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Recurrent and unstable mutations are set in brackets by Phylotree [4].
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The overall distribution of mutations is set out in Figure 1.
The remaining five sampling years showed signs of bottlenecks in the vast majority of parameter combinations, except when the parameters p s (the fraction of mutations larger than a single step) and Δ g (the mean size of larger mutations) were set at their maximum (see Additional file 3 Table S2).
A single point mutation was set via site-directed mutagenesis using the primers 5'-CCTAAAAACTGCATGGAGGCACAATATC-3' and 5'- GCAGTTTTTAGGACGACATCTGGCCTTAAAAG-3' leading to the amino acid E(1584)–K substitution on protein level (sequence confirmed by sequencing).
Haplotypes in control individuals were estimated using PHASE, and the relative position of the mutation was set within the haplotype.
Although the threshold for calling a mutation was set to 2%% of base changes, not all base changes above 2%% were called as mutations.
The selection coefficient was set as 0.01, and the frequency of the advantageous mutation was set to range between 10% and 100%, in increments of 10%.
The population size is 100 and the number of generations is 300; 2. The number of hill-climbing iterations for both crossover and mutation is set to 100; 3.
Again, this was due to the fact that 16278T for haplogroup C4a3 was reported as missing in the haplotype even though this mutation was set in brackets in Phylotree.
A mutation probability and a mutation fraction are set by the designer as a design parameter.
Note that this uncertainty is not accounted for in the simulation as values for the mutation rate are set a priori.
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