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This MD analysis has also shed light into the origin of the position dependence on mutation of β-sheet polymerization that was found experimentally for this model system.
In particular, the speed limit Vmax and its power law dependence on mutation rates should be quantifiable in evolving microbial colonies.
Both the existence of a speed limit Vmax for large habitats and its dependence on mutation rates contrast with the well-mixed case, where the adaptation speed depends logarithmically on both population size and mutation rates (see Discussion).
The error threshold shows a phase transition for collective order parameters such the consensus sequence [ 11, 16], but not, for example, for the average fitness of the population, whose value does not greatly vary at the error threshold, although its dependence on mutation rate does [ 13].
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Two key features of this model are the dependence of mutation rates on microsatellite length and a mutation process that includes both strand slippage and point mutation events.
One hundred sets of random passenger mutations were obtained for SIM II in a similar way, but accommodating the dependence of mutation rate on replication timing and expression level.
The dependence of mutation rate on sequence context is well known; the effect of sequence surrounding a mispair on MMR recognition has been well studied, for example, Marsischky and Kolodner (1999).
To facilitate comparisons with existing methods, the simulation study considers two types of simulations: SIM I simulations that ignore the dependence of mutation rate on replication timing and expression level and SIM II simulations that do not.
Simulations show a weak dependence on the mutation parameters, see Fig. 1.
Both mouse models greatly differ in the potential of inducing apoptosis and proliferation, and in their dependence on additional mutations.
In fact, the entire section "Dependence of speciation on mutation rate" is very weak, with almost no mechanistic explanation.
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