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

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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 52, 887-97.), a recently developed method for sequence comparison uses the Iterative Canonical Form of Boolean functions. It considers sequence information in a way entirely different from standard phylogenetic methods (i.e. Maximum Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The performance and reliability of Boolean analysis were tested and compared with the standard phylogenetic methods, using artificially evolved - simulated - nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At the outset, we assumed that the phylogeny of Hominidae is generally well established, and the guide tree of artificial sequence evolution can also be used as a benchmark. These offer a possibility to compare and test the performance of different phylogenetic methods. Trees were reconstructed by each method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We also introduced a special re-sampling method for Boolean analysis on permuted sequence sites, the P-BOOL-AN procedure. Considering the reliability values (branch support values of consensus trees and Robinson-Foulds distances) we used for simulated sequence trees produced by different phylogenetic methods, BOOL-AN appeared as the most reliable method. Although the mitochondrial tRNA sequences of great apes are relatively short (59-75 bases long) and the ratio of their constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach produced the same tree-topology as the established phylogeny, while the outcomes of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were equivocal. We conclude that Boolean analysis is a promising alternative to existing methods of sequence comparison for phylogenetic reconstruction and congruence analysis.

Original languageEnglish
Pages (from-to)193-202
Number of pages10
JournalMolecular Phylogenetics and Evolution
Volume63
Issue number1
DOIs
Publication statusPublished - Apr 2012

Fingerprint

Hominidae
Pongidae
Transfer RNA
phylogenetics
phylogeny
methodology
Bayes Theorem
Phylogeny
analysis
comparison
method
Benchmarking
Bayesian analysis
Mitochondrial Genes
Bayesian theory
Base Composition
topology
Sequence Analysis
sequence analysis
nucleotide sequences

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes. / Ari, Eszter; Ittzés, Péter; Podani, János; Thi, Quynh Chi Le; Jakó, Éena.

In: Molecular Phylogenetics and Evolution, Vol. 63, No. 1, 04.2012, p. 193-202.

Research output: Contribution to journalArticle

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