BIO1130 - PopGen exercise 2023 edit

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Module 4 – PopGen Exercise sIntroduction to computer simulation of Population genetics using PopGen. I- PopGen basic instructions: PopGen is a simulation of population biology software developed by Bob Sheehy at the Radford University in Virginia. You can access the simulation from their website: https://sites.radford.edu/~rsheehy/Gen_flash/popgen/ .). This program runs on MacOS and Windows. You TA will demonstrate how to use PopGen during the live session dedicated to this exercise. Follow the instructions below and write your answers directly in this document. **You can zoom in any region of the display window by selecting the region of interest with the left mouse button (drag the selection rectangle around the region you want to zoom in). II- Genetic drift: By default, you can enter values for four parameters: population size (N), initial frequency (freq A 1 ), number of populations and number of generations. Simulation 1-1: First, let’s simulate a population of 250 individuals and observe what will happen to an allele with an initial frequency of 0.5 . In the “Population Data” column, select Finite and enter N=250. Input the following parameters in the “Allele Frequency” column: # of populations=6, # of generations=300 and freq A 1 =0.5 allowing us to observe 6 simulated populations at a time. Click on GO to start the simulation. Below the table, a graph representing the allele frequency over time is showing. Each coloured broken line represents a population. You will notice that a certain number of broken lines may have reached the value 0 or 1. This phenomenon is called allele fixation . If an allele frequency reaches 0, the allele is lost in the population. On the other hand, if the frequency reaches 1 it is said to be fixed . To the right of the graph, you can see whether there are fixed alleles (# with A 1 Fixed) or lost (# with A 1 Lost). Question 1 How many alleles reached fixation at 1? Which allele (blue, red…)? None 1

Module 4 – PopGen Exercise Question 2 What does it mean in term of genetic diversity for the population when an allele becomes fixed? Run the simulation again (in the same conditions) by pressing the “ GO ” button in the output window. Question 3 Did you get the same result? No Question 4 How many alleles have been fixed this time? 2 Question 5 Are they the same than during the previous simulation? No, they are different Question 6 Why do you get different results when you run the same simulation several times? Because genetic drift has different effect on each population at each point in time, making it difficult. Simulation 1-2 Now let’s reduce the population size to N=100 without changing the other parameters and run the simulation (You can repeat the simulation by clicking on ‘ GO’ ). Question 7 Did you observe the same number of fixed alleles compared to previous conditions? Question 8 Based on the two previous simulations, what would be your hypothesis regarding the effect of the population size on genetic drift: 2 When an allele becomes fixed in a population, it means that all individuals carry that allele, resulting in a loss of genetic diversity.

Module 4 – PopGen Exercise To test your hypothesis, run the simulation 10 times with 6 populations each time and write down the number of alleles that have been either lost or fixed after 100 generations with the following population size: N=25 , 75 and 150 . You will use a quick statistical test to help you to compare your results for each population size: the 95% confidence interval. The 95% interval tells us that we can be 95% confident that the average is located between its lower and upper limits. Thus, if the 95% intervals limits of two averages do not overlap, it is a good indication the averages are different. Use your calculator and/or Excel to calculate the 95% CI: 1. Calculate the average number of fixed allele ( ¯ m ) for each population size. 2. Calculate the standard deviation (SD) of the sample by choosing the STDEV.S function in excel ( your TA will demonstrate how to do that in the live session ). 3. SE = SD √ n Calculate the standard error (SE) using this formula: where SD represents the standard deviation and n the sample size (number of measurements). 4. The 95% confidence interval is centered on the mean value and has two limits: Upper limit L1= ¯ m + 2 x SE Lower limit L2= ¯ m – 2 x SE Enter your results in table 5 below. Table 5: 95% Confidence interval results: Population size Average number of fixed alleles ( ¯ m ) Standard error (SE) 95% interval L1 95% interval L2 N=25 2.6 0.19321836 2.98643671 N=75 N=150 Question 9 Was your hypothesis correct? (Briefly explain why) 3

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Module 4 – PopGen Exercise Simulation 1-3 Set the population size to N=10 and run the simulation for 50 generations . Try different values of initial frequency ( freq A 1 and run the simulation several times for each value tested. Count the number of fixed alleles, and the number of lost alleles. Question 10 What is your conclusion regarding the effect of initial frequency on allele fixation in a small population? III- Drift and selection In previous simulations, we observed how genetic drift can affect a population by changing allele frequencies. We will see now what is happening if we introduce a new parameter in our simulation: selection . Selection is controlled in the simulation by assigning relative fitness values to the different genotypes. The relative fitness of each genotype is the combination of the survival rate until reproductive age and the reproductive success (=how many offspring they produce) of individuals of a certain genotype relative to the maximum survival and reproductive rate of other genotypes in the population. In summary, the relative fitness of a genotype is indicative of the success of individuals with this genotype to successfully reproduce and transmit their genotype. In the real world, both selection and genetic drift act simultaneously. The goal of this exercise is to observe the effect of selection on allele frequency and the combined effect of both genetic drift and selection. Simulation 2-1 **** (Number of Population? Do 6) In the input window, enter the following parameters: Set the fitness values to A 1 A 1 =0.8 , A 1 A 2 =1 , A 2 A 2 =0.8 , population size to N=500 . Start with an initial frequency freq A 1 =0.5 and run the simulation for 100 generations . Question 11 What do you observe? Has one of the alleles been fixed? 4

Module 4 – PopGen Exercise Simulation 2-2 Change the population size to N=250 , then to N=50 Question 12 What do you observe with these parameters? Is there any change in the probability of the allele to be fixed? How would you measure the genetic drift strength? Simulation 2-3 Now let’s give a selective advantage to one of the genotypes and set fitness values to A 1 A 1 =1 , A 1 A 2 =1 , A 2 A 2 =0.55 in a population of 300 individuals, an initial frequency freq A 1 =0.5 and run the simulation for 200 generations. Question 13 Which allele possesses a selective advantage in this case? Question 14 Run the simulation for 500 generations several times (at least 10 times). What do you observe? Simulation 3 Change the population size to N= 200, 100, 50, 25, 10 and run the simulation several times (at least 10 times for each population size). Question 15 What do you observe when population size decreases? 5

Module 4 – PopGen Exercise Question 16 What are the evolutionary forces in action? 6 This exercise was modified from a laboratory proposed by Dr J. Brown at Grinnel College in 1998.

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