ADVICE FOR USING EVOLGENIUS 5.6 EFFICIENTLY

A number of the processes simulated in EvolGenius require a lot of computational effort. If those processes are irrelevant to a particular study, they should be set such that the least amount of computation is required.

Population Size. To a first approximation, the time it takes to complete an iteration will be proportional to N², where N is the population size. This is because (i) the program must create N individuals every generation and (ii) gene copy fixation time is proportional to N under neutral conditions.

Fitness. Keep all nine values at 1.0 to minimize run time.

Mutation. Keep all four values at 0.0 to minimize run time.

Linkage. Keep the distance between Alpha and Beta at 0 cM to minimize run time. This is especially relevant if the user is interested in only one gene.

Mating Preferences. Keep all six value at 1.0 to minimize run time.

Migration. Keep migration disabled to minimize run time.

Gene Copy History. To minimize run time, do not track gene copy history. This is especially true for large populations, since the expected fixation time is 4N_e generations (where N_e is the effective number of breeding individuals in the population).

Maximum Number of Generations. If fixation is unlikely (e.g., if a selection-mutation balance has been established), set the maximum number of generations to a reasonable value -- one that is sufficient to allow equilibrium to be reached.

A Few More Thoughts...

Dominance. There is nothing special about upper- and lower-case alleles. Dominance is determined solely by fitness values. Thus, if aa and Aa have equal fitness, and if this value exceeds the fitness of AA, then the a allele is dominant to the A allele.

Independent Assortment. If the linkage map distance is set to 50 cM, the Alpha and Beta genes are behaving as if they are on separate chromosomes.

What if the user wants to start at Hardy-Weinberg equilibrium? The user must calculate the expected genotype frequencies in advance, and multiply these by the desired total population size (N).