Mendelian Pigs GIRP
We have spent the quarter developing a theory of evolution. It includes a theory of variation and inheritance.
How well does our theory predict how populations will evolve? We have looked at data from populations of insects living in bottles, and we will look at a couple of examples involving human populations. This assignment will let you do experiments of your own.
To make theoretical predictions using the equations of the Hardy-Weinberg Equilibrium principle, you can use a customized version of the AlleleA1 calculator called PigCheck.
To observe what happens in a “real” population, you can use the SimUText’s Mendelian Pigs—Section 3, Page 10 “Hungry Wolves.” Mendelian Pigs employs an individual-based model of an evolving pig population. That is, it tracks individual virtual pigs as they move around in space, bump into each other and mate, and die—either of old age or in the jaws of a wolf. You may find find is useful to refer to this table of genotypes and phenotypes:
The Pig Check assignmment has more detailed instructions on how to proceed. Once you have completed Questions 1-3, take a look at the aggregated data from 20 randomly-chosen students in a previous class.
I have created customized versions of the population genetics calculator, using spreadsheet software, that will draw graphs showing both the theoretical prediction and data from a dozen replicate runs in Mendelian Pigs:
Your Task
As a group, pick one of these questions to investigate (or develop a different question in consultation with me):
- What happens to allele frequencies in a population when heterozygotes have higher fitness than either homozygote?
- Use PigCheck first, to investigate a wide variety of different starting frequencies for allele A1 and different relative fitnesses for the three genotypes.
- Does PigCheck accurately predict what happens in populations of virtual pigs where heterozygotes have higher fitness than either homozygote?
- Use PigCheck first, to investigate a wide variety of different starting frequencies for allele A1 and different relative fitnesses for the three genotypes.
- What happens to allele frequencies in a population when heterozygotes have lower fitness than either homozygote?
- Use PigCheck first, to investigate a wide variety of different starting frequencies for allele A1 and different relative fitnesses for the three genotypes.
- Does PigCheck accurately predict what happens in populations of virtual pigs when heterozygotes have lower fitness than either homozygote?
- Use PigCheck first, to investigate a wide variety of different starting frequencies for allele A1 and different relative fitnesses for the three genotypes.
- Can immigration impede local adaptation?
- Use PigCheck to consider scenarios in which selection favors one allele over the other. Set up populations in which migrants bring the other allele into the population every generation. Look for combinations of parameters that are interesting.
- Once you’ve found an interesting set of parameters in PigCheck, set up similar scenarios in Mendelian Pigs to see if PigCheck accurately predicts their behavior. (How will you simulate immigration?)
- Use PigCheck to consider scenarios in which selection favors one allele over the other. Set up populations in which migrants bring the other allele into the population every generation. Look for combinations of parameters that are interesting.
- In a finite population, how strongly must selection favor a rare allele to give it a reasonable chance of rising to fixation?
- Use PigCheck to consider scenarios in which selection in a finite population favors a rare allele. You will want to use population sizes similar to those you can set up in Mendelian Pigs. Look for combinations of parameters that are interesting.
- Once you’ve found an interesting set of parameters in PigCheck, set up similar scenarios in Mendelian Pigs to see if PigCheck accurately predicts their behavior.
- Use PigCheck to consider scenarios in which selection in a finite population favors a rare allele. You will want to use population sizes similar to those you can set up in Mendelian Pigs. Look for combinations of parameters that are interesting.
- Develop a hypothesis to explain why predictions based on the Hardy-Weinberg Equilibrium Principle (that is, predictions using AlleleA1 or PigCheck) were less accurate for the scenario in the Pig Check Assignment, Question 3 than for the scenarios in Questions 1 and 2. Design and run an experiment to test your hypothesis. (My students and I have come up with three hypotheses—each with some experimental support.)
More details
Group Collaboration Agreement
Please discuss and compelte a group collaboration agreement
Written Report
Please read the following documents under the Info tab in the main menu:
- Dr. Herron’s List of Common Prose Errors, Plus some Pet Peeves
- Citation Format
- Research Report Format
For this assignment, your question will be something along the lines of: “How do populations evolve when heterozygotes have highest fitness?” or “How does population size affect how populations evolve?” or “Does migration influence the extent to which populations evolve to adapt to local conditions?” State your hypothesis about what the answer will be and explain your reasoning. Your hypothesis will be, in essence, “Populations will evolve as predicted by the theory of population genetics”—although you should be able to provide a little more detail in your group’s particular case.
Note that there are (obviously) many ways in which a prediction could be wrong. The simplest one to use for this assignment is the null model: The population will not evolve. That is, the population will behave like the idealized population imagined by the Hardy-Weinberg Equilibrium Principle. With random mating, no selection, no migration, no mutation, and no sampling error, allele frequencies will not change from one generation to the next. You can produce a graph of this with the calculator by changing the starting allele frequency to the one(s) you will use and leaving all other parameters at their default settings.
You want to provide an answer to your question that is a general as possible. This will mean two things: (i) Try different parameter values. For example, if you’re looking at what happens when heterozygotes have the lowest fitness, try different values for the fitness of heterozygotes; also look at what happens when the fitness of the homozygotes are the same versus different (but still higher than the heterozygtoes); (ii) For each combination of parameters, perform several replicate experiments in Mendelian Pigs. Something a little different happens every time; you need to make sure the results you present are not a fluke.
It would be a nice touch to run some replicate experiments in Mendelian Pigs to see if the pig population behaves as expected under the null model when the model’s assumptions are satisfied.
- Dr. Herron’s List of Common Prose Errors, Plus some Pet Peeves
Grading
Your grade will be based on the clarity of your question, the acuity of your scientific reasoning, the design and conduct of your study, and the lucidity of your report. Your grade will not be be based on whether your hypothesis turned out to be right or wrong.
Before uploading your finished report, please be sure to check it against the rubric on the Canvas assignment page.