Colin Wikholm's Individual Journal Assignment Week 2

Purpose

The purpose of this assignment was to use the Aipotu program as a model of real life biological manifestations. Our project was specific to evolution and examined changes in alleles frequencies within simulated populations. The assignment was performed with respect to Hardy-Weinberg Equilibrium and the presence or absence of evolutionary forces within the model. The undertaking was meant to both improve our understanding of evolution and models in biology. Finally, this assignment was meant to master working with our electronic notebook.

Methods and Responses/Results

Setup

1. Download the Aipotu program and unzip the files
2. Run the program
3. Click on the "Evolution" tab
4. Go to "File," click on "Preferences," then "Mutation Rates," and finally and turn off "Mutations Enabled"

Section A: "Select for Red"

1. Holding the shift key, click once on both the Red and White organisms.
2. Click on "Controls" and select "Load." The population will consist of approximately 50 red and 50 white organisms (to check, look at the Settings panel).
3. Click the "Settings" tab and select "Fitness." Set the fitness of red organisms to 10 and the others to 0.
4. Predict what will happen to the number of red and white organisms over several generations:
   • A: I predict that the allele for white flowers will go extinct in a few generations and the entire population will consist of red flowers.
5. Test the prediction by going to the "Controls" clicking "One Generation Only"
6. State the results of the test. How many generations passed before the population was pure red and white organisms stop appearing as offspring. Why can all-red populations have white offspring?
   • A: It took 26 generations for the white flowers to stop appearing completely. The allele for whiteness might be recessive, and thus may not show up in heterogeneous parents but appear in their offspring (if they are homogeneous recessive).

Section B: "Select for White"

1. Select both the Red and White organisms as in Section A
2. Select "Load" to create a population with 50 Red and 50 White organisms. Check this in the Settings panel as in Section A.
3. Got to "Settings" and this time change the "Fitness" setting so that the fitness of white is 10 and the fitnesses of other colors are set to 0.
4. Predict what will happen to the amount of red and white organisms after several generations.
   • A: I predict that the allele for white flowers will dominate and, in a few generations, the entire population will consist of white flowers (the red flowers will stop appearing)
5. Test the results again as in Section A, number 5
6. Report the results as more generations are tested. How many generations pass before the population consists of only white organisms?
   • A: It takes only 1 generation for the red flowers to stop appearing.

Why does it require more generations to have a pure red population than a pure white population? To help answer this question, select "Preferences" and got to "World Settings." Check "Show colors of both alleles."

• A: The white flowers are homozygous, while the red alleles are heterozygous. Red is the dominant allele, so each parent generation starts with an allele frequency of 75% white : 25% red. Because there is a higher frequency of the white alleles, they take greater time to eliminate even with very low fitness. When the white phenotype confers greater fitness, the white alleles dominate the population quickly."

Section C: "Hardy-Weinberg Equilibrium & Natural Selection

1. Load the world as before, but with a population of all Red.
2. If not already shown, show the allele of the population as in Section B.
3. Change the Fitnesses of all organisms to 5
   • Is the population in Hardy-Weinberg Equilibrium (HWE)?
     • A: The population is almost at HWE, but not quite. The population is undergoing low levels of evolutionary forces and the allele frequency of the population is not changing substantially over a short period of time. However, running the population over a long period of time undergoes evolution due to genetic drift (small population size of 100 individuals). In this case, the frequency of alleles in the population changes.
4. Determine the frequencies of alleles in the initial population
   • frequency of R (p) = .50
   • frequency of r (q) = .50
5. Determine what the genotype frequencies that would occur at HWE:
   • frequency of RR = p2 = .25
   • frequency of Rr = 2pq = .50
   • frequency of rr = q2 = .25
6. Is the population at HWE? Explain.
   • A: The population is at HWE. The frequency of the alleles in the population has not changed. It will still have a ratio of .50R : .50r
7. Run one generation and determine if the population is at HWE. Combine group results if your individual population is too small and influences HWE.
   • A: The population is very close to Hardy-Weinberg equilibrium. There following are the frequencies of the simulated population:
     • frequency of RR = .24
     • frequency of Rr = .46
     • frequency of rr = .30
   • The following allele frequency thus follows:
     • frequency of R(p) = .47
     • frequency of r(q) = .53
   • Although the actual population does not follow HWE perfectly because of the small population size, it nearly approximates it.
8. Change the fitness of red to 10 and the other colors to 0
9. Predict what will happen to p and q after multiple generations.
   • A: The frequency of the red allele should increase and the white decrease.
10. Test your prediction one generation at a time.
11. Calculate p and q as before.
    • frequency of RR = .74
    • frequency of Rr = .24
    • frequency of rr = .02
    • frequency of R(p) = .84
    • frequency of r(q) = .16
12. Report your results and compare to your predictions. Do they match? Explain.
    • A: The results matched the predictions. Because of the higher fitness conferred by the allele for red color, the population increased its frequency of red alleles and decreased its frequency of white alleles.

Scientific Conclusion

I found that the Aipotu program was a useful tool for testing evolutionary forces. The software was straightforward and easy to work with. It was also complex enough to model evolution in a way that was educative. For example, even when no evolutionary forces were intentionally placed upon a population, the software accounted for genetic drift due to the small size of the population. Although this was not initially apparent to me, the discovery showed me that models can be effective modes of learning about topics which I may have overlooked or taken for granted. In addition, I was able to observe allele frequencies stay the same over a few generations and then change over many generations. I applied HWE to examine the change in allele frequencies and learned the interface for using this model software. I believe that I both improved my understanding of evolutionary forces and how models may be used as learning tools for real life biological occurrences. As far as working with my electronic workbook, I feel that I also greatly improved my note-taking and syntax skills.

Data and Files

No data or files were saved for this project.

Acknowledgments

I worked with my partners Anindita Varshneya and Courtney L. Merriam to answer some of the above questions and on technicalities of using the Aipotu software. I would also like to thank Dr. Kam D. Dahlquist for her assistance in problem-solving and with software interface. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Colin Wikholm 02:12, 13 September 2016 (EDT)

References

Assignment Page: BIOL368/F16:Week 2

Direct link to directions (and link from which methods were adapted): Part IV: Evolution

Aipotu software

Author of Page: Colin Wikholm

Important links

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

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