AV BIOL368 Week 2

Purpose

The purpose of this assignment was to use and observe an already created modeling system to see how it is structured and how it follows the definition of a model as previously defined in class. These definitions can also be found in the Week 2 Class Journal. This assignment also helps us determine what we think is important and not important when creating a model by determining the best and most frustrating aspects of working with this program.

Methods & Results

1. Go to [1] and download the software.
2. Unzip the folder and run the executable. Switch to the Evolution tab.
3. Turn off mutations.
   • Select: File > Preferences
   • Click on Mutation Rates, and uncheck the "Mutations Enabled" checkbox.

Part A: Select for Red

1. Select both the red organism and the white organism in the Greenhouse by pressing shift while clicking on the organisms.
2. Click the load button in the controls.
   • The setting screen indicated 55 white organisms and 45 red organisms.
3. Set the fitness of the red to 10 and all other colors to 0.
4. Prediction: After several generations, there should be only red organisms.
5. Click the "One Generation Only" button in the controls menu box. The starting organisms contribute to the offspring according to their fitness. Each offspring flower will get two alleles randomly chosen from the gene pool.
6. Results: As we simulated more generations, more red organisms and fewer white organisms appeared. It took about 14 generations to get to pure red. The reason there were sometimes white offspring from all-red generations is because some of the red may have been heterozygous and produced a homozygous recessive white organism.

Part B: Select for White

1. Select both the red organism and the white organism in the Greenhouse by pressing shift while clicking on the organisms.
2. Click the load button in the controls.
   • The setting screen indicated 56 white organisms and 44 red organisms.
3. Set the fitness of the white to 10 and all other colors to 0.
4. Prediction: After several generations, there should be only white organisms.
5. Click the "One Generation Only" button in the controls menu box. The starting organisms contribute to the offspring according to their fitness. Each offspring flower will get two alleles randomly chosen from the gene pool.
6. Results: Almost immediately there were only white organisms in the world. It took only one generation to reach an all-white generation. This is most likely because only white organisms have a successful fitness, and they are produced by homozygous recessive organisms. Because white offspring had the maximum relative fitness, and all of the other organisms had 0 fitness, only recessive alleles made it to the next generation, preventing any red organisms from being created.
   • It took more generations to get all red than all white because only the recessive allele survived from the first generation and the recessive allele codes for white. However, for red, any organism with at least one dominant allele survived, so there were more instances of heterozygous organisms. This is because heterozygous organisms survived and contributed recessive alleles to the next generation. Because there were recessive alleles, it was possible for some offspring to be white.
7. Turn on the setting to "Show colors of both alleles" in the "World Settings" part of "Preferences"
   • When I turned on that setting, I did not see any changes on the world screen.

Part C: Hardy-Weinberg Equilibrium & Natural Selection

1. Load the world with only red organisms from the greenhouse.
   • The world appeared entirely red. I already turn on the setting to show colors of both alleles. It is now clear that the reason I did not see the white alleles in the previous step because they just appeared as white boxes on a white square.
   • I now see that each red organism has a red and white allele as represented by a small red and small white rectangle in the top corner of the organism.
2. Set all fitnesses to 5.
   • This population is in Hardy-Weinberg Equilibrium.
     • When I initially went through this protocol, I mistakenly thought that the population was in HWE, but after completing more of the protocol, I became aware of how this population was not in HWE. More information about how I made this discovery is noted below.
3. Calculate allele frequencies for the starting population.
   • Allele frequencies for the starting population: 50% R, 50% r
4. Calculate genotype frequencies expected at HWE.
   • Genotype frequencies: 25% RR, 50% Rr, 25% rr
5. Is the population in HWE?
   • The population is in HWE because both the allele frequencies and expected genotype frequencies add up to 100%.
6. Run one generation.
   • My group member Colin Wikholm let several generations run and noticed that eventually *after hundreds of generations) the program would favor one or the other organism. This debunked our initial belief that the population was at HWE. After some analysis we realized that this is most likely because the population size is about 100 organism which does not constitute a large population. For that reason, this population does not follow the principles of HWE.
   • The population is not at HWE because 79% of organisms are either RR or Rr and 21% of organisms are rr. Though these rations are very close to HWE expected values, they are not exactly 75/25 as expected. This is mostly likely because with only 100 organisms, this population does not follow the HWE rule of large populations.
7. Set the fitness of red to 10 and all other colors to 0.
8. Prediction: There should be an increase in allele frequency for R (p) and a decrease in allele frequency for r (q) over several generations.
9. Click "One Generation Only" a couple times.
   • Genotype frequencies after 5 generations: 72% RR, 28% Rr, 0% rr
   • Allele frequencies after 5 generations: 86% R, 14% r
10. Results: The results of the allele frequencies after 5 generations does match my predictions. After just 5 generations, the allele frequencies shifted from about 50/50 R and r alleles to about 85/15. I am confident that after a few more generations, these frequency of the r allele would be almost 0% and the frequency of the R allele would be almost 100%. This is because the population is not in HWE because of the increased fitness of the red organism vs. all other organisms.

Conclusion

The purpose of this assignment was to observe a modeling program and to identify key characteristics that are common to all models. We made these observations on a program created by Aipotu. Our group worked specifically with their Evolution module and supporting instructions. The purpose of that module is to observe Hardy Weinberg Equilibrium with red and white flowers in which color was determined by a single gene. The program took us through several different scenarios where we manipulated relative fitness and the starting population of organisms (red and/or white organisms). The program allows us to manually adjust relative fitness, which adjusted how many organisms of different colors we started with, and how the allele and genotype frequencies were affected throughout different generations. It also provided us with some information about the genetic make up of the organism by providing small colored rectangles in the top right corner of each organism signifying the color of each of the alleles in the organism.

A screenshot of how the model was set up including the allele make-up of each organism.

The program that we used had a great interface and was easily manipulated for different scenarios. I found the model itself to be intuitive to read with exception of the genotypes of each organism. When showing the colors of each allele for each organism, the alleles often just blended in with the color of the organism since there was no border around the alleles. This functionality of the model made it difficult to discern what the genotypes were until I played around with the program longer and made some guesses about what was happening. Aside from that difficulty, I found the program to easily understood, and think it was a great example of a modeling program.

Data & Files

No files were created as a part of this assignment.

Acknowledgements

Thank you to Colin Wikholm and Courtney Merriam for collaborating with me on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

• Aipotu
• Week 2 Assignment Page

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

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

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Links: Electronic Lab Notebook