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Classical mutation rate estimation is based on counting mutations in father son pairs (or other known geneologies).
A fundamental flaw of all Y-STR mutation rate estimation approaches, including our own, is the limiting assumption they make about the nature of Y-STR mutation processes.
To date there are only two studies that deal with the empirical mutation rate estimation of coding mtDNA region [ 31, 35].
The MAL8 method used in this study was applied to a small, previously published dataset, consisting of only <4000 samples, which were collected for other uses and not customized for Y-STR mutation rate estimation in any way.
Because we investigate the mutation rates for different lethality levels, it is desirable to know whether a slight deviation of the optimal parameters will lead to a significant difference in the subsequent mutation rate estimation and hypothesis testing.
The phenotype can be selected for in the presence of αF; this allows for mutation rate estimation by fluctuation assays, for the isolation of spontaneous sterile mutations in the ancestral background, and provides a means for amplifying these mutations in culture.
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It must be stated that coalescence ages are only rough estimations biased by mutation rate estimations, small sample size, demographic history and, possibly, selection.
Radiation ages for M1 and its subhaplogroups have been estimated on the basis of complete coding and HVSI sequences using different mutation rate estimations (Table 4).
Finally, PAR-inferred demographic scenarios offer the opportunity of being incorporated in coalescence-based Bayesian mutation rate estimations, and this way more accurate substitution rates can be obtained [ 52].
While the validity of applying this mutation rate estimate to a phylogenetically distant taxon is untested, it does currently represent the only option for a rough estimation of divergence times among L. chagosensis clades.
Coalescence times for mtDNA haplogroups were calculated by the rho statistic according to the mutation-rate estimation of Mishmar et al. [ 32].
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