The purpose of the population experiments is to observe Hardy-Weinberg equilibrium as various forces are applied by measuring the resulting changes in allele frequency as a function of generation. In the simulation, we can look at the allele frequency by either calculating the allele frequency directly under various conditions (what we call the Hardy-Weinberg option) or by actually performing crosses for multiple generations using multiple parents (the Crosses option).
The Crosses option is really a modified Mendelian experiment where, instead of restricting the number of parents to two for the F2, F3, etc. crosses, we provide various options to select or define multiple parents in each generation. As succeeding generations are produced, allele and genotype frequencies can be tracked for various genetic models.
The Hardy-Weinberg option is a different experiment than the Mendelian type experiments. In this experiment, a specific species is not selected but a generic species is used to represent an arbitrary allele and genotype frequency. A population experiment is performed by selecting or defining the forces that will be applied to the Hardy-Weinberg population and then calculating the allele and genotype frequencies as a function of generation. The forces that can be applied to the system include (a) the initial allele frequency, (b) population size, (c) the number of generations to track, (d) whether genetic drift or inbreeding is turned on, (e) the mutation rate, (f) the relative fitness parameters for different genotypes, (g) the degree of assortative or disassortative mating, and (h) linkage disequilibrium. Given below is an outline of the general steps involved in performing a population experiment.
- Make sure the Population option is selected in the Setup menu and then select either the Hardy-Weinberg option or Crosses option. The Hardy-Weinberg option is selected by default.
- For the Hardy-Weinberg option, use the following steps:
- For this experiment the species selector reduces itself to allow only one generic species. Selecting a species is not necessary.
- In the initial or default state, the Hardy-Weinberg parameters are set to cover 100 generations, using a population size of 1000, and an initial allele frequency, pA, of 0.75. Random Genetic Drift is also turned on but all other variables are set to not contribute to the calculation.
- Choose or set the variables you wish to observe by either typing in the number or using the slider to the right of the variable.
- Click on the Calculate button to show the results in Live Data. Parameters can be changed and the results re-calculated easily.
- For the Crosses option, use the following steps:
- The first step is to select a species in the Species menu. Depending on the species selected, the laboratory will change to reflect the type of species chosen. The default room is for plant species.
- After selecting a species, a list of traits for that species will be listed in the Setup menu. Select one or more of the traits you wish to follow as crosses are performed. Use Ctl-click (Windows) or Cmd-click (Mac) to select multiple traits.
- For plant species, self-crosses are allowed. Select whether there will be one or two parents for the cross.
- After the traits have been selected, the genotypes for each parent must be defined. This can be done randomly by clicking on the Randomize button, or the genotype can be defined manually using the dropdown list for each allele. Note that some traits are defined by multiple loci and for some presets the genotypes of the parents could be hidden.
- Now the number of offspring per cross must be defined. In most cases, you will use the default number, but the number of offspring that can be produced from each cross can be changed within a range of values that is typical for the selected species.
- Finally, click on the Cross button to perform the cross for the defined parents. The results will show in Live Data. In many cases, you will need to perform multiple crosses to generate enough offspring to obtain some reasonable statistics. Just return to Setup and click Cross again as many times as needed.
- After producing the necessary population size, subsequent generations of offspring can be produced by clicking on the Next Generation button. The Setup menu will be reconfigured to allow you to select the set of parents that will produce the next generation of offspring. The parents can be selected manually from the list of offspring, randomly, and all possible combinations of parents. Remember that for the Crosses experiment, multiple sets of parents can be selected to produce the next generation of offspring.