

Evolutionary Bioinformatics

Volumn 2012, Issue 8, 2012, Pages 357-371

  Ishikawa, Sohta A ^a   Inagaki, Yuji ^a   Hashimoto, Tetsuo ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Compositional heterogeneity; Long branch attraction; Model misspecification; Non homogeneous model; RY coding

Indexed keywords

PURINE; PYRIMIDINE;

AMINO ACID SUBSTITUTION; ARTICLE; DNA BASE COMPOSITION; MAXIMUM LIKELIHOOD METHOD; MODEL; MONTE CARLO METHOD; NON HOMOGENOUS MODEL; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMULATION;

EID: 84863632996     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S9017     Document Type: Article

References (33)

1. Philippe H. Opinion: long branch attraction and protest phylogeny. Protist. 2000;151:307-16.
2. Huelsenbeck JP. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol. 1995;12:843-9.
3. Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Roger JS. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol. 2001;50:525-39.
4. Hasegawa M, Hashimoto T. Ribosomal RNA trees misleading? Nature. 1993;361:23.
5. Foster PG, Hickey DA. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol. 1999;48:284-90.
6. Chang BSW, Campbell DL. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol Biol Evol. 2000;17:1220-31.
7. Mooers A, Holmes EC. The evolution of base composition and phylogenetic inference. Trends Ecol Evol. 2000;15:365-9.
8. Tarrio R, Rodríguez-Trelles F, Ayala FJ. Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. Mol Biol Evol. 2001;18:1464-73.
9. Galtier N, Gouy M. Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A. 1995;92:11317-21.
10. Conant GC, Lewis PO. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol Biol Evol. 2001;18:1024-33.
11. Ho SYW, Jermiin LS. Tracing the decay of the historical signal in biological sequence data. Syst Biol. 2004;53:623-37.
12. Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol. 2004;53:637-43.
13. Lockhart PJ, Steel MA, Hendy MD, Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol. 1994;11:605-12.
14. Steel MA. Recovering a tree from the leaf colourations it generates under a Markov model. Appl Math Lett. 1994;7:19-23.
15. Rodriguez-Trelles F, Tarrio R, Ayala FJ. Fluctuating mutation bias and the evolution of base composition in Drosophila. J Mol Evol. 2000;50:1-10.
16. Singh ND, Arndt PF, Clark AG, Aquadro CF. Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol. 2009;26:1591-605.
17. Inagaki Y, Simpson AGB, Dacks JB, Roger AJ. Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origin as a case study. Syst Biol. 2004;53:582-93.
18. Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. 2007;56:389-99.
19. Phillips MJ, Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol. 2003;28:171-85.
20. Phillips MJ, Delsuc F, Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol. 2004;21:1455-8.
21. Cavender JA, Felsenstein J. Invariants of phylogenies in a simple case with discrete states. J Classif. 1987;4:57-71.
22. Galtier N, Gouy M. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 1998;15:871-9.
23. Strope CL, Abel K, Scott SD, Moriyama EN. Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen Version 2.0. Mol Biol Evol. 2009;26:2581-93.
24. Hasegawa M, Kishino H, Yano T. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:160-74.
25. Swofford DL. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4 beta 10. Sinauer Associates, Sunderland, Mass; 2003.
26. Galtier N, Tourasse N, Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Science. 1999;83:220-1.
27. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307-21.
28. Janouškovec J, Horák A, Oborník M, Lukeš J, Keeling PJ. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci U S A. 2010;107:10949-54.
29. Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H. Additional molecular support for the new chordate phylogeny. Genesis. 2008;46:592-604.
30. Herbeck JT, Degnan PH, Wernegreen JJ. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (w-Proteobacteria). Mol Biol Evol. 2004;22: 520-32.
31. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and GaC-content biases. Mol Biol Evol. 1992;9:678-87.
32. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A. 2008;105:20356-61.
33. Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Biotttsuite of libraries and programs. BMC Evol Biol. 2008;8:255-5.