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However, there is an increasing discrepancy between the overall mutation rate estimated from likelihood analysis and that from the classical estimator when the rate is significantly higher than 1%.
The average mutation rate estimated over 7680 gametes was in the range reported within fish (3.9 × 10− 4) and did not compromise parentage analysis.
This could explain that we observe a higher diversity than the one expected with the phylogenetic mutation rate estimated for Bovidae (i.e., 30.1 % of divergence per Myr on the total control region sequence based on the Bos/Bison divergence [26]).
To assess whether individual loci were inconsistent with expectations under the best-fit neutral demographic model, coalescent samples of ARGs conditional on the best-fit model were generated placing mutations on the ARG conditional on the scaled mutation rate estimated for all loci within the coding and promoter locus classes, respectively.
The mutation rate estimated from human-chimpanzee divergence based on a constant molecular clock [25] yielded age estimates for these SNPs (Table S6A) far older than the generally accepted time of human speciation, further testifying to the process of positive selection acting on the region.
We assume here that synonymous mutation are neutral and that the synonymous divergence gives an estimate of the mutation rate; although, there is a discrepancy between mutation rate estimated from pedigrees and the level of synonymous divergence, this is probably a consequence of the methods used to infer the pedigree mutation rate [17].
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Divergence and mutation rate estimates [95% highest posterior density intervals] from BEAST and Path-O-Gen analyses, and consensus values across these two methods.
If striking, such differences between soma and germline should, among other things, make attempts at evaluating somatic-mutation advantages on the basis of germline mutation rates estimated from inferred evolutionary substitutions into problematic, if not directly hopeless, undertakings.
STR median-joining networks were drawn by Network 4.201 [30], and ages were estimated in the networks according to the mutation rates estimated by Zhivotovsky et al. (6.9×10−4 per 25 years) [31].
Table 1 shows the mutation rates estimated by three strategies.
The mutation rates estimated by the first two strategies were quite similar.
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