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Genetics, Vol 143, 1457-1465, Copyright © 1996
INVESTIGATIONS |
F. Tajima
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113, Japan
The expectations of the average number of nucleotide differences per site ({pi}), the proportion of segregating site (s), the minimum number of mutations per site (s*) and some other quantities were derived under the finite site models with and without rate variation among sites, where the finite site models include Jukes and Cantor's model, the equal-input model and Kimura's model. As a model of rate variation, the gamma distribution was used. The results indicate that if distribution parameter {alpha} is small, the effect of rate variation on these quantities are substantial, so that the estimates of {theta} based on the infinite site model are substantially underestimated, where {theta} = 4Nv, N is the effective population size and v is the mutation rate per site per generation. New methods for estimating {theta} are also presented, which are based on the finite site models with and without rate variation. Using these methods, underestimation can be corrected.
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