Reliability of phylogenetic analyses strongly depends on
models assumed for the substitution processes of nucleotides
and amino acids. Here we propose a new codon-based model in
which codon replacements with single and multiple base
changes occur in the same order of time, and a new
evaluation of the selective restraints on amino acid
replacements is used. The codon substitution process is
modeled as the time-reversible Markov process and the codon
mutation rates are assumed to be proportional to the
equilibrium codon frequencies. All codon replacements are
assumed to be lethal or neutral, and the mean fraction of
neutral replacements is approximated by the exponent of a
linear combination of two terms, mean increment of contact
energies between an amino acid and surrounding amino acids
due to an amino acid exchange in a protein structure and
volume difference between an amino acid and its replacement.
This codon-based model is examined by maximizing its
likelihoods to the amino acid substitution matrices, JTT
tallied by Jones et al., mtREV estimated for mitochondria-
and cpREV for chloroplast-encoded proteins. The maximum
likelihoods indicate that the present evaluation of the
selective restraints better fit the JTT than both Grantham's
and Miyata's distances. The Akaike information criterion
scores indicate the significance of multiple base changes.
The estimated values of parameters confirm
transition/transversion rate bias and codon usage bias, and
reproduce characteristic features in the temporal changes of
the log-odd matrix.