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Originally published as Genetics Published Articles Ahead of Print on March 4, 2007.
Genetics, Vol. 176, 467-476, May 2007, Copyright © 2007
doi:10.1534/genetics.106.067199
Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus 
6
Christina L. Burch*,1,
Sebastien Guyader*,2,
Daniel Samarov
and
Haipeng Shen
* Department of Biology and Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, North Carolina 27516
1 Corresponding author: Department of Biology, University of North Carolina, CB 3280, Chapel Hill, North Carolina 27516.
E-mail: cburch{at}bio.unc.edu
Although the frequency and effects of neutral and nearly neutral mutations are critical to evolutionary patterns and processes governed by genetic drift, the small effects of such mutations make them difficult to study empirically. Here we present the results of a mutation-accumulation experiment designed to assess the frequencies of deleterious mutations with undetectable effects. We promoted the accumulation of spontaneous mutations by subjecting independent lineages of the RNA virus 
6 to repeated population bottlenecks of a single individual. We measured fitness following every bottleneck to obtain a complete picture of the timing and effects of the accumulated mutations with detectable effects and sequenced complete genomes to determine the number of mutations that were undetected by the fitness assays. To estimate the effects of the undetected mutations, we implemented a likelihood model developed for quantitative trait locus (QTL) data (OTTO and JONES 2000) to estimate the number and effects of the undetected mutations from the measured number and effects of the detected mutations. Using this method we estimated a deleterious mutation rate of U = 0.03 and a gamma effects distribution with mean 
and coefficient of variation = 0.204. Although our estimates of U and 
fall within the range of recent mutation rate and effect estimates in eukaryotes, the fraction of mutations with detectable effects on laboratory fitness (39%) appears to be far higher in 6 than in eukaryotes.
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Genetics 2007 176: NP.
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