PART 1: Worked Problems

1. The Alert allele (A) is dominant to the asleep allele (a), and the Big Head allele (B) is dominant to the small head allele (b). An Alert, Big Headed student is identified. (i) What are the possible genotypes of this individual? Assume you could mate this student to another student and look at their offspring. (ii) To what type of student should the Alert, Big Headed student be mated to determine her/his actual genotype? (iii) Why? (one short sentence)

2. In Drosophila, the "purple" locus affects eye color [two alleles are pr (purple) and pr+ (wild-type red)] and the "vestigial" locus affecting wing size [two alleles are vg (vestigial) and vg+ (wild type)]. In a cross of
 

3. In class we worked through a dihybrid cross of AaBb x AaBb. Assuming dominance of A and B (over a and b) we produced the typical phenotype ratios of 9:3:3:1. We then worked through a dihybird cross of AaBb x AaBb assuming the A and B loci were linked together with r =0.02 (2%). 3a) Assuming co-dominance, write down the proportions of 2-locus phenotypes for this cross where linkage is involved (AA = alert, Aa = drowsy, aa = asleep, BB = bighead, Bb = medium head, bb = small head; for example, AaBb would be a drowsy, medium-head). 3b) You will see that there are three common phenotypic classes; why do the proportions of these classes resemble the proportions of a one-locus cross ( i.e., 1:2:1)?

4 (four parts). The following numbers of allozyme (protein) genotypes at a shell deposition locus of the barnacle (Semibalanus balanoides) were identified in a sample of 1000 barnacles from coastal Rhode Island before a hurricane hit: 90 FF, 420 FS and 490 SS individuals (F stands for fast migrating protein allele, S = slow migrating allele in gel electrophoresis). 4a) What are the allele frequencies for the F and S alleles? 4b) Are the barnacles in Hardy-Weinberg equilibrium? Show your work. After the hurricane, the following genotypes were observed in a sample of 860 barnacles : 90 FF, 378 FS and 392 SS. 4c) Determine the relative fitnesses (W_FF, W_FS, W_SS) of the genotypes and the selection coefficients. (hints: see page 129 in the Texbook). 4d) What are the new allele frequencies after selection.

5. What is the average fitness of the population of barnacles immediately AFTER the hurricane?

6. The leucine amino peptidase (LAP) locus regulates osmotic pressure in the cell. In a brackish estuary with intermediate salinity levels that lies between a freshwater stream and the ocean, the following genotypes were found at the LAP locus of the aquatic plant Halophilia intermedia in a sample of 1000 plants: 250 CC, 600 Cc, 150 cc. Assuming the level of salinity is fixed in the estuary, what are the relative fitnesses of the three genotypes in this habitat? What will be the equilibrium frequency of the C allele? (hints: you will need to use H-W to answer this question; define fitnesses as the ratio of observed/expected genotype frequencies).

7. If a population of snails on the mainland has an allele frequency of p = 0.75 and the allele frequency on an island is p = 0.25, what will the allele frequency be on the island after one generation of migration with m = 0.1 ?

Population Genetics Simulations using Populus

For PC users, you can download Populus from the Bio48 web page. This will install Populus on your hard drive, which will be most convenient. At a Public Cluster First launch Windows 95. Most IBMs will already have Win95 running. If not, and some sort of C:\ prompt is on the screen, type Win95. After some delay you will be prompted for your Network ID (Firstname_Lastname) and password(your personal password). Once Win95 is ready, double-click on the Network Neighborhood icon in Windows Explorer. Double-click on Entire Network, double click on Cluster, double click on Cluster_PC. A Populus folder should be listed. Double click on it, and then double-click on populus.exe to start Populus. An introductory screen will come up. Everything in Populus has on-screen instructions or is menu driven, i.e., you move the cursor up and down with the arrow (or tab) keys and press return to select an option. Type F1 key for general help (do it now!).

BRING the Selection handout AND your Text READ THE INSTRUCTIONS: You will select different options from the menus (e.g., Selection, Differentiation Models) by selecting the specific options. You will have to 1) draw some of the graphs, and 2) answer questions about specific simulations. You select options by pressing the Return (Enter) key. When you enter an option, a screen of text will; Read all pages of the text on the screen. There may be more than one screen so press page down to see the next page. When you are running a specific part of Populus, the F1 key presents a screen with help/information on it. Pushing the F1 key twice will bring up the general help screen.

PART 2. Selection: Choose "Selection" Then choose "Autosomal selection"

You will be presented with a menu for changing various conditions of the simulation. Start with p vs. t (allele frequency vs. time), the Fitness option (input fitnesses rather than selection coefficients), and six-frequency stability analysis (simultaneously runs six different simulations with different starting frequencies). Set the fitnesses to the values listed below. Set the number of generations to 500 (you can change this for different strengths of selection to let the simulation approach equilibrium). When you run the simulation (by pressing the Return key), a graph will appear. To zoom in on the plot, press Alt-Z and then use the arrow keys (down and left) to resize the view window. By pressing the Space Bar, a new graph will appear plotting different information about the simulation (e.g., genotype frequency vs. time(generations); Æp vs. p; wbar vs. time). Run the simulation for each of the following conditions (two different sets of values for each general condition) and sketch your results on paper (you do not need to hand these drawings in, but it will help to label your axes and keep track of the individual lines). Now press the space bar and a plot of genotypes vs. time graph appears. Press space bar again to see the Æp vs. gene frequency (p); wbar vs. gene frequency (p) plots. Draw the graphs of wbar vs. gene frequency so that you can compare the shapes of the plots for each condition. You will have to hand in the wbar vs. gene frequency drawings. THINK about what the graphs mean when you draw them. When you have run them all, answer the questions below.
 

Condition Run	wAA	wAa	waa
Selection against 1A one genotype 1B	0.9 0.5	1 1	1 1
Selection with codominance 2A 2B	1 1	0.95 0.8	0.9 0.6
Selection with overdominance 3A 3B	0.8 0.6	1 1	0.9 0.4
Selection against heterozygote 4A 4B	1 0.8	0.8 0.6	0.9 1

 

8. For all the runs in general, what is the relationship between the size of the selection coefficient and the time to (apparent) equilibrium of allele frequency ? _______________

________________________________________________________________________ .

9. For Runs 1A and 1B, what is the relationship between the size of the selection coefficient and the apparent equilibrium frequency of the A allele (do both simulations for 2000 generations, and use the Alt-Z zoom option to see the "equilibrium" frequency at time=2000). ______________

____________________________________________________________________________.

10. For selection against the heterozygote, how does initial frequency affect the trajectories. Is there a polymorphic equilibrium? Explain your answer _________________ _____________________________________________________________________________________________________________________________________________________ .

• Using your drawings of the Wbar vs. gene frequency (p) plots for each run, explain the following facts (you should write these answers on the page with your drawings).

11) why does wbar take on the specific values shown on the graphs when p = 0 and p = 1.0? Answer this for each graph.

12) why is the slope of wbar vs. p opposite in direction for the plots in runs 1A&B vs. 2A&B?

13) why does wbar reach a maximum at an intermediate value of p in runs 3A&B, but wbar reaches a minimum at intermediate values of p in runs 4A&B?

14. Cavener and Clegg (1981) grew fruit flies under normal conditions and on food containing ethanol. They used protein electrophoresis to survey the frequencies of the Alcohol dehydrogenase locus (Adh) in these experimental populations (Adh S = slow allele, Adh-F = fast allele; see page 131-132 of the text). Assuming that the experimental populations had a starting frequency of f(Adh-S) = 0.65, and a final frequency of f(Adh-S) = 0.05 (see figure 5.7), use Populus to calculate the selection coefficients needed to reconstruct these data. 14a) assume Adh-F is dominant, 14b) assume codominance between Adh-S and -F. (you will need to write down two sets of fitnesses : W_FF, W_FS, W_SS).