Download Simulating Random Events in Evolution: Genetic Drift, Founder

Simulating Random Events in Evolution: Genetic Drift, Founder Effect and Bottlenecks
Integrated Science 4 Honors
Name
Per.
Introduction
The Vertebrate Evolution unit studied the results of evolution. In that context, we considered
changes in both traits and DNA for evidence of evolutionary change and evolutionary relationships.
The current unit on Islands focuses instead on the mechanisms producing observed evolutionary
change. We looked at evidence from finch beak sizes to evaluate natural selection as an evolutionary
mechanism. Natural selection is considered a deterministic process, one that yields predictable
results. In this activity, we use genetic evidence to model genetic drift as an alternative mechanism to
natural selection. Genetic drift is considered a stochastic process, producing results that are random.
In 1908 G.G. Hardy and W. Weinberg independently suggested a model that measured
evolution changes by the changes in the frequency of alleles in a population of organisms. (remember:
alleles are different copies of the same gene located on different chromosomes.) They reasoned that if
A and a are alleles for a particular gene and each individual in the population has two alleles, then the
allele frequency for both A and a can be measured in the population. If allele frequencies change from
generation to generation, then evolution has occurred.
The purpose of this simulation is to examine the conditions necessary to change allele
frequency. We will use both a physical model and a computer-based model for this purpose. The
physical model will provide the basis to understand the overall simulation, while the computer
simulation will allow us to run the large number of trials needed to best observe the random events
necessary in genetic drift.
Physical Simulation
1. Construct a Generation 1 population of (10) individuals, each heterozygous for the alleles.
• Represent (10) A alleles with (10) dark beans
• Represent (10) a alleles with white beans
2. Simulate random mating in Generation 1
• Shake the cup
• Randomly select (2) and record the combination
• Return the bean to the cup
• Repeat (10) times
3. Construct Generation 2
• Add dark and white beans to match the alleles selected in step #2
4. Simulate random mating in Generation 2
• Repeat step #2
5. Repeat the entire procedure for (5) generations
6. Graph the allele frequencies for each generation.
7. Respond to the following prompt:
Ø The theoretical probability for selecting either allele is 0.5 (50%). Consequently, the theoretical
allele frequency for each new generation should be A = 0.5 and a = 0.5. Compare your actual
results to this theoretical value and then compare another group’s actual results to the
theoretical value. Write a brief explanation accounting for any observed discrepancies.
Additional Research
Use the following resources to further develop your understanding of what you observed in the
physical simulation.
Watch the following video introduction:
https://www.youtube.com/watch?v=mjQ_yN5znyk
View the following website:
https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-evolution-ofpopulations-19/population-genetics-131/genetic-drift-531-11736/
Computer Based Simulation- Genetic Drift
Go to the website:
http://virtualbiologylab.org/PopulationGenetics.htm
1. Select the ‘Genetic Drift’ option. Read the instructions.
2. This simulator runs the same experiment you conducted with the beans – randomly
combining alleles to simulate reproduction – but does so much faster and for many more
trials. The simulation tracks two alleles of an eye color gene: red and brown.
3. Run the simulation with the following parameters:
• Set the population size = 10
• Run the simulation for 30 generations (you will manually start and stop the process)
4. Note the following values at the end:
• Mean fix time (in number of generations)
• # colonies fixed
• Which colonies are fixed?
• Which alleles are fixed?
5. Repeat the simulation and data collection for population = 40.
6. Compare your results with another group.
7. Respond to the following prompt:
Ø Summarize the differences in the two simulations you ran. Write a brief explanation accounting
for those observed differences.
Computer Based Simulation – Genetic Bottleneck
Go to the website:
http://virtualbiologylab.org/PopulationGenetics.htm
1. Select the ‘Random Effects’ option. Read the instructions.
2. This simulator runs a version of the experiments you conducted with beans and with
computerized fruit flies – but allows you to incorporate additional variables. This simulation
tracks three alleles for body color: Yellow; Blue and Red. These alleles show incomplete
dominance in producing body color phenotype: Y/B = green; Y/R = orange; B/R = purple;
Y/Y = yellow; B/B = blue; R/R = red.
3. Set the starting parameters as follows:
•
Population (Mainland-K) = 800
•
Bottleneck size =20.
•
Note the starting frequencies (Mainland Allele Proportions) for each color.
4. Run the simulation for 30 generations. You will need to manually stop the simulation. As it
runs, you can track the allele frequencies on the graph.
•
Note the allele frequencies after 30 generations.
5. Re-start the simulation and click the ‘bottleneck’ button. This randomly reduces the
population to your set bottleneck size.
6. Continue to run the simulation until the population returns to the starting value of 800. As it
runs, you can track the allele frequencies on the graph.
• Note the final allele frequencies.
7. Compare your results with another group.
8. Respond to the following prompt:
Ø Summarize the results of this simulation. Write a brief explanation accounting for the observed
changes.
Computer Based Simulation – Founder Effect
1. Using the same ‘Random Effects’ simulator from above, click the “Reset’ button to clear the
last simulation.
2. This simulation allows you to model the effects of island colonization by a small, random
population. It uses the same (3) color alleles as the Genetic Bottleneck simulation.
3. Set the starting parameters as follows:
•
Population (Mainland –K)=800
•
Founding N-1 = 4
•
Isle 1-K = 80
•
Founding N-2 = 2
•
Isle 2-K = 40
4. Note the starting frequencies (Mainland Allele Proportions) for each color.
5. Run the simulation for (5) generations. Stop the simulation at this point.
• Note the allele frequencies.
6. Re-start the simulation and click ‘colonize 1’ to create the migration to Island 1. Allow the
simulation to run until the N-1 population = 80. Stop the simulation at this point.
• Note the allele frequencies for the Island 1 population.
7. Re-start the simulation and click ‘colonize 2’ to create the migration to Island 2. Allow the
simulation to run until the N-2 population =40. Stop the simulation at this point.
•
Note the allele frequencies for all three populations: mainland; island 1; island 2.
8. Compare your results with another group.
9. Respond to the following prompt:
Ø Summarize the results of this simulation. Write a brief explanation accounting for the observed
changes.
Computer Based Simulation – Your design
1. Using the same ‘Random Effects’ simulator from above, click the “Reset’ button to clear the
last simulation.
2. Design your own simulation that combines the founder effect and genetic bottleneck.
3. Clearly organize and present both your parameters and your results.
4. Compare your design and result with another group.
5. Respond to the following prompt:
Ø Summarize the results of this simulation. Write a brief explanation accounting for the observed
changes.