ATH 255 Lab 3 Exercise

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Miami University *

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255

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Anthropology

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Dec 6, 2023

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Foundations of Biological Anthropology GENETICS AND THE FORCES OF EVOLUTION For this lab exercise, you will be using two different models in NetLogo to explore the four forces of evolution. Go to https://netlogoweb.org/ and launch the NetLogo web version to get started. NetLogo is an online and free program that helps to simulate and understand natural and social phenomena that develop over time. NetLogo was authored in 1999 by Urin Wilensky, and the Center for Connected Learning & Computer-Based Modeling has continued to improve it. Based on the modeling environment, NetLogo allows the user to explore the connection between micro-level behaviors and emerging macro-level patterns. NetLogo allows students, professors and researchers to create new simulations and “play” with them, exploring the effects under different conditions. PART 1. MUTATION & NATURAL SELECTION USING THE “PEPPERED MOTHS” MODEL For, part 1 you will be using a simulation of peppered moth color evolution. This models a classic example of natural selection - the peppered moths of Manchester, England. The color of the peppered moths provide camouflage from the birds that would eat them (Note that in this model, the birds act invisibly). Historically, light-colored moths predominated because they blended in well against the white bark of the trees they rested on. However, due to the intense pollution caused by the Industrial Revolution, Manchester's trees became discolored with soot, and the light-colored moths began to stick out, while the dark-colored moths blended in. Consequently, the darker moths began to predominate because Natural Selection will favor the darker phenotype. Now, in the past few decades, pollution controls have helped clean up the environment, and the trees are returning to their original color. Hence, the lighter moths are once again thriving at expense of their darker cousins. PART 1a. NATURAL SELECTION Natural selection occurs as the result of non-random, differential reproductive success in the transmission of heritable traits. Remember that natural selection is acting on the phenotype of the moths in this simulation as you proceed through. You may need to run this simulation a few times to get the hang of it before you answer the questions. Let’s get started! 1. Search for the peppered-moth model in the NetLogo search bar. 2. Leave the parameters for this model in their default settings. Click SETUP and then click GO. 3. As the simulation runs, repeatedly hit the POLLUTE button to increase the pollution to 75% (see next page). 1

Foundations of Biological Anthropology 4. Allow the simulation to run 200 ticks (a tick is the unit of time used in NetLogo) 5. Pause the simulation by clicking GO again 6. What is the count of each type of colored moth at 200 ticks? (scroll over the line on the graph to see the count) (1pt) a. Dark: __________________ b. Medium:________________ c. Light:___________________ 7. Click GO again to continue the simulation 8. Use the CLEAN UP button to reduce the pollution to 25% as the simulation runs. 9. Allow the simulation to run to 400 ticks and click GO to Pause. 10. What is the count of each type of colored moth at 400 ticks? (1pt) a. Dark: __________________ b. Medium:________________ c. Light:___________________ 11. Describe the shape of the curves of the 3 lines representing the moth colors and how they are related to the percent-of-pollution line. (You may want to draw the curves to help with your description) (2pts) 2

Foundations of Biological Anthropology Which color had the selective advantage in higher levels of pollution and which had an advantage in lower levels? Why? (2pts) 1b. MUTATION Mutations, or changes to the DNA sequence, are the ultimate source of all genetic variation. Mutations have advantageous, neutral, or negative effects. Let’s see how mutation rates impact frequencies of 3 colors of moths. In this simulation the light colored moths have the selective advantage due to the lack of pollution. Mutation rate is the only parameter that is changing. 1. Click SETUP. Note that the default Mutation rate is 15. Leave the pollution at 0% 2. Click GO and allow the simulation to run 100 ticks. Then pause the simulation. 3. What is the count of each type of colored moth at 100 ticks? (1pt) a. Dark: ___________________ b. Medium:_________________ c. Light:____________________ 4. Now increase the Mutation rate to 60. Click GO and allow the simulation to run to 200 ticks. Pause the simulation. 5. What is the count of each type of colored moth at 200 ticks? (1pt) a. Dark: ___________________ b. Medium:_________________ c. Light:____________________ 6. What effect did increasing the mutation rate have on the number of each color of moth? (1pt) 7. Think back to Part 1a. In what situation would this increase in mutation rate be beneficial? (1pt) 3

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Foundations of Biological Anthropology PART 2. GENETIC DRIFT & GENE FLOW USING THE “GENDRIFT T INTERACT MODEL” You will now be modeling genetic drift and gene flow. This model starts with a random distribution of colored “turtles”. The colors represent the phenotypes for which you will be observing frequencies. Turtles move by wiggling randomly across the environment (black rectangle). When two turtles come in contact with each other they mate. When they separate they now represent their offspring. The two offspring will be the same color because they take on the color of dominant allele (producing the dominant phenotype). Remember that simulations are not perfect representations and in this case, the effects of heterozygotes are ignored. Also, note that if a color dies out, it can never come back because there are no mutations in this model. PART 2a. GENETIC DRIFT This exercise will investigate how random genetic drift can affect gene frequencies under the absence of natural selection. First, you will be modeling a large population of turtles with no natural or artificial barriers. 1. Search for “GenDrift T interact” in the NetLogo search bar. 2. Change the number of colors to 2. Leave number at 300. Click SETUP. 3. Click GO and allow the simulation to run until it stops on its own (Hint: you can increase the speed of the simulation using the sliding bar above the simulated environment) 4. Record the number of ticks as well as the color that has taken over. This is equivalent to the allele that has reached fixation. Run the simulation 8 times. (2pts) Round Color with 300 Turtles 1 2 3 4 5 6 7 8 Did one color reach fixation more often than the other? Since genetic drift is a random process, if you did 20 more rounds what would you expect to see? (2pts) Genetic drift has the largest and fastest impact on small populations. In order to model this, you will be placing a wall within the simulation environment to prevent the turtles of the two subpopulations from 4

Foundations of Biological Anthropology breeding with one another. Modeling two subpopulations divided by a wall represents either natural or artificial barriers such as when part of a river dries up or a road is built. 1. Change the number of colors to 7. Decrease the model speed to about a quarter of the possible speed. These two settings will help you to visualize the different changes going on in the subpopulations. Click SETUP. 2. List the colors of turtles below. (Hint: there are usually very subtle shades of green used) (1pt) 3. Click PLACE WALL, then hover over the environment and click to place that wall (a thick white line will show up) to block off a small portion of the turtles from the rest. (You can remove and replace the wall as many times as you want until you are happy with size of the smaller subpopulation you are isolating) 4. Click GO. Allow the simulation to run 150 ticks. Then click GO again to pause the simulation. 5. Now that you’ve run the simulation, what colors are in your subpopulations? (1pt) a. Larger subpopulation colors: b. Smaller subpopulation colors: 6. Which subpopulation changes more in the proportion of colors and why? (2pts) PART 2b. GENE FLOW Lastly, you will be modeling gene flow by allowing your subpopulations to mate with one another once again. First, pick a color in your smaller subpopulation that is not in (or that there is not a lot of in) your larger subpopulation and draw dots (at least 20) to represent where the turtles of that color lie in the environment on the first box below. Also, draw a line indicating where you placed your wall. (2pts) 1. Click the “remove-all-walls” button. Click GO. 2. Run the simulation to 250 ticks. Click GO to pause. 5

Foundations of Biological Anthropology 3. In the second box above, indicate where the turtles of your selected color now lie within the environment. Draw dots for at least 20 turtles to represent the distribution of that color. Draw a dashed line to indicate the position of the removed wall. How did removing the wall affect the distribution of the color you chose? (1pt) 4. By removing the wall, what evolutionary force did you allow to happen? (1pt) 6

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ATH 255 Lab 3 Exercise

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