WS1 Drosophila - MMJ edit(1)

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Apr 3, 2024

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Drosophila Population Genetics Worksheet Name_____________________ Biology 301L The genetic simulation program is available at https://www.radford.edu/~rsheehy/Gen_flash/popgen/ Ecologists often use mathematical models to understand the dynamics of population change. In this exercise you will 1) investigate how initial allele frequency, relative fitness, and Mendelian genetics affect evolution in a population; 2) use a model to make predictions of final allele frequency for our Drosophila evolution experiment; 3) create testable hypotheses for the experiment; and 4) create a figure showing your predicted/hypothesized results. The models used here include the following parameters: • population size (N ) = the number of individuals in the population (number of individuals) at generation 0. This parameter ranges from 1 to 10 000. • initial allelic frequency (p) = the proportion of the initial population that has the p allele. This parameter ranges from 0.0 to 1.0. • Generations (runtime) = the maximum number of generations to run the model simulation. Note: the actual number of generations the model completes may be less than the runtime if the population reaches fixation before the number of generations you designated. • w = relative fitness . This parameter must be assigned independently by you to all three genotypes. Remember, fitness acts on the phenotype, not the genotype directly. Preparatory Exercises Using the following scenario, run the population simulator to answer these questions. In peacocks, a long tail diminishes ability to escape from coyotes. Assume tail length is controlled in a simple Mendelian fashion, and longer tails are homozygous for the recessive allele (l), and short tails are either homozygous for the dominant allele (L) or heterozygous. Answer the following preparatory questions based on a simulation using the following parameters: Population size (N) = 300 Initial allele frequency (p) = 0.5 Generations = 500 Fitness: w AA = 1.0 w Aa = 1.0 w aa = 0.1 Questions: 1. Run 5 simulations and record A) the allele frequency at 5 generations and B) the number of generations until the population reaches fixation. A. Average of all 5 simulations at generation 5: B. Average number of generations to fixation/loss, and which allele reaches fixation?
2. All coyotes have been shot. Thus, there is little predation on peacocks. (w aa = 0.9) . Run 5 simulations and record A) the allele frequency at generation 5, and B) the number of generations to fixation. A. Average of all 5 simulations at generation 5: B. Average number of generations to fixation/loss, and which allele reaches fixation? 3. Adjust the initial allele frequency (p) to 0.1. (Lots of long tails in the initial population). Adjust fitness to the original values for each genotype . Run 5 simulations and record: A) the allele frequency at generation 5 and B) the number of generations to fixation. What are the averages and what differences did you see when compared to the results of question 1? A. Average of all 5 simulations at generation 5: B. Average number of generations to fixation/loss, and which allele reaches fixation? Experimental Predictions Next, we will use models to make predictions for the experiment we are beginning today. Using the same models as above, input relative fitness values based on the table below. Record the proportion of p for generations 0, 1, 2, 3, 4, 5, and record the number of generations to fixation. Each model is a separate set of PopGen runs with the indicated selection coefficients. Use the values produced by the model to create a figure that illustrates our predicted results. I recommend recording all your values in the provided excel notebook on BB and submitting this in addition to this worksheet. Initial population parameters : Population size (N) = 100 Initial allele frequency (p = A1) = 0.2 (q) = 0.8 Selection Coefficients Why do we expect the heterozygote (w Aa ) to have the same selection coefficient as the wild-type homozygote (w AA )? Model 1 Predictions from PopGen Simulation number Proportion p at 0 generations Proportion p at 1 Proportion p at 2 Proportion p at 3 Proportion p at 4 Proportion p at 5 Generations To Fixation Model w AA w Aa w aa 1 1 1 0.4 2 1 1 0.8 3 1 1 1 4 0.8 0.8 1 5 0.4 0.4 1
generation generations generations generations generations 1 2 3 4 5 Model-predicted average allele frequency at generation 5: ( p ) = ( q ) = What is the average number of generations until one of the alleles (which?) reaches fixation? Model 2 Predictions from PopGen Simulation number Proportion p at 0 generations Proportion p at 1 generation Proportion p at 2 generations Proportion p at 3 generations Proportion p at 4 generations Proportion p at 5 generations Generations To Fixation 1 2 3 4 5 Model-predicted average allele frequency at generation 5: ( p ) = ( q ) = What is the average number of generations until one of the alleles (which?) reaches fixation? Model 3 Predictions from PopGen Simulation number Proportion p at 0 generations Proportion p at 1 generation Proportion p at 2 generations Proportion p at 3 generations Proportion p at 4 generations Proportion p at 5 generations Generations To Fixation 1 2 3 4 5 Model-predicted average allele frequency at generation 5: ( p ) = ( q ) = What is the average number of generations until one of the alleles (which?) reaches fixation?
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