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Molecular Biology and Evolution, Vol 15, 336-344, Copyright © 1998 by Society for Molecular Biology and Evolution
X Xia
Substitution rates at the three codon positions (r1, r2, and r3) of
mammalian mitochondrial genes are in the order of r3 > r1 > r2, and
the rate heterogeneity at the three positions, as measured by the shape
parameter of the gamma distribution (alpha 1, alpha 2, and alpha 3), is in
the order of alpha 3 > alpha 1 > alpha 2. The causes for the rate
heterogeneity at the three codon positions remain unclear and, in
particular, there has been no satisfactory explanation for the observation
of alpha 1 > alpha 2. I attempted to dissect the causes of rate
heterogeneity by studying the pattern of nonsynonymous substitutions with
respect to codon positions in 10 mitochondrial genes from 19 mammalian
species. Nonsynonymous substitutions involve more different amino acid
replacements at the second than at the first codon position, which results
in r1 > r2. The difference between r1 and r2 increases with the
intensity of purifying selection, and so does the rate heterogeneity in
nonsynonymous substitutions among sites at the same codon position. All
mitochondrial genes appear to have functionally important and unimportant
codons, with the latter having all three codon positions prone to
nonsynonymous substitutions. Within the functionally important codons, the
second codon position is much more conservative than the codon position.
This explains why alpha 1 > alpha 2. The result suggests that
overweighting of the second codon position in phylogenetic analysis may be
a misguided practice.
ORIGINAL ARTICLE
The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes
Department of Ecology and Biodiversity, University of Hong Kong. xxia@hkusub.hku.hk
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