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In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data.
In addition, the interplay of replication and transcription, known to induce a strand bias in mutation rate, gives rise to variation in substitutional strand asymmetries.
Equating U d with the genomic mutation rate gives a range of 6.7×10−5< s d <6.7×10−4for u=10−6, but U d is generally smaller than U for finite values of β.
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Therefore, the proposed mutation rate gave an expected heterozygosity of 0.5.
This maximum value is dictated by the number of cells in the population as well as the mutation rate giving rise to new cell types.
In a previous work analyzing dN/dS ratio in four closely related yeast species (S. cerevisiae, S. mikatae, S. bayanus, and S. paradoxus), the dN/dS ratio for YER067W was 0.03, indicating a relatively slow mutation rate given that the whole genome mean for dN/dS ratios in S. cerevisiae was 0.10 [21].
This estimates divided by per locus mutation rate give the absolute age of the genealogy and corresponding standard errors.
Mutation starts with a random change to the mutation rate, given by (8) for i ∈ { μ + 1,..., λ} and j ∈ {1,..., n}, where and are tuning parameters.
Therefore, HCV replication is associated with a high mutation rate, giving rise to a mixed and changing population of mutants known as quasispecies [ 4, 8].
Our extensive simulations were designed to test whether natural selection could shape the optimum mutation rate, given the initial configuration of the population.
This condition defines an upper bound for the mutation rate, given by Simulations are started with a population devoid of genetic variation.
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