Interact box Genotype frequencies

PopGene.S2 (short for Population genetics simulation software) is a population genetics simulation program that will be featured in several Interact boxes. Here we will use PopGene.S2 to explore interactive versions of Figs 2.5 and 2.6. Using the program will require that you download it from a website and install it on a computer running Windows. Simulations that can be explored with PopGene.S2 will be featured in Interact boxes throughout this book.

Find Interact box 2.1 on the text web page and click on the link for PopGene.S2. The PopGene.S2 website has download and installation instructions (and lists computer operating system requirements). But don't worry: the program is small, runs on most Windows computers, and is simple to install. After you have PopGene.S2 installed according to the instructions provided in the PopGene.S2 website, move on to Step 1 to begin the simulation.

Step 1 Open PopGene.S2 and click once on the information box to make it disappear. Click on the Allele and Genotype Frequencies menu and select Genotype frequencies. A new window will open that contains a picture like Fig. 2.5 and some fields where you can enter genotype frequency values. Enter 0.25 into P(AA) to specify the frequency of the AA genotype. After entering each value the program will update the p and q values (the allele frequencies). Now enter 0.5 into P(Aa). Once two genotype frequencies are entered the third genotype frequency is determined and the program will display the value. Click the OK button. A dot will appear on the graph corresponding to the value of P(Aa) and the frequency of the a allele. Changing the P(AA) and P(Aa) frequencies to different values and then clicking OK again will add a new dot. Try several values for the genotype frequencies at different allele frequencies, both in and out of Hardy-Weinberg expected genotype frequencies. Step 2 Leave the Genotype frequencies window open but move it to one side to make room for another window. Now click on the Mating Models menu and select Autosomal locus. A new window will open that contains a triangular graph like that in Fig. 2.6. To display a set of genetype frequencies, enter the frequencies for P(AA) and P(Aa) in the text boxes and click OK. (Frequency of the aa genotype or P(aa) is calculated since the three genotype frequencies must sum to one.) The point on the De Finetti diagram representing the user-entered genotype frequencies will be plotted as a red square and displayed under the heading of "Initial frequencies". Hardy-Weinberg expected genotype frequencies are plotted as a blue square based on the allele frequencies that correspond to the user-entered genotype frequencies. These Hardy-Weinberg expected genotype frequencies are displayed under the heading of "Panmixia frequencies". Try several sets of different genotype frequencies to see values for genotype frequencies at different allele frequencies, both in and out of Hardy-Weinberg expected genotype frequencies. Step 3 Compare the two ways of visualizing genotype frequencies by plotting identical genotype frequencies in each window.

A single generation of reproduction where a set of conditions, or assumptions, are met will result in a population that meets Hardy-Weinberg expected genotype frequencies, often called Hardy-Weinberg equilibrium. The list of assumptions associated with this prediction for genotype frequencies is long. The set of assumptions includes:

• the organism is diploid,

• reproduction is sexual (as opposed to clonal),

• generations are discrete and non-overlapping, the locus under consideration has two alleles, allele frequencies are identical among all mating types (i.e. sexes), mating is random (as opposed to assortative), there is random union of gametes, population size is very large, effectively infinite, migration is negligible (no population structure, no gene flow), mutation does not occur or its rate is very low, natural selection does not act (all individuals and gametes have equal fitness).

Frequency of Aa

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