Beyond Labz

The purpose of the Genetics laboratory is to (a) allow students to perform Mendelian experiments to explore how a variety of different genetic models reveal themselves through phenotypic frequencies and (b) to explore Hardy-Weinberg equilibrium through the application of various forces on a population. The outcomes for the Mendelian and Population experiments are handled quite differently and are described below.

Mendelian Experiments. In a Mendelian experiment, students first select a species they wish to study from the species selector, which then populates a list of traits for that species that can be selected and studied by performing crosses. (A list of traits available for each species is given below.) Once the traits have been selected, students then assign genotypes for each parent for each trait, select the number of offspring per cross, and then perform the selected cross. The results from the cross (and any subsequent crosses) are displayed as a summary of phenotypic frequencies and a list of individual offspring where the phenotype of each individual offspring can also be viewed.

The phenotype for each trait for each offspring as a result of a cross is determined using the following process:

1. An allele from each parent for each loci is selected randomly, and the two alleles are then combined to define the genotype for the offspring. In the case of a self-cross for a plant, the two alleles are each selected randomly from the parent plant. This random selection of alleles simulates independent assortment and assumes the selected traits are independent or reside on separate chromosomes. However, a few traits for selected species in the database are linked and if these traits happen to be selected at the same time then the selection of alleles is not fully random but weighted by their relative distance from each other on the chromosome.

2. Once the genotype has been defined for each loci, the phenotype is determined based on the genetic model that has been defined for that trait or combination of loci in the database. These genetic models include, but are not limited to, simple Mendelian or complete dominance, incomplete dominance, codominance, sex linked, epistasis, recessive epistasis, three allele systems, dominant mutant, lethal alleles, pleiotropy, duplicate gene action, and dominant suppression.

The following is the list of traits that can be selected for each of the available species in the Genetics laboratory. Please note that for a very few commonly used examples, the genetic models are known to be complex but have been approximated here with a much more simple model.

Population Experiments. 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. For these experiments, 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 actually 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 very different experiment than the Mendelian type experiments described above. In this experiment, a specific species is not selected but a generic species is used to represent an arbitrary allele frequency and genotype. A population experiment is performed by selecting or defining the forces that can be applied to a population in Hardy-Weinberg equilibrium 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.

The actual equations and models used to determine the allele and genotype frequencies in the simulation were adapted from those described in the text An Introduction to Genetic Analysis 3e by David T Suzuki, Anthony J. F. Griffiths, Jeffrey H. Miller, and Richard C. Lewontin. The following are a few assumptions that should be noted.

1. Genetic Drift and Inbreeding are assumed to have the same effect on the allele frequency and are treated identically.

2. Genetic Drift and Inbreeding are modeled using a random number generator and the population size to calculate the statistical noise in the allele frequency.

3. In an actual Hardy-Weinberg system, all the forces that can affect the allele frequency are applied simultaneously. In the simulation this was not possible, and the forces were applied in a hierarchical order in the calculation. While strictly speaking this has the potential to cause some inaccuracies, we have not observed it to be a problem.