Carolyne week 2

Purpose

The purpose of this experiment is to use Hardy-Weinberg Equilibrium to determine if the population of Aipotian flowers is undergoing evolution. In addition, this study hopes to understand how selection pressures can lead to the fixation of alleles within the population over-time.

Methods and Results

Methods

I used the program Aipotu, which utilizes digital flowers called Aipotipian flowers to help model how organisms evolve over time (Aipotu, 2020). The protocol used in parts A, B, and C came from the Aipotu website and content from the Week 2 Assignment page (Aipotu, 2020; OpenWetWare, 2020). After opening the Aipotu program, I went to the Evolution program. To strictly test the relationship between selection and evolution, I turned off the mutations by going to the File menu, then Preferences, then Mutation Rates, and unchecking the box that enabled mutations.

Part A: Selecting for Red Flowers

To select both red and white organisms, I clicked on the red flower icon in the Greenhouse, then pressed shift so I could also select the white flower icon. With these two organisms selected, I clicked on "Load." A group of 100 red and white flowers popped up on the screen and I recorded the number of red flowers and white flowers displayed in the "Settings" Panel in a Google Sheets spreadsheet.

To understand how selection for red would impact the phenotypic distribution of the flowers, the fitness of the flower colors was manipulated. The fitness of the red flowers was set to 10 (maximum fitness), while the fitness of all of the other flower colors was set to 0 (minimum fitness). Data regarding how the counts of red and white flowers over generations were collected by clicking "One Generation Only," which would make current flowers contribute to the gene pool, die, and produce a new generation of exactly 1000 flowers (Aipotu, 2020). Each of the new flowers would have randomly inherited two alleles from the population's gene pool. The data regarding the number of red and white flowers in each new generation was recorded in a Google Sheets spreadsheet.

Part B: Selecting for White Flowers

Using the same process outlined in Part A, I selected both the red and white flowers in the Greenhouse and clicked on "Load" to generate a sample size with roughly 50 red and 50 white flowers. To examine how selection pressures that favor white would affect the population, I maximized the fitness of White by setting its Fitness value to 10 and minimized the fitness of all other colors by setting their Fitness values to 0. A new generation of flowers was generated by clicking "One Generation Only" until all the flowers in the new generation were white. The number of generations that passed until all white flowers were attained and the number of red and white flowers in each generation was recorded.

Part C: Exploring Natural Selection and HW Equilibrium

A new world was created with only Red flowers. To show the alleles that give rise to the red flower color, I clicked on Preferences, clicked on World settings, and checked the box that would allow me to observe both allele colors. To determine if this new population was in Hardy-Weinberg Equilibrium (HWE), I went to the Fitness section and changed the Fitness values of all flowers to 5. I recorded the data regarding the genotypes present in the population, then used that data to find the frequency of the R allele and the r allele within the population in Google Sheets. The data was also used to calculate the expected frequencies of each allele in Google Sheets. I then used the "One Generation Only" function to create a new generation of flowers. In Google Sheets, I recorded the number of RR, Rr, or rr genotypes present in the new population and used that data to find the HWE values for the newly generated population.

This part of the experiment also aimed to determine how natural selection effects evolution within the population. To model this, I changed the Fitness value for Red flowers to 10 while the values for the other colors were set to 0. I selected "One Generation Only" until there were only Red flowers present in the population. For the final all-red population, I recorded the number of genotypes present, then used that data to determine the HWE values for that population.

For each population where HWE values were calculated, I completed a Chi-Squared test to determine if the genotypic frequencies observed in the population are in Hardy-Weinberg Equilibrium or not.

Results

All calculations for this assignment were done in Google Sheets.

Part A

Prediction (A4): I predicted that if red was dominant, then in a couple of generations the number of read flowers will completely dwarf the number of white flowers leaving little to no white flowers in the population.
Results (A6): As more generations are simulated, the number of red flowers increases and the number of white flowers decreases. It takes about 6 generations to attain a purely red generation (Fig. 1). It took multiple attempts because some generations that seemed mostly red, such as generation 3 could still produce white offspring. This is due to white alleles that remain masked by the dominant red allele, producing a red phenotype despite the presence of a white color gene.

Part B

Prediction (B4): If selection pressures favor the white color allele over other colors, then the number of red flowers should decrease and the number of white flowers should increase over successive generations.
Results (B6): It only took one generation of flowers to attain a purely white flower population. This shows that the counts of red flowers decrease relative to white flowers as the number of simulated generations increases. It takes more generations to attain a purely red flower population rather than a purely white flower population because the Red allele is dominant and the white allele is recessive. This affects trying to attain a population of all red flowers because it is possible to produce a red flower with one red allele and one white allele. This allows allowing the white allele to remain hidden in the population and occasionally leads to the occurrence of a white flower. In contrast, a white flower can only arise if there are two white alleles present because the white allele is recessive. Thus, all white flowers must be homozygous recessive. Any flower that does not have two white alleles will be selected against, so they die off and leave only the flowers that have two white alleles.

Part C

The Chi-squared value is 5.99 and df=2 (Boston University, 2018).

Starting Population
- C4: Starting population allele frequencies
  - Frequency of R(p): 0.5
  - Frequency of r(q): 0.5
- C5: Genotype frequencies expected at HWE
  - Frequency of RR: p^2 = 0.25
  - Frequency of RR: 2pq = 0.5
  - Frequency of rr: q^2 = 0.25
  - Chi squared:100 > 5.99
- C6: Is the population at HWE?
  - Answer: The population is not at HWE. The result of the Chi-Squared test shows that the null hypothesis should be rejected. The observed genotypic frequencies are significantly different from the expected genotypic frequencies for this population.
Offspring of Starting Population
- C7: Starting population allele frequencies
  - Frequency of R(p): 0.54
  - Frequency of r(q): 0.46
- C7: Genotype frequencies expected at HWE
  - Frequency of RR: p^2 = 0.21
  - Frequency of RR: 2pq = 0.50
  - Frequency of rr: q^2 = 0.29
  - Chi squared:0.218 < 5.99
- C7: Is the population at HWE?
  - Answer: The population is at HWE. The result of the Chi-Squared test shows that the null hypothesis should be accepted. The observed genotypic frequencies are not significantly different from the expected genotypic frequencies for this population.
Selection for Red Allele and Evolution
- C9: Prediction: With this selection, it is expected that the frequency of p will increase towards 1 and the frequency of q will decrease towards 0, and the population will be evolving.
- C11: Starting population allele frequencies
  - Frequency of R(p): 0.93
  - Frequency of r(q): 0.07
- C11: Genotype frequencies expected at HWE
  - Frequency of RR: p^2 = 0.865
  - Frequency of RR: 2pq = 0.130
  - Frequency of rr: q^2 = 0.005
  - Chi squared:0.567 < 5.99
- C12: Is the population at HWE?
  - Answer: Initial genotype frequency values for HWE were taken after 7 generations, which is when only red squares were present in the population. This matches my prediction that the red allele would become more frequent over time because the frequency of the red allele increases to p=0.97 while the white allele is at q=0.03. Based on the results, however, the population is at HWE. The result of the Chi-Squared test shows that the null hypothesis should be accepted. The observed genotypic frequencies are not significantly different from the expected genotypic frequencies for this population. This does not match my prediction that the population is evolving because the population remains in HWE despite major phenotypic and genotypic frequency changes

Scientific Conclusion

The purpose of this experiment was to determine how selection pressures affect allele fixation within the Aitopian flower population and if the flowers are evolving over time. Based on the calculated Chi-squared values, evolution is not occurring within the populations despite selection pressures. My results also suggest that allele fixation can occur if the fixed allele has a great fitness advantage over the other alleles. The number of generations needed for an allele to become fixed within a population is greater for a dominant allele compared to a recessive allele.

Acknowledgements

The content of my entry was dictated by the Week 2 Assignment page for the course. I copied and modified the procedure from the Aipotu website to reflect the work that I did, however, I largely followed the given procedure. I worked with my homework partners Jenny and Christina in class and over text to complete the experimental procedures and understand Hardy-Weinberg Equilibrium. I also consulted the website page on Hardy-Weinberg Equilibrium created by The Insitute of Environmental Modeling to further understand how to use the model to determine if a population is undergoing evolution. I utilized the Chi-squared critical values from a chart from Boston University. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Carolyne (talk) 23:36, 29 January 2020 (PST)

References

Aiptou. (2020). Evolution Lab Manual. Retrieved January 22, 2020, from http://aipotu.umb.edu/
OpenWetWare. (2020). BIOL368/S20:Week 2. Retrieved January 22, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_2
The Institute for Environmental Modeling. (1999). Hardy-Weinburg Equilibrium. Retrieved January 22, 2020, from http://www.tiem.utk.edu/~gross/bioed/bealsmodules/hardy-weinberg.html
Boston University School of Public Health. (2018). Chi-Squared Tests. Retrieved January 25, 2020, from http://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717_ComparingFrequencies/PH717_ComparingFrequencies2.html

User Page and Template Links

User page: Carolyn C. Egekeze
Template: Template:Carolyne

Individual Journal Pages

Weekly Assignments

Class Journal Pages