Icrespin Journal Week 2
Contents
Evolution: Electronic Lab Notebook
Purpose
The purpose of Aipotu IV: Evolution is to be able to understand evolution by stimulating it. In this program, the user uses Aipotian flowers as part of a large population. The user begins with a size of 100 flowers. Each flower has a lifespan of one year and immediately dies after the production of seeds for a new generation. This simulation uses colors (Red and White) and shows how natural selections is happening with a the qualities noted above. Fitness plays a key role and by simulating different levels of fitness, the user will be able to better understand how there are mutations and which colors survive in the flowers.
Methods/Results*
In order to do the Evolution portion, user will use the program named Aipotu.
Aipotu can be downloaded using this link: Aipotu Home Page
Once link is clicked, user will go to the Download tab, and follow instructions to acquire program.
After downloading, user will click on the fourth tab titled Evolution.
Part A
- In Greenhouse, user will click on Red and White flowers
- User will click on Load
- User changes fitness of red to 10 and the other flower colors to 0
- Answer prediction question
- Test prediction by clicking on One Generation Only in Controls
Prediction: Overall, after changing the fitness, it can be predicted that red flowers will dominate after several generations with this selection.
Result: After clicking loading, there was a count of 52 red flowers and 48 white flowers. It can be seen that there is roughly a 50:50 ratio between the two colors with a fitness of 5 for each color. Once fitness was changed, the count of the red flowers increased. Therefore, the prediction that was made follows with the results. After loading one generation only, the red flowers count went up to 69 and the white flowers went down to 31. After one generation, white is still visible, but it is the recessive trait in this pool. After 3 simulations, the red flower count increases and the white flower count decreases. By 11 generations, there is a pure red generation. Some all-red generations can have some white offspring because all-red flowers can be considered as homozygous or heterozygous dominant alleles. Therefore, if it is considered heterozygous, then there is a chance that there would be white offspring.
Part B
- Click on Red and White flowers
- Click on Load
- Change Fitness settings for the White flowers by making it 10 and the other colors to 0
- Answer prediction question
- Test by clicking on One Generation Only button
Prediction: If fitness is at 10 for white flowers, the number of red would decrease and the number of white would increase. After several generations, there should be a world of all white flowers.
Result: When first 2 steps were done, there was a 50:50 ratio of red and white flowers. After changing fitness to 10 for white flowers, all of the flowers where white. In one generation, the world was covered in pure white. As more simulations occur, it can be seen that white flowers are dominant. It takes more generations to get to pure red than pure white because in this specific simulation, the recessive is the white. Therefore, with a fitness at 10, white is being naturally selected to come out. Whereas, in red, it takes either homozygous or heterozygous alleles to appear in the pool.
Part C
Section 1
- In World settings, click on Preferences
- Click on Show colors of Both Alleles
- This will allow World to display the genotype of each flower
- Load World by clicking on the Red flowers
- Make sure both alleles for the flowers are showing
- User can confirm this by seeing little red/white rectangles in the upper left corner of each flower
- Set all colors to have Fitness to 5
- Calculate the allele frequencies using table provided in results
- Calculate genotype frequencies expected
- Run one generation only
Result: After setting up the world, it can be seen that all of the flowers are red. However they have one red and white allele making the genotype Rr. This can be seen with the white rectangle described in methods.
The following table shows the allele frequencies in the starting population:
| Genotype | Number | #R's | #r's |
|---|---|---|---|
| RR | 0 | 0 | 0 |
| Rr | 100 | 50 | 50 |
| rr | 0 | 0 | 0 |
| TOTAL: | 50 | 50 |
- Frequency of R (p) = 50/100 = 0.50
- Frequency of r (q) = 50/100 = 0.50
This following information is the calculations of the genotypes frequencies expected at HWE:
- Frequency of RR = p2 = 25/100 = 0.25
- Frequency of Rr = 2pq = 50/100 = 0.50
- Frequency of rr = q2 = 25/100 = 0.25
After calculating the genotype frequencies expected, the population that is listed in the table above does not follow HWE because there aren't any RR or rr visible. In this specific population, all of the flowers have a genotype of Rr. This makes them red.
After running a one generation only, the results were 81 red and 19 white. There are 19 rr, 32 RR, and 49 Rr. This run is somewhat similar to the HWE because as mentioned about the frequency of each genotype, RR and rr should be at 0.25 each. Each one is roughly there. Also, Rr is roughly 0.50 as the frequency.
Section 2
- Set Fitness in red to 10 and the other colors to 0
- Create a prediction
- Test by clicking on One Generation Only button
- Click on that button for a couple of times
- Calculate p and q using table provided in results
Prediction: If fitness changes to 10 for red, then p will be greater than q. P would stand for the color red and there would be a lot more with that color trait.
Result: After 2 generations, there are 89 red and 11 white. In 3 generations, there are 97 red and 3 white. By 8 generations, it is 100 red and 0 white.
| Genotype | Number | #R's | #r's |
|---|---|---|---|
| RR | 90 | 90 | 0 |
| Rr | 10 | 5 | 5 |
| rr | 0 | 0 | 0 |
| TOTAL: | 95 | 5 |
- Frequency of R (p) = 95/100 = 0.95
- Frequency of r (q) = 5/100 = 0.05
- Does the result match your prediction?
- Expected Hardy - Weinberg Equation
- Frequency of RR (p2) = 0.25
- Frequency of Rr (2pq) = 0.50
- Frequency of rr (q2) = 0.25
- Simulation Calculations
- Frequency of RR (p2) = (0.95)2 = 0.9025
- Frequency of Rr (2pq) = 2(0.95)(0.05) = 0.0950
- Frequency of rr (q2) = (0.05)2 = 0.0025
- Expected Hardy - Weinberg Equation
The prediction matches with the results because it was predicted that an increase in fitness on a certain color will increase the amount of flowers that would be in that specific color. After calculating the actual frequencies, the expected genotype frequencies do not match with the actual frequencies that were acquired from the Evolution Simulation. By looking at it, it can be seen that an increase in fitness doesn't follow the HWE.
*The results portion is combined with the answers to the questions portion of this assignment.
Scientific Conclusion
After using an Evolution Simulation, the user was able to better understand allele frequencies. This simulation gives a real-world scenario of using flowers to determine an offspring's physical traits. The purpose was fulfilled because the user saw what fitness can do to an organism. It helped further evaluate the definition of natural selection and see why many organisms are the way they are. In this project, flowers and variation of colors was used to see that the parent's traits were seen in the offspring. This interconnects with genetics because it deals with the different alleles that gives that certain color to the organisms.
Data/Files
Methods were acquired from pages 5-9 of the Aipotu IV: Evolution PDF. Link is provided: Evolution PDF
Aipotu was downloaded from the following link:
Acknowledgements
My homework partner for this week was Naomi Tesfaiohannes. She assisted in organization/structure of the notebook. Also, we discussed about evolution and why the results are the way they are.
New skills were used in this assignment. They were learned from the following links:
These skills were used frequently in emphasizing on results and answers to questions. Making a table was very tricky, at first, but this link helped a lot on how to format it.
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Icrespin (talk) 17:40, 11 September 2019 (PDT)
References
Aipotu. (2017). Aipotu. Retrieved September 11, 2019, from http://aipotu.umb.edu
Week 2 Assignment page is: LMU BioDB 2019. (2019). Week 2. Retrieved September 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_2
