Simulation Parameters and Settings

Note: all parameters can be set to resolution finer than values shown on the screen.

Starting Population and Relative Fitness (Populations Tab):

• Starting Population (changes can be made on the populations tab).
  The user sets the number of individuals with each genotype. As a consequence, this sets the population size and the initial genotype frequencies.
  Default: Each allele is present at an initial frequency of 0.5, and genotype frequencies reflect Hardy-Weinberg equilibrium. The population size (N) is 160 individuals (i.e., 2N=320 copies of each gene).
  
  
• Relative Fitnesses of Genotypes (changes can be made on the populations tab).
  The user sets the fitnesses of the nine genotypes. Maximum fitness can not exceed 1.0.
  Default: All genotypes confer equal relative fitness.
  
  
• Mutation Rates (Mutation and Mating Tab)
  Self-explanatory.
  Default: No mutation.
  
  
• Mating Preferences (Mutation and Mating Tab)
  The user determines the relative mating preferences for the six possible pairings of parental Alpha genotypes. Mating rates range from 1 (product of the tow parental genotype frequencies) to 0.0 (matings never occure). To prevent a mating, the user should simply set the mating preference to 0.0.
  Default: No mating preferences. The probability of any given mating is simply the product of the two parental genotype frequencies.
  
  
  
• Linkage Map Distance (cM) (Status pane)
  The user sets the linkage map distance between the Alpha and Beta genes by clicking on the slider. A map distance of 0.0 cM prevents recombination; a map distance of 50.0 cM means that the genes are effectively independently assorting.
  Default: Complete Linkage. (Note: the fastest run times will be obtained with complete linkage).
  
  
  
• Fertilization Allowed (Status pane)
  The user can choose to permit self-mating, to prevent self-mating or to enforce monogamy.
  Default: Self-ferteilization is permitted.
  
  
  
  
• Number of Iterations
  This is the number of times that the program will repeat the simulation with the same starting parameters.
  Default: 1 iteration.
  
  
• Maximum Number of Generations
  Unless otherwise set (see Stop at Fixation and Gene Copy Tracking), the program stops each iteration when (i) allele fixation occurs as specified (see Allele Fixation); and (ii) when a single Generation 0 copy of each gene is fixed in the population. While gene copy fixation is guaranteed to occur eventually, the allele fixation may not occur (e.g., if a mutation-selection balance is established). For various reasons, the user may wish to halt each iteration after a set number of generations.
  Default: 30,000 generations.
  
  
  
  
• Migration Settings
  The user can set the genotype frequencies in a source (immigrating) population, as well as the average number of immigrants per generation. Note: If migration is permitted, then gene copy tracking is turned off.
  Default: No immigration.
  
  
  
  
• Gene Gene History
  This setting allows the user to keep track of gene history. The user can decide to not track and report the number of generations required for fixation of Alpha and Beta gene copies (coalescents). This will speed up the simulation.
  Default: Track gene copies.
  
  
  
  
• Stop at Fixation?
  The user may want to prevent the program from stopping an iteration upon allele and gene copy fixation. If this option is set to "no," the iteration will continue until the specified maximum number of generations is reached (see Maximum Generations).
  Default: Iterations stop at fixation.
  
  
  
  
• Allele Fixation
  The user may want finer control over the allele that must be fixed (if any) to end the iteration. For example, a population could begin with the A allele fixed, but permit A to a mutation. In such a case, it would make more sense either to stop the iteration at fixation of a or to ignore fixation of either Alpha allele.
  Default: stop at fixation of either allele for both genes.