Assignments for majors

For your ease in completing the following assignments, the background text relevant to the experiment that you will perform is in black text, instructions for each assignment are indicated by plain text, and questions or activities that you will be asked to provide answers for are indicated by bold text.

Assignment 1: Getting to Know PopGenLab: Testing the Hardy-Weinberg Theorem
This assignment is designed to help you become familiar with the operation of PopGenLab by applying the Hardy-Weinberg theorem to learn about Hardy-Weinberg equilibrium parameters. The first screen that appears in PopGenLab shows you an input parameter page with a table listing the default parameters for the laboratory conditions that you can manipulate when setting up your experiments.

Before you can set up any experiment in PopGenLab, you must be familiar with the input parameters that you can manipulate for this population of moths. You will study the effects of these different parameters in future assignments. A brief description of each input parameter is provided below. Refer back to this section as needed when you are working on different assignments.

Click on the Change Inputs button to see all the parameters you can manipulate for this lab. A new page will open with buttons for each of the input parameters located at the left side of each page (genotype frequency will be open as the first input parameter). Click on each input parameter and read the descriptions below. Change each parameter so that you can become familiar with how each input parameter operates.

Genotype Frequency - allele frequency for wing color (controlled by a single gene) is shown for two alleles, A and a, as a pie chart of the phenotype resulting from each of the three possible genotypes: AA (black moths), Aa (brown moths), and aa (white moths). Notice that the default frequency is 50% for each allele.

Tree Types - three different types of trees are available. These trees provide habitat and food for the moths. Each tree has a different color of bark, which corresponds to the color of each of the three moths. Moth survival from birds as natural predators depends on a moth's ability to blend against tree bark with a color similar to the moth's wings. Notice that the default value provides an equal proportion of each tree type.

Number of Stands - the number of groups (stands) of trees determines the number of moth populations. The default value is one tree stand (one moth population).

Stand Size - the number of trees in an individual stand. Stand size directly influences the number of moths that can live within the stand. The maximum number of moths that the stand can support over time is called the carrying capacity of the stand. The default value is set to accommodate a large population, 4000 moths. This is the largest carrying capacity available in the simulation.

Migration Rate - controls the rate of migration and mixing of populations between different tree stands. Note: The Migration Rate button is shaded and inactive as the default because you must select at least two different populations (tree stands) for this input parameter to be active.

Mating Pattern - the type of mating can be selected as either assortative (individuals select partners with phenotypes similar to their own), random, or disassortative (individuals select partners with different phenotypes). The default is random mating. You can alter the degree of assortative or disassortative mating.

Disaster Frequency - controls the frequency of tornadoes, hurricanes, and the weather effects that typically accompany these natural disasters. Any population of organisms can be influenced by environmental disasters such as drought, flooding, hurricanes, tornadoes, and disease. In PopGenLab, the default value is for a benign environment with no disasters (Never). This frequency can be changed to produce occasional disasters (Sometimes) or frequent disasters (Often).

After you have finished this introduction to the input parameters, click the Reset button at the left of the screen to return all input parameters to their default values.

1. Testing the Hardy-Weinberg Principle: Now that you are familiar with the basic parameters in PopGenLab, set up the following experiment to help you understand Hardy-Weinberg equilibrium and the factors that influence a state of equilibrium in a population.

Leave all input parameters at their default values. Check the genotype frequency value and note the allele frequency values for comparison after you have run the experiment. You now have an experimental paradigm with equal allele frequencies; genotype frequencies of 50% brown, 25% white, 25% black; equal proportions of each tree type; one tree stand with a carrying capacity of 4000 (this is a large population of moths); random mating; and because the disaster frequency is set at "Never," the population size of these moths will remain constant.

Based on these conditions, does each moth genotype have an equal chance of survival or is there a selective pressure (positive or negative) on one or more genotypes? Explain your answer.

Return to the initial page of the simulation if you are still in the Change Inputs view. Find the popup menu, showing the number of generations, in the lower left corner of the screen. Leave generation number set at its default value of 100. Click the Run Experiment button to run this simulation.

When the experiment has finished running, a separate page will appear that presents the results of your experiment. Note: Any of the following data views can be saved to disk or printed by clicking the Export button. Clicking on this button will open a separate window with your plot or table. From this window you can then save your data to your hard drive or a disk, and you can print your data by using the print feature of your browser software. The following data can be examined:

Genotype Frequency - click and drag the slider to show genotype frequency as the frequency of AA (black), Aa (brown), and aa (white) genotypes for each generation. Data is represented as a pie chart showing the percentage of each different colored moth in the total population for each generation.

Allele Frequency - click on the check boxes to show a plotted view of allele frequency for each allele (A or a). Data is represented as the percentage of an allele in each generation.

Heterozygosity - plots the percentage of heterozygous moths in each generation over time.

Population Size - plots the number of moths in each generation over time.

Allele Distribution - plots the frequency of the A allele vs. the number of populations in each generation over time.

Textual Data - text columns of raw data for allele frequencies.

Input Summary - a summary table of the input parameters for the experiment that you carried out.

Look at the allele and genotype frequencies. Is there a change in allele frequency over time? Is there a change in genotype frequency over time? What did you observe? Explain your answers.

How do the actual genotype frequencies compare to the Hardy-Weinberg predictions?

Repeat this experiment at least three or four times to determine if the results from this experiment are consistent.

Repeat this experiment with a different set of initial genotype frequencies, but before you run the experiment, use the Hardy-Weinberg equation to predict what will happen to this population.

What did you discover? Did the results agree with your predictions? Why or why not?

2. Extending Hardy-Weinberg Principles (for use by advanced students): Repeat the experiment described above and use Chi-square analysis with one degree of freedom to test your prediction.

How many generations does it take for a population to reach Hardy-Weinberg equilibrium?

Can different initial genotype frequencies lead to the same Hardy-Weinberg equilibrium?

Assignment 2: Genetic Drift
Random changes in the genotypes of a population are known as genetic drift. Genetic drift has the potential to change the genetic composition of populations. Carrying capacity of an environment can influence how a population changes in response to genetic drift because carrying capacity is an important factor that determines the size of a population. Large populations rarely show strong effects of genetic drift; however, genetic drift in a small population can have a great influence on allele and genotype frequencies in that population. The following exercise is designed to help you understand important aspects of genetic drift as a potential cause of microevolution.

Influence of Carrying Capacity
Formulate a hypothesis to predict the effect of a decrease in tree stand carrying capacity on allele and genotype frequencies.

Set up an experiment with default values for all of the Hardy-Weinberg conditions. Run this experiment and make note of what happens to allele and genotype frequencies (especially if you did not do assignment 1).

Run a series of experiments with default parameters for all conditions except tree stand size. For each experiment, reduce tree stand size by one-half (for example, run an experiment at 2000, half of the default value, then change tree stand size to 1000, and so on) After each experiment, make notes of what you observed for allele and genotype frequencies. Be sure to repeat each experiment several times. After you have completed this series of experiments, answer the following questions.

What happened to allele and genotype frequencies in this experiment? How do these results compare with what you observed for allele and genotype frequencies under the default conditions? Explain these results.

What happened to the percentage of heterozygotes? Explain these results.

In the following experiment, you will study several populations in different isolated tree stands.

Set up an experiment with the number of tree stands set to the maximum value of 100 and perform a series of experiments with different tree stand carrying capacities. Study genotype and allele frequencies that result from each experiment. When you are examining genotype and allele frequencies, and heterozygosity, use the text box or arrows in the lower right corner to change your view so you can see the results for the population in each tree stand as well as the average results. For each experiment, go to the Allele Distribution view and use the slider to examine allele frequency among the populations. In addition, examine what happens to population size. For each experiment, answer the following questions.

What happened to the average genotype frequencies? What happened to the genotype frequencies in each population? What happened to the allele frequencies in each population? What happened to the average allele frequencies? Explain these results.

What happened to the average heterozygosity? What happened to the heterozygosity in each population? Explain these results.

How does population size (carrying capacity) affect the changes in genotype and allele frequencies that you observed in these experiments?

What do these experiments tell you about the effect of population size on genetic variation?

Did any of the populations that you studied become extinct? If so, which ones? Why did these populations become extinct while others avoided extinction? What can you say about the relationships between carrying capacity and the risk of extinction?

Assignment 3: The Influence of Mating Patterns on Population Genetics
One of the conditions required for maintaining Hardy-Weinberg equilibrium in a population is random mating. When individuals select mates with a particular heritable trait-for example, color or size-this is a form of nonrandom mating known as assortative mating. Similarly, inbreeding is another form of nonrandom mating in which closely related individuals within a population mate. In this experiment, you will examine how different forms of mating among moths influence Hardy-Weinberg equilibrium.

1. Assortative Mating
Set up an experiment at default conditions for Hardy-Weinberg equilibrium for all parameters except the number of tree stands. Set tree stand number to 100. Carry out the first experiment with random mating. Then conduct a number of experiments where there is assortative mating. Use the slider to choose different degrees of assortative mating in values ranging from 0% (random mating) to 100% (only like phenotypes mate).

What is the effect of assortative mating on genotype frequencies? Allele frequencies? Heterozygosity? Explain your answers.

Compare the effects of assortative mating to those of genetic drift (you will need to carry out additional experiments to complete this assignment). Carry out experiments similar to those that you did for genetic drift, but change mating to different degrees of assortative mating.

How do the effects of assortative mating compare to those created by genetic drift? In particular, are the effects of assortative mating and the effects of genetic drift the same at different population sizes? Why or why not? Explain any differences you encountered between population size and the effects of assortative mating, and population size and the effects of genetic drift.

2. Disassortative Mating
Conduct a series of experiments where there is disassortative mating. Choose different degrees of disassortative mating at values between 0% (random mating) and 100% (only unlike phenotypes mate).

What is the effect of disassortative mating?

3. Genotype Frequencies and Mating Style
For both assortative and disassortative mating, conduct more experiments where you vary the initial genotype frequency. Try experiments where the initial allele frequency is not equal to 0.5.

Based on the results of these experiments, can you draw any other conclusions about the effects of assortative and dissassortative mating on allele frequency?

Assignment 4: Modes of Natural Selection
It is possible for natural selection to affect allele and genotype frequencies in several ways depending on the mode of natural selection occurring within the population. Different modes of natural selection can select for or against a particular trait, thus affecting the balance of phenotypes in the population. For example, in a mode of natural selection called directional selection, selection favors individuals with one of the extreme phenotypes--a phenotype at either end of the range of phenotypes. For example, all black or all white moths are at the extremes while brown moths represent an intermediate phenotype. In stabilizing selection, extreme phenotypes are selected against and intermediate phenotypes have higher rates of reproduction or survival. Conversely, diversifying (disruptive) selection favors individuals with a range of extreme phenotypes over individuals with an intermediate phenotype.

In the following experiment you will investigate how fitness--the probability that a particular phenotype will survive and produce offspring (which is a measure of survival and reproduction of different genotypes)--affects changes in allele frequency in the population.

Begin an experiment with default conditions for Hardy-Weinberg equilibrium for all parameters except the number of tree stands and genotype frequencies. Set the number of stands to 100. (Recall that the survival of the three types of moths depends on the distribution of tree types within the stand). Change genotype frequency to set up several different experiments under conditions of directional selection for dark color, directional selection for light color, balancing selection, and diversifying selection. For each experiment, look at genotype and allele frequencies.

Try experiments with the different conditions of selection and initial allele frequencies near zero and one.

What happens to allele frequency in the case of directional selection? Does directional selection for dark color produce the same result as directional selection for light color?

What happens to allele frequency in the case of balancing selection?

What happens to allele frequency in the case of diversifying selection?

Are small differences in fitness effective in changing allele frequencies? (Conduct additional experiments with varying proportions of tree types to help answer this question.)

Under what mode of selection might genetic variation be maintained? Explain your answer.

Under what mode of selection might there be a "founder effect," where the final allele frequency depends on the initial allele frequency? Explain your answer.

Assignment 5: Migration
Random genotypic and phenotypic changes in isolated populations can be overcome by migration. Both movement of organisms into a population and the migration of organisms out of a population can influence genotype frequencies. Migration can result in new alleles being introduced into a population. Conversely, when organisms migrate out of a population the frequency of certain alleles in the population can decline.

Run an experiment with a large amount of genetic drift occurring in 100 isolated populations by setting the number of stands to 100. To create migration among these populations, click on the Migration button and use the slider to change migration rate. Design and carry out experiments where there are different levels of migration occurring among the populations. For each of these experiments, carefully study what has happened to the populations by analyzing each category of results (genotype frequency, allele frequency, etc.).

Does migration modify the effects of genetic drift? If so, how? Explain.

Assignment 6: Population Bottlenecks
Occasionally populations undergo "crashes," when the population size gets too small. For example, a rapid reduction in population size can occur due to natural disasters such as flood, fire, tornadoes, drought, and other extreme weather conditions. These natural disasters are frequently unselective in nature--they kill individuals throughout the population and are not selective for a particular phenotype. Even if population numbers recover, the effect of a natural disaster can have an impact on the gene pool in a population for many generations because the range of genotypes (both frequency and number) in the population that survived the disaster may not be the same as it was in the original population. Biologists call this effect a bottleneck effect.

Conduct an experiment in which there is very little genetic drift. Repeat the experiment with moderate and high frequencies of "disasters" that reduce population numbers to small values.

What is the impact of these population bottlenecks?

How do these disasters affect the probability of population extinction?

Can these effects be mitigated by allowing migration to occur among the population? Yes or no? Design and carry out experiments to examine this idea. Based on your results from these experiments, if you were a conservation biologist, what would these data suggest to you about the design of natural reserves?

Assignment 7: Group Assignment
The experiments that you have conducted so far were designed to help you learn about the many parameters that influence population genetics. Typically, each of the experiments you set up analyzed the effects of a single parameter; however, it is important to realize that in nature, population genetics for any population is typically affected by changes in multiple parameters at the same time. The following experiments are designed to help you study the effects of different combinations of factors. Work together in a group of four students to complete these exercises.

Divide your group into pairs. For each pair of students, design and carry out a set of experiments with a different combination of parameters--for example, different rates of migration with different modes of selection, different modes of selection with different types of mating, and so on. Consider changing parameters to create situations that act in opposite directions (e.g., balanced selection with assortative mating). Before you run each experiment, formulate a hypothesis to predict the effects of your experimental conditions. Discuss this hypothesis with the other pair of students in your group and reformulate a hypothesis if necessary. Run the experiment, then analyze your results. Be sure to repeat each experiment at least twice to confirm your results.

Did the results of your experiment support your hypothesis? If not, reformulate a new hypothesis and carry out additional experiments. Explain how the experimental conditions you set up were responsible for your results. Once you think you have an explanation for your findings, design and carry out additional experiments to support or refute your thesis.

Discuss the results of your experiment with your instructor to clarify questions that you may have about interpreting the results of your experiment and understanding the effects of the experimental conditions you created.