This is expected, since increased mutation rates correspond to a larger number of mutations that contribute to fitness and make the SBD model a better approximation.
After including confidence intervals on mutation rate, this corresponds to a point estimate of Ne equal to 2632 with 95% density in (0, 40 000).
Thus, in these cases, an optimum value for the mutation rate exists that corresponds to the lowest value of the characteristic time for quasispecies evolution.
Assuming the same mutation rate as above this corresponds to migration rates ranging between 0.001 and 0.010.
Because we consider a number of offspring reaching the first year, before the viability selection, equal to 10, a mutation rate equal to 10-5 correspond to 3 allelic mutations every generation.
The mutation rate of U = 1.5 corresponds to our best estimate of the somatic mutation rate for the whole macronucleus of T. thermophila and can be interpreted as the probability of somatic chromosomal lost/gain per Mac genome per generation.
Assuming the estimated mutation rate of 2.81 × 10-4 this corresponds to 2482 years before present (90% credible interval 641 – 4344 years).
In P. aeruginosa, deficiencies in MMR increased the BPM rate by 267-fold, a value that corresponds to a mutation rate similar to that reported in other MMR-deficient strains in other bacterial species (0.09 to 0.18 mutations per genome per generation, Table 4).
Then, the insertion time of each element was estimated by the formula T = k/2 r (Li 1997), where T corresponds to the insertion time in millions of years, k corresponds to the number of nucleotide substitutions per site, and r corresponds to the neutral mutation rate of the species lineage.
The distributions shown in Figure 2(a) and 2(b) correspond to a mutation rate μ = 0.004, which yields a fraction ρ ≃ 0.34 of correctly folded sequences.
