Evolve ----Lab Copy

Program Description

Evolve is a simulation program that models microevolution. It depicts a sexually reproducing species with a single genetic locus and two alleles represented as • and ◊ . The genotypes found in the population are •• (homozygous), •◊ (heterozygous), and ◊◊ (homozygous). By selecting parameters in the simulation, you can specify:

-starting frequency of alleles

-population size

-survivability of each genotype

-number of offspring produced

-number of generations over which the simulation runs.

The program will mate (cross) parents from a designated parental population gene pool to give a new generation. The designated mating process (where you varied population size, or allele frequencies or survivability) will be repeated for the number of generations you specify. The program offers the choice of graphing the frequency of each of the three genotypes, the frequency of the alleles, and/or the total population size over the number of generations specified.

According to the Hardy-Weinberg theorem, genotypic and allele frequencies should not significantly change if a mating population is large with random mating and selection does not occur, provided no mutation occurs, and there is no migration into or out of the population. allows you to test this theorem and see what the effects are when the HW conditions are not met. .

If a section is highlighted in gray, data or answers should be recorded on your assignment sheet.

To start the EVOLVE program...

double click EVOLVE icon on desktop to open

click license box to proceed

click "Default Problem" to select

click "Start Problem"

click box within a box at the upper right of the screen to enlarge screen

A. Simulation: Effect of No Natural Selection in a Large, Randomly Mating Population

Question to be answered: Do allele frequencies change significantly in the gene pool of a large randomly mating population over several generations when there is no selection, mutation or migration?

Set parameters for Simulation: Population of 8,000 over 200 generations with NO natural selection

1. Click "Change Params" (lower left)

2. In the "Title" box enter ‘Large Pop No Select’ (Press Return)

3. Under "Generations" "Final:" enter value 200. Press Return.

4. In the "Allele Frequencies" boxes change frequency of the " • " allele to 0.3 and frequency of "◊" to 0.7 Press Return.

5. In the "Total Pop:" box enter 8000. Press Return

6. Under "Genetic Drift" change "Maximum Pop" and "Post-crash Pop" to 8000. Press Return.

7. The program parameters are now set for a population of 8,000 individuals which will produce a population of 8,000 in the next generation for 200 generations. The starting frequency of alleles is • = 0.3 and ◊ = 0.7. Do not change any other parameters, but note under the natural selection area that all genotypes have equal probabilities of surviving and all produce equal numbers of offspring. Also, note there is no migration into or out of the population.

8. Name the five assumptions (or conditions) that must be met for the Hardy Weinberg Law to be true. Have the parameters been set to reflect these assumptions? If so, the Hardy Weinberg Law should predict the results of this simulation.

9. Using the Hardy Weinberg Law what do you predict will the allele frequencies in 200^th generation?

10. Click Done (lower right of screen)

11. Before running the simulation, check the following settings to ensure that the program graphs the allele frequencies and not the frequency of genotypes. Move your cursor to the menu bar and click and hold "Graphs". Select (if not checked) Frequency • allele and Frequency ◊ allele by clicking on it. Checks in front of these options indicate these parameters are to be graphed. If a check appears before Frequency •• Genotype, Frequency •◊ Genotype or Frequency ◊◊ Genotype, deselect by clicking on them. This will remove check marks in front of those lines.

Running the simulation

Click Start at the lower right. The simulation will run through 200 generations and plot allele frequencies in each generation.

Analyzing the results –

In the upper right corner, find the box containing this symbol. Click once on it to show the grid markings on the graph.

Figure 1.

Below the graph, find the table containing the values used to make the graphs. By temporarily clicking and holding on the titles in each column such as "•• Frequency", the graph will display the data in that column for the last run of the simulation. By doing this, you can see how the frequency of genotypes change over 200 generations.

12. On your assignment sheet, sketch the graphical output from your simulation.

13. Repeat the simulation by clicking on "New Trial" and then "Start" at least 2 more times. Do you get the same results? Why or why not? How do you answer the question posed at the beginning of this section? Write answers on your assignment sheet..

B: New simulation: Effect of natural selection against a recessive allele in a large population.

Question to be answered: Do allele frequencies change significantly in the gene pool of a large randomly mating population over several generations when there is selection against the recessive allele?

14. You will now use the EVOLVE program to investigate the effects of natural selection. Go to the File menu and select NEW PROBLEM..

Select "Selection for the Dominant Allele" (against recessive)

click "Start Problem"

click box within the box at the upper right of screen to enlarge the screen

Set parameters for Simulation Population of 8,000 over 200 generations with natural selection against recessive allele

15. Click "Change Params" (lower left)

16. In the "Title" box enter ‘Nat Sel against Res. (Press Return)

17. Under "Generations" "Final:" enter value 200. Press Return. (you may need to click GENERATIONS box to get the data cell to reveal itself.)

18. In the "Allele Frequencies" boxes change frequency of the " • " allele to 0.3 (this will be dominate allele) and frequency of "◊" to 0.7 (this will be the recessive allele) Press Return.

19. In the "Total Pop:" box enter 8000. Press Return

20. Under "Genetic Drift" change "Maximum Pop" and "Post-crash Pop" to 8000. Press Return.

21. Leave the rest of the parameters unchanged. However, note the entries under Natural Selection. All genotypes do not have the same probability of surviving, nor they produce the same number of offspring. Note which genotype(s) have the advantage and which is disadvantaged. With this knowledge, you should be able to make a prediction concerning changes in allele frequencies in the gene pool over the next 200 generations. Write your predictions on your assignment sheet.

22. The program parameters are now set for a population of 8,000 individuals which will produce a population of 8,000 in the next generation for 200 generations using the survivability factors and offspring projections shown under the Natural Selection parameters. After you run the initial simulation, you might consider changing these values to see what happens.

23. click Done (lower right of screen)

24. Before running the simulation, check the following settings to ensure that the program graphs the allele frequencies and not the frequency of genotypes. In the menu bar under "Graphs" click and hold. Select (if not checked) Frequency • allele and Frequency ◊ allele with a click. Checks in front of these options indicate these parameters are to be graphed. If a check appears before Frequency •• Genotype, Frequency •◊ Genotype or Frequency ◊◊ Genotype, deselect with a click. This will remove check marks in front of those lines.

Running the simulation

Click Start at the lower right. The simulation will run through 200 generations and plot allele frequencies in each generation according to the parameters set on the previous screen.

Analyzing the results

In the upper right corner, find the box containing this symbol. Click once on it to show the grid markings on the graph.

25. On the assignment sheet, sketch the graphical output from this run of the simulation. Label all axes and lines. Is this what you predicted in #21? How do you answer the question posed at the beginning of this section?

26. To see what has happened to genotypic frequencies, do the following. Below the graph, find the table containing the values used to make the graphs. By temporarily clicking and holding on the titles in each column such as "•• Frequency", the graph will display the data in that column for the last run of the simulation. By doing this, you can see how the genotypic frequencies change over 200 generations.

27. Answer this question on your assignment sheet: Why does the recessive allele persist in the population after 200 generations when there has been selection against it?

C. New Simulation: Selection for recessive allele and answer questions

Question to be answered: If there is selection against a dominant allele, will the pattern of change be the same as was seen for selection against the recessive allele in the previous simulation?

28. Go to the FILE menu and choose New Problem. Choose “Selection for Recessive Allele” (against the dominant allele). Set the population parameters as you did in #15 through #20. Note that the symbols for dominant and recessive have switched due to a bug in the program: • is no longer them dominant allele; it is the recessive; and ◊ becomes the dominant one. Also note the entries under natural selection. All genotypes do not have an equal chance of survival nor do they produce the same numbers of offspring.

29. Predict what would happen to allele frequencies in a gene pool if there was selection against the dominant allele. Write you prediction on the assignment sheet.

30. Be sure to change to graphing allele frequencies under Graph in the menu bar. Run the simulation to test your idea by clicking Start at the lower right. The simulation will run through 200 generations and plot allele frequencies in each generation.

31. Describe what happens to allele frequencies on your assignment sheet.

32. Use the shortcut described in # 26 to look at the frequencies of genotypes. How does this result differ from what you saw in # 26 when selection was against the recessive allele? How do you answer the question posed at the beginning of this section?

D. New Simulation: Genetic Drift (Effect of Small Population Size (100))

Question to be answered: Does the gene pool of a small population respond in the same way as that of a large population under the conditions of the H-W equilibrium,?

33. To start your experiment, go to FILE on the menu bar and choose New Problem.

34. Choose the “Genetic Drift, 80-100 pop” and set parameters as in first experiment.

35. Click the "Change Parameters" button at the bottom of the screen.

36. Under "Generations" "Final:" enter value 200. Press Return.

37. In the "Allele Frequencies" boxes change frequency of the " • " allele to 0.3 and frequency of "◊" to 0.7 Press Return.

38. Change Total Population to 40. Press return.

39. Change Maximum Population and Post-crash Population to 40. Press return.

40. The parameters here are very similar to those in the first simulation with one major difference, population size. Thus, this is an experiment to determine if population size can affect outcomes as Hardy and Weinberg indicated. What would you predict the outcomes to be, i.e. what will happen to allele frequency in the gene pool of small population over 200 generations?

41. Click Done. Check that you will graph allele frequencies by clicking on GRAPH in the Menu bar.

42. Click "Start" as before.

43. Repeat the simulation by clicking "New Trial" & "Start", so that you have you have three trials displayed . Review your results. Use the shortcut described in # 26 to look at the frequencies of genotypes. Did you get the same result for each trial or were they quite different? Why is this happening? What assumption of the HW law is not being met? Write your answers on the assignment sheet. How do you answer the question posed at the beginning of this section?

E. New Simulation: Genetic Drift and Natural Selection together.

Question to be answered: What are the combined effects of a small population size and natural selection against a recessive allele?

44. Devise an experiment that will allow you to determine the combined effects of genetic drift and natural selection on a small population.

45. State the question that you are asking in this trying this simulation.

46. Start a New Problem again as you have done before. “Genetic Drift, 80-100 pop” and enter information for population size using a small population. Also change the natural selection parameters and be sure to record them so you remember what your starting conditions are for the simulation.

47. Give the parameters for your simulation.

48. Sketch the results of the simulation. Label all axes, lines and give the graph a title.

49. Explain how this experiment answers or does not answer your question.