AP Biology: Allele A1 Lab

Transcription

1 AP Biology: Allele A1 Lab Allele A1 Download: In today s lab we will use a computer program called AlleleA 1 to study the effects of the different evolutionary forces mutation, natural selection, genetic drift, and gene flow (migration). AlleleA 1 simulates the evolution of a single genetic locus (with two alleles, A 1 and A 2) in a randomly mating population. The program is easy to use and will allow you get a feel for the relative strengths of the different evolutionary forces. It is worthwhile trying many different kinds of cases and asking what values of parameters are needed to make one evolutionary force be influential in the presence of another. Open the program and familiarize yourself with the screen and input variables. AlleleA 1 allows the user to control several parameters including: Initial frequency of the A 1 allele Fitness values of the three genotypes, A 1A 1, A 1A 2, and A 2A 2 Mutation rate from A 1 to A 2 Mutation rate from A 2 to A 1 Fraction of migrant individuals per generation Frequency of allele A 1 in the source population Population size (from 1 to infinite) Inbreeding coefficient (F) As the program runs, it plots a graph of the frequency of allele A 1 over many generations (see figure at right). You can select a different variable to plot using the triangle on the y-axis; the program can plot the frequency of either allele (A 1 or A 2) or any of the three possible genotypes (A 1A 1, A 1A 2, or A 2A 2). The user can also change the number of generations to simulate using the triangle button on the right side of the x-axis. Lastly, you can select the color of the line used to plot a particular simulation using the color swatches in the lower right of the screen. If the Single button is selected, then only one simulation is plotted at any one time (i.e., the previous simulation is cleared before each new run). However, for many of the exercises in this lab you will want to compare the results of two (or more) simulations. In this case, you should select Multiple and designate the color for the run in question. During lab we will explore the various capabilities of AlleleA 1 and run several simulations to familiarize you with the program. Your assignment is to work through the questions included in this packet. We will work through these questions in class and you must answer them in your packet.

2 Quick Reference for AlleleA 1 AlleleA 1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus has 2 alleles, allele A 1 and allele A 2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A 1 over time. Setting the parameters Set the parameters by entering values in the boxes in the AlleleA 1 window. For example, to set the initial frequency of allele A 1 to 0.01, double click in the box labeled Starting frequency of allele A 1, then type Running the simulation Run the simulation by going to the Simulation menu and selecting Run, by pressing command-r, or by clicking on the Run button. Setting the number of generations By default, the simulation will run for 500 generations. You can select a different number of generations in the popup menu at the lower right corner of the graph. Setting the graph line mode & color By default, the graph will clear itself at the start of each run. To overlay the graph for a new run onto the graph for the previous run, click on the Multiple radio button under Graph lines at the bottom right of the AlleleA 1 window. To change the color of the graph line for your next run, click on the color you want in the palette at the lower right of the AlleleA 1 window. The currently selected color is shown in the larger rectangle to the left of the color palette. If you select Auto, the software will automatically cycle through all eight colors. Clearing the graph & restoring all settings to default values To clear the graph, but leave the parameters unchanged, go to the Simulation menu and select Clear, or press command-k, or click on the Clear button. To clear the graph and restore all settings to their default values, go to the Simulation menu and select Reset, or press command-d, or click on the Reset button. Parameters Starting frequency of allele A 1 As it's name suggests, this parameter controls the frequency of allele A 1 at the start of the simulation. The frequency of allele A 2 is determined automatically (1-A 1). The starting frequency of allele A 1 should not be less than zero or greater than one. Fitness of genotypes A 1A 1, A 1A 2, and A 2A 2 These parameters determine the relative fitness values of the three genotypes. The values should be positive, but what matters is the values relative to each other. Mutation rates These parameters determine the rate at which copies of allele A 1 turn into allele A 2 and vice versa. The mutation rates should not be less than zero or greater than one. Fraction of migrants This parameter controls the fraction of individuals in each generation that are migrants newly arrived from another population. The fraction of migrants should not be less than zero or greater than one. Frequency of allele A 1 in the source population This parameter controls the frequency of allele A 1 among the newly arrived migrants. It should not be less than zero or greater than one. Population size By default, the population size is infinite, and the population evolves according to a deterministic equation. Entering a positive integer for the population size makes the population finite. Each generation, the allele frequencies are determined by sampling from the previous generation's gene pool. Coefficient of inbreeding This parameter, also known as F, determines the probability that an individual's two alleles are identical by descent. A value of 0 represents outbreeding; a value of 1 represents selfing.

3 Simulating Hardy-Weinberg Equilibrium The default settings encompass initial frequencies of 0.5 for both alleles, and the assumptions of no selection, no mutation, no migration, no genetic drift, and random mating. 1. Run the simulation to verify that under these conditions the allele frequencies do not change. 2. Try different values for the starting frequency of allele A1. 3. Does your experimentation verify that any starting frequencies are in equilibrium so long as there is no selection, no mutation, no migration, and no drift? How do you know? Selection as a Mechanism of Evolution There are three boxes that let you set the fitnesses for the three genotypes. The fitnesses allow you to play with the effects of selection (that is, differences between the genotypes in survival or reproduction). Setting the values to 1, 0.8, and 0.2, for example, is equivalent to specifying that for every 100 individuals of genotype A 1A 1 that survive to reproduce, 80 individuals of genotype A 1A 2 survive, and 20 individuals of genotype A 2A 2 survive. 1. Predict what will happen if you set the fitnesses of A 1A 1, A 1A 2, and A 2A 2 to 1, 0.8, and 0.2, respectively. Then run the simulation. Was your prediction correct? Explain. 2. Now set the initial frequency of allele A 1 to 0.01, and the fitnesses to 1, 1, and What happens when you run the simulation? Why? Now try fitnesses of 1, 1, and Can you explain the difference?

4 Mutation as a Mechanism of Evolution There are 2 boxes in AlleleA1's window that let you play with the mutation rate. One controls the rate at which copies of A 1 turn into A 2 s; a mutation rate of means that each generation one out of every thousand A 1 s turns into an A 2. The other box controls the mutation rate in the other direction. Note that the mutation rate should be a number between 0 and 1 because a 1 represents 100% of the alleles mutating to the other allele. 1. Return all parameters to their default values, then set the mutation rates to and 0. Predict what will happen. Migration as a Mechanism of Evolution AlleleA1 uses the one-island model of migration described on pages of the text. The simulation tracks the frequency of allele A1 in an island population. The parameter called Fraction of migrants each generation determines the number of individuals that move from the mainland to the island every generation, as a fraction of the island population. For example, setting the parameter to 0.1 means that each generation ten percent of the individuals in the island population are new arrivals from the mainland. The parameter called Frequency of A1 in the source pop'n determines the frequency of allele A1 on the mainland (and thus among each generation's migrants). 1. Click on the Reset button to restore all parameters to their default values. Predict what will happen when you set the fraction of migrants each generation to 0.01 and the frequency of A1 in the source population to 0.8. Then set the parameters to these values and run the simulation. Explain what caused the change in the population.

5 Genetic Drift as a Mechanism of Evolution We have so far used AlleleA1 to simulate evolution in populations of infinite size. In reality, of course, populations are finite. Is evolution in finite populations different from evolution in infinite populations? 1. How much does genetic drift change with population size? Return all parameters to their default settings. Set the number of generations to 100. Set the graph line mode to multiple, and the graph line color to auto. Now investigate the power of genetic drift at different population sizes: a) Set the population size to 4 and run the simulation several times. b) Clear the graph. Set the population size to 40 and run the simulation several times. c) Clear the graph. Set the population size to 400 and run the simulation several times. d) Compare your results for parts a, b, and c to graphs a, b, and c in Figure 7.15 on page 247. Why are the results different for populations of different sizes? 2. Conservation biologists generally consider genetic diversity to be a good thing. That is, populations are more likely to escape extinction if there are several alleles present for each gene. a) What does drift do to the genetic diversity in a population as the population nears extinction? b) Reset all parameters to their default values. Note that the starting frequencies for alleles A1 and A2 are 0.5. Roughly how big does the population have to be for the chances to be reasonably good that both alleles will persist for 500 generations?