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Haplogroup D has a likely pre-LGM time depth characterized by an overall coalescence time estimate of 35 37 kya, depending on the mutation rate used.
The other major branch of the tree, C5 has a coalescence time of 14 17 kya, depending on the mutation rate used.
For instance, subcluster U5b2a2 is frequent in central Europe (with the highest frequency of its subcluster U5b2a2a1 in Poles) and dated as arising between 12 18 kya, depending on the mutation rate used (Table 1).
Subhaplogroup U5a dates to ∼16 20 ky, implying that it evolved during the LGM, in contrast to subhaplogroup U5b that suggests a pre-LGM time of divergence of 20 24 ky, depending on the mutation rate used.
For this purpose, we chose to apply a strict molecular clock with the same mutation rate used to estimate coalescences.
Generations were converted to dS using a factor of 10−4, an approximation to the mutation rate used in the simulation.
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Cells ensure the maintenance of genome stability and a low mutation rate using a plethora of DNA surveillance and correction processes.
The problem is that scientists often calculate the mutation rate using dates from fossils of other primate species, then applying this rate to the African apes and humans.
To resolve the limitation of low spontaneous mutation rate using ALE natural selection (Lee et al. 2012), various mutagenesis approaches using chemical, physical, or molecular methods have been developed and employed for microbial strain improvement such as chemical mutagenesis, transposon mutagenesis, genome shuffling, or error-prone PCR.
Clune et al. [20] explored the optimization of mutation rate using the Avida model, in which computer programs compete as digital organisms, with their success at performing certain computational operations serving as a measure of fitness.
The mutant frequencies were used to calculate the number of mutation events and the mutation rate, using Equation 3 above.
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