Improving phylogenetic inference with a semiempirical amino acid substitution model

Molecular Biology and Evolution

Volumn 30, Issue 2, 2013, Pages 469-479

  Zoller, Stefan ^a,b   Schneider, Adrian ^c  

^a ETH ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Amino acid substitution model; Atlantogenata; Markov model; Origin of mammals; Principal component analysis; Semiempirical substitution model

Indexed keywords

AMINO ACID;

AFROTHERIA; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ATLANTOGENATA; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; GENETIC CODE; INFERENTIAL STATISTICS; MAMMAL; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL MODEL; VARIANCE; XENARTHRA; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC DATABASE; GENETICS; HUMAN; MOLECULAR EVOLUTION;

AMINO ACID SUBSTITUTION; ANIMALS; COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; HUMANS; MAMMALS; MODELS, GENETIC; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS;

MLCS; MLOWN;

EID: 84879304797     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss229     Document Type: Article

References (39)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automatic Control. 19: 716-723.
2. Burnham K, Anderson D. 2002. Model selection and multimodel inference: a practical information-theoretic approach. New York Springer Verlag.
3. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17: 540.
4. Dayhoff MO, Schwartz RM, Orcutt BC 1978. A model for evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure, Vol. 5. Washington (DC): National Biomedical Research Foundation, p. 345-352.
5. Dessimoz C Cannarozzi G, Gil M, Margadant D, Roth A, Schneider A, Gonnet G. 2005. OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: introduction and first achievements. Lect Notes Comput Sci. 3678: 61-72.
6. Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11: 725-736.
7. Gonnet G, Cohen M, Benner S. 1992. Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445.
8. Guindon S, Delsuc F, Dufayard J., Gascuel O. 2009. Estimating maximum likelihood phytogenies with PhyML Methods Mol Biol. 537: 113-137.
9. Hallström B., Kullberg M, Nilsson M., Janke A. 2007. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol Biol Evol. 24: 2059-2068.
10. Halpern A, Bruno W. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol Biol Evol. 15: 310-917.
11. Hurvich C, Tsai G 1989. Regression and time series model selection in small samples. Biometrika 76: 297-307.
12. Jones D, Taylor W, Thornton J. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8: 275-282.
13. Katoh K, Kuma K, Toh H., Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
14. Kawashima S, Pokarowski P, Pokarowska M., Kolinski A, Katayama T, Kanehisa M. 2008. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36(SUPPL. 1):D202-D205.
15. Klosterman PS, Uzilov AV, Bendana Y.R., Bradley RK, Chao S, Kosiol C Goldman N, Holmes I. 2006. Xrate a fast prototyping, training and annotation tool for phylo-grammars BMC Bioinformatics 7: 428.
16. Koshi J, Goldstein R. 1998. Models of natural mutations including site heterogeneity. Proteins 32: 289-295.
17. 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.
18. Le S, Dang C Gascuel O. 2012. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol. 29: 2921-2936.
19. Le S, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25: 1307-1320.
20. Le S, Gascuel O. 2010. Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial. Syst Biol. 59: 277-287.
21. Le S, Lartillot N, Gascuel O. 2008. Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci. 363: 3965-3976.
22. Murphy W, Eizirik E, O'Brien S, et al. (11 co-authors). 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
23. Murphy WJ, Pringle TH, Crider T.A., Springer MS, Miller W. 2007. Using genomic data to unravel the root of the placental mammal phyl-ogeny. Genome Res. 17: 413-421.
24. Murrell B, Weighill T, Buys J., Ketteringham R, Moola S, Benade G., du Buisson L, Kaliski D, Hands T., Scheffler K. 2011. Non-negative matrix factorization for learning alignment-specific models of protein evolution. PLoS One 6:e28898.
25. Nikolaev S, Montoya-Burgos JI, Margulies E.H., NISC Comparative Sequencing Program, Rougemont J, Nyffeler B, Antonarakis SE 2007. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet 3:e2
26. Novacek MJ. 1992. Mammalian phytogeny: shaking the tree. Nature 356: 121-125.
27. Pagel M, Meade A. 2005. Mixture models in phylogenetic inference. In: Gascuel O, editor. Mathematics of evolution and phylogeny. Oxford (United Kingdom): Oxford University Press, p. 121-142.
28. Prasad A, Allard M, Green E. 2008. Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol. 25: 1795-1808.
29. Schneider A, Cannarozzi G. 2009. Support patterns from different out-groups provide a strong phylogenetic signal. Mol Biol Evol. 26: 1259-1272.
30. Shoemaker J, Fitch W. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol. 6: 270-289.
31. Shoshani J, McKenna M. 1998. Higher taxonomie relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol Phylogenet Evol. 9: 572-584.
32. Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 17: 57-86.
33. Thorne J, Goldman N, Jones D. 1996. Combining protein evolution and secondary structure. Mol Biol Evol. 13: 666-673.
34. Waters P, Dobigny G, Waddell P., Robinson T. 2007. Evolutionary history of LINE-1 in the major clades of placental mammals. PLoS One 2: e158.
35. Whelan S, de Bakker P, Goldman N. 2003. Pandic a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19: 1556-1563.
36. 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.
37. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites approximate methods. J Mol Evol. 39: 306-314.
38. Zoller S, Schneider A. 2010. Empirical analysis of the most relevant parameters of codon substitution models. J Mol Evol. 70: 605-612.
39. Zoller S, Schneider A. 2012. A new semiempirical codon substitution model based on principal component analysis of mammalian sequences. Mol Biol Evol. 29: 271-277.