Molecular Biology and Evolution, Vol 6, 636-647, Copyright © 1989 by Society for Molecular Biology and Evolution
JH Gillespie
Recent efforts to estimate the index of dispersion [R(t)] of molecular
evolution-i.e., the ratio of the variance in the number of substitutions on
a lineage to the mean number-have suffered from an inability to adjust the
data for lineage effects. These effects may include the generation-time
dependency of the rate of evolution or improper assumptions about the
branching pattern of a phylogenetic tree. In the present paper a method for
correcting for lineage effects in the estimation of R(t) is presented for
trees made up of three species. The recent data published by Li et al. for
20 loci in three orders of mammals is examined, and the average R(t),
corrected for lineage effects, is shown to be 7.75 for replacement
substitutions and 3.3 for silent substitutions. Thus the high values
reported earlier may not be dismissed as due to generation-time effects or
improper assumptions about phylogenies. Computer simulations are presented
to give confidence in the estimate for replacement substitutions but also
to demonstrate that the estimate for silent substitutions is sensitive to
corrections for multiple substitutions and is not as reliable. This work's
implications for our understanding of the mechanism of molecular evolution
are discussed, and the arguments in favor of the hypothesis that
replacement substitutions are mostly selected while silent substitutions
are mostly neutral is presented.
ORIGINAL ARTICLE
Lineage effects and the index of dispersion of molecular evolution
Department of Genetics, University of California, Davis 95616.
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