Molecular Biology and Evolution, Vol 15, 1600-1611, Copyright © 1998 by Society for Molecular Biology and Evolution
Z Yang, R Nielsen and M Hasegawa
Models of amino acid substitution were developed and compared using maximum
likelihood. Two kinds of models are considered. "Empirical" models do not
explicitly consider factors that shape protein evolution, but attempt to
summarize the substitution pattern from large quantities of real data.
"Mechanistic" models are formulated at the codon level and separate
mutational biases at the nucleotide level from selective constraints at the
amino acid level. They account for features of sequence evolution, such as
transition-transversion bias and base or codon frequency biases, and make
use of physicochemical distances between amino acids to specify
nonsynonymous substitution rates. A general approach is presented that
transforms a Markov model of codon substitution into a model of amino acid
replacement. Protein sequences from the entire mitochondrial genomes of 20
mammalian species were analyzed using different models. The mechanistic
models were found to fit the data better than empirical models derived from
large databases. Both the mutational distance between amino acids
(determined by the genetic code and mutational biases such as the
transition-transversion bias) and the physicochemical distance are found to
have strong effects on amino acid substitution rates. A significant
proportion of amino acid substitutions appeared to have involved more than
one codon position, indicating that nucleotide substitutions at neighboring
sites may be correlated. Rates of amino acid substitution were found to be
highly variable among sites.
ORIGINAL ARTICLE
Models of amino acid substitution and applications to mitochondrial protein evolution
Department of Biology (Galton Laboratory), University College London, England. z.yang@ucl.ac.uk
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