When the master phenotype is composed of more than just one sequence, the genetic information of the master phenotype is lost for any value of mutation rate different from zero, beyond which the population wanders through the master neutral network [ 28, 59].
To evaluate the significance of mutation rate differences across different species, strains, chromosomes, chromosome regions, and coding regions, we employed X goodness-of-fit tests.
These include differences in mutation rates in different lineages, different patterns of evolution being apparent in different sources of data, including convergent evolution, and long branch attraction.
We adapted SFS_CODE such that individual loci can have different mutation rates and different proportions of selected sites.
This discrepancy cannot have arisen from demographic processes affecting markers with different mutation rates to different extents: rarefying diversity to the slowest mutation rate should always give equivalent estimates, as the underlying distribution of gene genealogies is the same irrespective of the marker of choice.
If male and female mutation rates are different, we expect different evolutionary rates for X and Y chromosomes and autosomes.
As for including non-mutated sites, we were concerned that this approach could lead to uncontrollable increase in the error rate due to the different and unknown intrinsic mutation rates of different sites.
It is unclear whether the differences in mutation rates among different genes are conserved in long-term evolution.
Indeed, we observed in this study, as well as others in previous works (Willuweit and Roewer, 2007), that there is the large difference in mutation rates between different STRs.
Several age estimates for the whole U6 mtDNA clade have been calculated with different sets of complete sequences, varying mutation rates and different coalescence-based approaches; including, mean pairwise distances, maximum likelihood, and internally calibrated Bayesian relaxed clock phylogenetics.
