Journal of Molecular Evolution

, Volume 42, Issue 4, pp 459–468 | Cite as

Model of amino acid substitution in proteins encoded by mitochondrial DNA

  • Jun Adachi
  • Masami Hasegawa
Articles

Abstract

Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.

Key words

General reversible Markov model Amino acid substitution Maximum likelihood method 

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Copyright information

© Springer-Verlag New York Inc. 1996

Authors and Affiliations

  • Jun Adachi
    • 1
  • Masami Hasegawa
    • 2
  1. 1.Department of Statistical ScienceThe Graduate University for Advanced StudiesTokyoJapan
  2. 2.The Institute of Statistical MathematicsTokyoJapan

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