Courtney L. Merriam Assignment 2

From OpenWetWare
Jump to: navigation, search

Purpose

The purpose of this experiment was to explore evolution with evolving digital organisms, test evolutionary hypotheses, and try out different evolutionary scenarios.

Methods and Results

  1. Go to Aipotu to download Aipotu as a zip file
  2. Unzip the file by right clicking and clicking unzip here
  3. Open the application and switch to the evolution tab
  4. Turn off mutations
    • File > Preferences > Mutation Rate > Uncheck the Mutations Enabled checkbox > click OKAY
  5. Run simulations of Natural Selection

A) Select for Red

  • Click the Red organisms in the Greenhouse
    • While holding the shift key, click on White organism in the Greenhouse
  • Click the Load button in the Controls
    • Note the count or red and white in the Settings panel
      • Red:47
      • White:53
  • Set the Fitness setting in the Settings panel to select for red
    • Set the fitness of red to 10 and all other colors to 0
  • Prediction:
    • What should happen to the number of red and the number or white flowers after several generations with this selection?
      • All the flowers should end up red
  • Test: Click the One Generation Only button in the Controls
  • Results:
    • What will happen to the counts of red and white flowers as you simulate more generations?
      • Red increased while the white decreased ending with a 100:0 ratio
    • Roughly how many generations does it take to get to pure red?
      • 9 generations
    • Some all-red generations can have some white offsprings why?
      • Generation 11 had a white offspring because the generations before may have had an allele for white and the two bred together getting a white flower.

B) Select for White

  • Click the Red organisms in the Greenhouse
    • While holding the shift key, click on White organism in the Greenhouse
  • Click the Load button in the Controls
    • Note the count or red and white in the Settings panel
      • Red:53
      • White:47
  • Set the Fitness setting in the Settings panel to select for red
    • Set the fitness of White to 10 and all other colors to 0
  • Prediction:
    • What should happen to the number of red and the number or white flowers after several generations with this selection?
      • All the flowers will end up white
  • Test: Click the One Generation Only button in the Controls
  • Results:
    • What will happen to the counts of red and white flowers as you simulate more generations?
      • White increased to 100% and red decreased to 0%
    • Roughly how many generations does it take to get to pure red?
      • 1 generations
  • Why does it take more generations to get pure red than it does to get pure white?
    • This is because the some of the red flowers will have an allele for white so there are opportunities to get white flowers while the white flowers only have two white alleles so there is no chance for a red flower.

C) Hardy-Weinberg Equilibrium and Natural Selection

  • Lode the World with only Red organism from the Greenhouse
  • Show the colors of both alleles in each organism by checking the Show colors of both alleles in the World settings part of the Preferences
  • Set all Fitnesses to 5
    • Is this population Hardy-Weinberg Equilibrium?
  • Calculate the allele frequencies in the starting population:
    • R: 50%
    • r:50%
  • Calculate the genotype frequencies expected at HWE:
    • RR: 0
    • Rr: 100
    • rr: 0
  • Is the population at HWE? Why or why not?
    • Yes because the allele frequency of R + r adds up to 100%
  • Run one generation only
    • Is that population at HWE?
      • No it is not HWE
  • Set the Fitness setting in the Settings panel to select for red. Set the fitness of red to 10 and all other colors to 0
  • Prediction:
    • What should happen to p and q after several generations with this selection?
      • p becomes greater while q decreases
  • Test: Click the One Generation Only button in the Controls. Do this a few times.
  • Results: Caculate p and q
    • RR: 74
    • Rr: 26
    • rr: 0
      • Frequencies of R(p)= 174
      • Frequencies of r(r)= 26
  • Does the results match your predictions? Why or why not?
    • Yes this does match my prediction because the frequency of R increased while the frequency of r decreased.

Data and Files

No files or data was used for this assignment.

Conclusion

The purpose of this experiment was to explore evolution with evolving digital organisms, test evolutionary hypotheses, and try out different evolutionary scenarios. The group I worked with on this project focused on the evolution module of the program. The module worked to view Hardy Weinberg Equilibrium with the representation of red and white flowers. I found the computer program Aipotu to be easy to use and understand. The program was useful in the fact that I could modify the variables to see how it would effect future generations. It would have been nice if the program generated the number of hybrids in order to easily count the allele frequency.


Acknowledgments

I collaborated with Anindita Varshneya and Colin Wikholm in class 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

Evolution. (n.d.). Retrieved September 6, 2016, from Aipotu This website and corresponding downloaded program were used to complete this assignment

Useful Links

Courtney L. Merriam

Clas Page: Bioinformatics Laboratory

Weekly Assignments Individual Journal Assignments Shared Journal Assignments