Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes

Molecular Phylogenetics and Evolution

Volumn 63, Issue 1, 2012, Pages 193-202

  Ari, Eszter ^a   Ittzés, Péter ^a   Podani, János ^a,b   Thi, Quynh Chi Le ^a   Jakó, Éena ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Boolean analysis; Congruence analysis; Discrete mathematical method; Mitochondrial tRNA; Phylogeny; Simulated sequences

Indexed keywords

MITOCHONDRIAL DNA; TRANSFER RNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENETICS; HOMINID; METHODOLOGY; PHYLOGENY; SEQUENCE ANALYSIS; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; HOMINIDAE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA;

HOMINIDAE;

EID: 84857234305     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.01.010     Document Type: Article

References (39)

1. Bjarnason A., Chamberlain A.T., Lockwood C.A. A methodological investigation of hominoid craniodental morphology and phylogenetics. J. Hum. Evol. 2011, 60:47-57.
2. Bryant D. A classification of consensus methods for phylogenetics. Bioconsensus DIMACS Series in Discrete Mathematics and Theoretical Computer Science 2003, vol. 61:163-184. American Mathematical Society, Providence, Rhode Island.
3. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
4. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
5. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
6. Felsenstein, J., 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
7. Fitzhugh K. The "requirement of total evidence" and its role in phylogenetic systematics. Biol. Philos. 2006, 21:309-351.
8. Fletcher W., Yang Z. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 2009, 26:1879-1888.
9. Goodman M., Tagle D.A., Fitch D.H.A., Bailey W., Czelusniak J., Koop B.F., Benson P., Slightom J.L. Primate evolution at the DNA level and a classification of hominoids. J. Mol. Evol. 1990, 30:260-266.
10. Goodman M., Porter C.A., Czelusniak J., Page S.L., Schneider H., Shoshani J., Gunnell G., Groves C.P. Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 1998, 9:585-598.
11. Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010, 27:221-224.
12. Hasegawa M., Kishino H., Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22:160-174.
13. Helm M., Brulé H., Friede D., Giegé R., Pütz D., Florentz C. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 2000, 6:1356-1379.
14. Hillis D.M. Approaches for assessing phylogenetic accuracy. Sys. Biol. 1995, 44:3-16.
15. Holder M.T., Zwickl D.J., Dessimoz C. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos. Trans. R. Soc. London Ser. B 2008, 363:4013-4021.
16. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
17. Jakó, É., 1983. Iterative canonical decomposition of Boolean functions and its application to logical design - Ph.D. thesis, Technical University, Moscow.
18. Jakó, É., 2007. Generalized Boolean descriptors for biological macromolecules. In: Special Issues of International Conference on Computational Methods and Engineering (ICCMSE), pp. 552-7.
19. Jakó É., Ari E., Ittzés P., Horváth A., Podani János BOOL-AN: a method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 2009, 52:887-897.
20. Jakó É., Ittzés P. A discrete mathematical approach to the analysis of spatial pattern. Abstr. Bot. 1998, 22:121-142.
21. Jukes T.H., Cantor C.R. Evolution of Protein Molecules. Mammalian protein metabolism 1969, 21-123. Academy Press, New York. H.N. Munro (Ed.).
22. Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences. PNAS 1981, 78:454-458.
23. Koga A., Notohara M., Hirai H. Evolution of subterminal satellite (StSat) repeats in hominids. Genetica 2011, 139:167-175.
24. Penny D., Foulds L., Hendy M. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 1982, 297:197-200.
25. Podani J. Introduction to the Exploration of Multivariate Biological Data 2000, Backhuys, Leiden.
26. Podani J., Oltvai Z.N., Jeong H., Tombor B., Barabási A.L., Szathmáry E. Comparable system-level organization of Archaea and Eukaryotes. Nat. Gen. 2001, 29:54-56.
27. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
28. Rannala B., Yang Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 1996, 43:304-311.
29. Reeck G.R., de Haen C., Teller D.C., Doolittle R.F., Fitch W.M., Dickerson R.E., Chambon P., McLachlan A.D., Margoliash E., Jukes T.H. "Homology" in proteins and nucleic acids: a terminology muddle and a way out of it. Cell 1987, 50:667.
30. Rodríguez F., Oliver J.L., Marín A., Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 1990, 142:485-501.
31. Robinson L., Foulds L. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
32. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
33. Ruvolo M. Genetic diversity in hominoid primates. Annu. Rev. Anthropo. 1997, 26:515-540.
34. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
35. Satta Y., Klein J., Takahata N. DNA archives and our nearest relative: the trichotomy problem revisited. Mol. Phylogenet. Evol. 2000, 14:259-275.
36. Schöniger M., Von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 1994, 3:240-247.
37. Stauffer R.L., Walker A., Ryder O.A., Lyons-Weiler M., Hedges S.B. Human and ape molecular clocks and constraints on paleontological hypotheses. J. Hered. 2001, 92:469-474.
38. Swofford, D.L., 2003. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4, Sinauer Associates, Sunderland, Massachusetts.
39. Tarver J.E., Donoghue P.C.J., Benton M.J. Is evolutionary history repeatedly rewritten in light of new fossil discoveries?. Proc. R. Soc. London Ser. B 2011, 278:599-604.