Bios 320 Computer Lab in Genetics: Populus Program Oct. 1997, Part I

(Fornari lab section)

Each lab group working with the Populus computer program and your Russell textbook will solve the following problems. Turn in a report, signed by all contributing members of the group, to me by the next laboratory session, Oct. 14^th. The report should contain detailed answers to each question below, and answers should be, when appropriate, supported by experimental data.

Populus program: Selection, then X-linked selection

(a)List the total number and types of genotypes for an X-linked locus with two alleles in both sexes. (Use an X^A, Y type of notation).

(b)List the H-W genotype frequencies for each sex, male and female, in which p = the frequency and an allele, and q = the frequency of the other allele at the A locus.

(c)If random mating is occurring in a very large population experiencing no evolutionary forces, then H-W genotype frequencies at autosomal loci are reached in one generation; but if alleles are X-linked and the population starts out with the alleles at differnt frequencies in each sex, then equilibrium frequencies are achieved only after several generations. EXPLAIN.

(d)How much is the difference in allelic frequency between the 2 sexes reduced in each generation? Illustrate or support your answer with two experimental examples.

(e)If the fitness values (w) for each possible genotype in both sexes (see your answer to parts a and b) are 1.0, and the initial alleles frequency (p) in males is 0.0, and in females is 1.0, then how many generations are required to reach an equilibrium allele (p) frequency in both sexes?

(f)If all fitness values (for each of the possible genotypes in both sexes) are 1.0 except the p(XY), and w(XY) = 0.1, do the allelic frequencies (p in both males and females) reach equilibrium values after the same number of generations as your answer to part (e)? Explain.

(g)As w(XY) decreases from 0.9 to 0.1, does it take longer or shorter for the allelic frequencies to reach H-W proportions (compared to Part E.)? Explain.

(h)If the initial allele frequency (p) is 0.3 in males and 0.8 in females, then how many generations are required to achieve H-W proportions?

(i)In general, are more or less generations required to reach H-W proportions in p as the initial allele frequency (p) difference between the sexes decreases? Illustrate your answer with at least 2 experimental results.

(j)What different intitial allele frequencies (p in each sex) will yield a final, H-W allele frequency (p) in both sexes of 0.5?
 

Bios 320 Computer Lab in Genetics: Populus Program Oct. 1997, Part II

Each lab group working with the Populus computer program and your Russell textbook will solve the following problems. Turn in a report, signed by all contributing members of the group, to me by the next laboratory session, Oct. 21^st. The report should contain detailed answers to each question below, and answers should be, when appropriate, supported by experimental data.

Populus program: Main Menu, Genetic Drift, Monte Carlo model for question #1,

1. Devise an experiment to test Matoo Kimura's hypothesis that, if initial allele frequencies at a locus are NOT equal, then the less frequent allele is more likely to be lost from the population.

Carefully explain and describe your experimental design, i.e., provide rationales for your choice of the following parameters:
 

(A)Population size (I recommend using two very different population sizes, while holding all other parameters constant; then how does population size affect your results?).

(B)Initial frequencies. Keep the number of loci at 6 (the maximum) and vary the p allele frequency at each locus in a systematic way, such that the results of your trials clearly support or refute Kimura's hypothesis

(C)Set up and run a controlled experiment. Ideally, what should the allele frequnecies be for such a controlled experiment?

Perform enough trials to give your results some statitical significance (i.e, try to avoid drift!), but provide graphs only for the following:
 

--your "best" run at each population size, i.e., the one that most clearly supports or refutes your hypothesis, and best illustrates the "solution" to the problem.

--the results of the control simulations for each population size

Then summarize the collected analyses of all your simulation runs in a table; in other words it is not necessary to provide a graph for each and every run, but it is necessary to provide the summarized results from all your runs.

Sources of information: Russell text, p.719-725; Figs. 21.1 and 21.12 for quest. #2

Populus program: Main Menu, Genetic Drift, Markov model for question #2.

2. Repeat Buri's (Fig. 21.11) and Fisher-Wright's (Fig. 21.12) experiments by using the same N and starting allele frequencies, but now determine exactly the total number of generations required to fix 99% of the populations for one allele or the other. Complete the following table and plot: #generations for 99% of populations with fixed alleles vs. initial A frequency. What do your results tell you about genetic drift in general and Kimura's hypothesis (i.e., loss of alleles in proportion to starting frequency) in particular? Explain and interpret your results in these terms, as well as in any other terms you observed during your experimenatation.