Ntesfaio Week 2
Contents
Electronic Lab Notebook
Purpose
The purpose of the Evolution section was to explore evolution with evolving digital organisms. The evolution tab used 100 flowers that are annual. These flowers live for one year and die after producing seeds for the next generation. The flower contributes to the gene pool for the next generation and is based of fitness. All parents die and the offspring begin crossing with one another. All that this simulation focuses on is fitness.
Methods
All instructions came from File:Tesfaiohannes Aipotu.pdf
1. Open Aipotu download
2. Click on Evolution located on the top of the screen next to Molecular Biology
3. Turn off mutation by clicking file, preferences, mutation rate, and unchecking the mutations enabled checkbox.
A) Select for Red
A1) Click on the red and white organisms while holding down the shift button so that both are highlighted by a green box
A2) Load the two by clicking on the "Load" button on the bottom left of the screen
A3) Set the fitness of the red flower to 10 while making all other fitnesses 0. This is located on the top left of the screen with boxed numbers that have up and down arrows to direct whether to add or subtract the fitness of the flower.
A5) Test: Click the One Generation Test button in the bottom left of the screen. Continue doing this to observe multiple generations.
B) Selecting for White
B1) Click on the red and white organisms while holding the shift button so that both are highlighted by a green box
B2) Load the two by clicking on the "Load" button on the bottom left of the screen
B3) Set the fitness in the setting panel so that the fitness of white is 10 and all other colors are 0. The instructions to do this are similar to A3, however how the white column should have a 10.
B5) Test: Click the One Generation Only button in the bottom left of the screen. Continue doing this to observe multiple generations.
Check the genotype of each flower by checking the "Show colors of both alleles" in the "World Setting" part of preferences.
C) Hardy-Weinberg Equilibrium & Natural Selection
C1) Load the world with only red organisms. The entire world should be red.
C2) Show colors of both alleles by going to Settings and selecting the designated tab show colors of both alleles.
C3) Set all fitnesses to 5.
C7) Run one generation only.
C8) Set the fitness to select for red. Set the fitness of red to 10 and all other color's fitness to 0
C10) Click the one generation only button
Results
Question A
Selecting for Red
A4) Prediction: What should happen to the number of red and the number of white flowers after several generations with this selection?
By making the fitness of red the highest (10) and all other fitnesses 0 the number of red flowers should dominate and the number of white flowers should be little to none. There should definitely be no other color shown unless a mutation were to occur (which is not the case here since the mutation tab was disabled for this fitness test).
A6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly, how many generations does it take to get to pure red. Some all-red can still have some white offspring (why)?
Number of white and red by generational stimulate:
1 stimulate: 27 white and 73 red
2 stimulate: 20 white and 79 red
3 stimulate: 19 white and 81 red
At 9 generations there were 100 red and 0 any other color. All red generations can also have white offspring since white can be autosomal recessive and if one recessive genes is taken from each parent then the recessive trait can show. Each red flowered parents can be Rr and Rr, and the offspring can take the r from both parents to be white. Throughout the generations the number of red selecting flowers increased.
Question B
Selecting for White
B4) Prediction: What should happen to the number of red and white flowers after several generations with this selection?
With the selection being white (10) and all other colors (0) the white flower has the greatest fitness and should dominate the grid.
B6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly how many generations does it take to get to pure white?
The number of white significantly increases by large amounts when selecting for white.
With 1 generation stimulate there were 100 white flowers. No other color appeared.
Why does it take more generations to get to pure red than it does to get to pure white?
With the fitness set for white, the recessive alleles (r) are more prominent to survive. This allows for more pure white genotypes. When the fitness is set for red, that incorporated r alleles since they are a part of Rr. It also enhances RR which when mixing with Rr can still make Rr. This allows for red flowers to be made, expressed by the R allele, but with the white allele present. This is why it is difficult to get pure red as the red flowers Rr and Rr have the potential to bring in a white flower. However, a white flower does not have R at all, making it easier to express the r allele as dominant.
Question C
C3) Is this population at Hardy-Weinberg Equilibrium?
| Genotype | Number | #R's | #r's |
|---|---|---|---|
| RR | 0 | 0 | 0 |
| Rr | 100 | 50 | 50 |
| rr | 0 | 0 | 0 |
Frequency of R (p): 50/100 or 1/2
Frequency of r (q): 50/100 or 1/2
C5) Calculate the genotype frequency expected at HWE:
Frequency of RR= p^2= 1/4
Frequency of Rr= 2pq= 2/4
Frequency of rr=q^2= 1/4
Is the population at HWE? Why or why not?
No, because the only genotype to appear was Rr. There were no RR or rr genotypes.
C7) Run one generation only. Is the population at HWE?
25 white and 75 red. This is very close to Hardy Weinberg RR being (1/4) approximately 25 Rr being (2/4) approximately 50 and rr (1/4) approximately 25. The data I collected is very close to these points as seen below.
| RR | 21 |
|---|---|
| Rr | 54 |
| rr | 25 |
C9) With fitness set to 10 for red what should happen to p and q?
There should be more p than q present on the world grid
C11) Result: Calculate p and q as you did in part (d)
Generation 7
88 red and 12 white
| Genotype | Number | #R's | #r's |
|---|---|---|---|
| RR | 40 | 40 | 0 |
| Rr | 48 | 24 | 24 |
| rr | 12 | 0 | 12 |
Frequency of R (p)= 64/100
Frequency of r (q)= 36/100
For Hardy Weinberg the equation would be:
Frequency of RR= p^2= 1/4
Frequency of Rr= 2pq= 2/4
Frequency of rr=q^2= 1/4
C12) Does the result match your prediction? Why or why not?
I predicted there to be more red coding alleles when the fitness for red is set to 10 and all other fitness is set to 0. However, this does not follow the Hardy Weinburg equation because it does not follow the RR (1/4) Rr (2/4) rr (1/4) since there were 40 RR, 48 Rr, and 12 rr
Scientific Conclusion
This week's assignment supported the idea that the alleles of both parents being passed down to offspring (one from each parents) is what determines the offspring's trait. The purpose of the Evolution assignment was fulfilled since the purpose was to observe the different offspring traits when comparing fitness of each organism (white or red). Everything was based on fitness. Having the greatest fitness, for example when one flower would have a fitness of 10 and all other flowers had a fitness of 0, allowed for one flower to dominate and after a few generations appear as the only color available. Although, having one color does not mean it will be this way for all resulting offspring. For example, a red flower can have the genotype Rr but if two flowers with this genotype were to have an offspring it can have rr which is white. Although Rr is expressed as red it holds the allele for white.
Data and Files
To complete this assignment I used the method enlisted on pages 5-9 of the Evolution section File:Tesfaiohannes Aipotu.pdf
The only other Data collector I used was the Aipotu download which can be located on the website [| Aipotu Download]
Acknowledgements
My homework partner this week was Iliana Crespin. We sat together in the class periods to discuss the week 2 assignment.
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Ntesfaio (talk) 11:44, 10 September 2019 (PDT)
Reference
Week 2 Assignment page is: LMU BioDB 2019. (2019). Week 2. Retrieved September 10, 2019, from [[1]]
