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The mutation rate creates a binary mutation string which modifies the new member.
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Such studies will tend to report both high rates of EPPs and high mutation rates, creating outlier points with high leverage on the regression.
The fast mutation rate that creates these high levels of polymorphism is widely recognized to increase levels of homoplasy as genetic distance increases (Estoup et al., 2002), although the use of multiple loci may mitigate the impact of homoplasy in a single locus.
Previous work has described how experimental measurements of amino-acid preferences can be combined with known mutation rates to create a parameter-free phylogenetic evolutionary model from deep mutational scanning data (Bloom, 2014).
It is possible that higher mutation rates may create a greater pool of standing variation from which adaptive substitutions can be derived.
The conclusion reached here is that the canalized character of HA evolution arises primarily from the two critical parameters in the model (mutation rate, immunological distance created by mutation) rather than from the functional constraints of viral invasion of the host, though the molecule must of course maintain its core activity.
Chromosomal position could create a mutation rate bias that results in a non-random distribution of mutations along the length of the circular genome.
In each simulation, a sample of haplotypes representing a single chromosome of 1 Morgan (100,000,000 base pairs) with the per-site mutation rate set to 10-8 was created using MaCS [ 8], which invokes a neutral coalescent model.
The behavior of the system is largely governed by two parameters: the mutation rate of the virus, and the immunological distance created by each mutation.
Significantly mutated genes (SMGs) were defined as the somatic mutations with higher mutated frequency than background mutation rate.
If higher growth rates also lead to faster diversification [ 51], then this could create an indirect link between the mutation rate and diversification.
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