When we allowed all SNP markers to mutate at a mutation rate equal to 10-6, we found a loss of accuracy of about 20-25% for HaploMax and about 50% for HAPimLDL (data not shown).
The mutation rate equal to 0 is set; 6b.
It has been labeled as string 5 and carried to the next generation (elitist strategy); The remaining four strings for reproduction, based on a deterministic tournament selection strategy, are chosen; Crossover with P c = 1 is applied; The mutation rate equal to 0 is set; Nominal convergence is checked.
On the other hand, an accelerated mutation rate equal to that of fast-evolving human mitochondrial DNA [26] yielded age estimates of 139.91±10.09 Kya for rs6556547, 113.31±18.35 Kya for rs187269, 92.82±19.06 Kya for rs1816071, and 69.44±20.14 Kya for rs1816072 in coalescence-based calculations with the Rho index [27] (Table S6; Figure 4).
For each coalescent tree, a microsatellite site pattern was simulated under the microsatellite model with mutation rate equal to 1.0.
Note that this inferred rate is significantly greater than an inferred rate for an individual of the same age, if the site had a mutation rate equal to the generally accepted genome average mutation rate.
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.
Exceptions were the pathogen genotypes with the highest aggressiveness on either the crop or the wild host – these mutated towards less specialized genotypes with a probability of 0.004 to keep their overall mutation rate equal to that of other genotypes.
To generate these parameters we first fit the cancer onset model parameters (mutation, death, and birth rates) to Surveillance, Epidemiology, and End Results (SEER) data for prostate cancer incidence.a We then fit the selenium model parameters to produce a mutation rate equal to the fitted cancer onset model mutation rate at baseline selenium levels.
