READINGS AND ASSIGNMENTS

  NOTE: Readings should be done before the indicated date; assignments should be
              handed in during class on the indicated date.

              Click on a reading to bring it up.

For 17 October:

         Text Readings:  H&C pp. 31-39,   pp. 45-53,   pp. 61-70.

For 22 October:
 

                POPULUS exercise:
 

a.  Download a copy of the POPULUS program following the directions at the POPULUS site.  You may also need to
download a copy of a JAVA RunTime program.  There is a link at the POPULUS site for this.  When you have
downloaded the POPULUS program, you will need to unzip it.  Once you have done this, you can click on the
"run.bat" file in the POPULUS directory to start the program.

 

 b.  Explore the following issues using the Genetic Drift Package of POPULUS and write a brief summary of what you learned (i.e. for each question i - vi below, report the results of your simulations and explain how your answers to the questions are supported by your simulation results):

  i.  Starting at an initial gene frequency of p=0.7, what is the probability of fixation of an allele due to drift?

  ii.  Ditto for initial frequency of p=0.2.

  iii.  Can you generalize, i.e. what is the probability of fixation given an arbitrary initial gene frequency?

  iv.  Derive a relationship inductively (e.g. by "experiment" on the computer) between population size and expected time to fixation (or elimination) for an allele starting out at an initial frequency of p=0.5.

  v.  Investigate whether the direction of change in gene frequency in one generation influences the direction of change in the next generation.

  vi.  What is the relationship between population size and the magnitude of gene frequency change in a single generation?

For 24 October:

                Text Readings:  H&C pp. 147-168.

                POPULUS exercise:

                    Using the Autosomoal Selection model in POPULUS, answer the following questions. For each question, report the results of your
                    computer analyses and explain how your answers to the questions are supported by your simulation results.

                        i.  How is the rate of evolution related to the intensity of selection?

                        ii.  How is the rate of fixation of a new mutation related to its dominance or recessiveness?

                        iii.  What are the final gene frequencies for the following sets of fitnesses for genotypes at a single locus?

                                a.  W_AA= .83,   W_Aa= .91,   Waa= 1.0

                                b.  W_AA= .83,   W_Aa= .91,   Waa= .68

                                c.  W_AA= .83,   W_Aa= .47,   Waa= 1.0

                        iv.  Does the equilibrium gene frequency correspond to a peak of the adaptive topography for the fitnesses
                                in part iii?
 
 

For 29 October:

                1.  Text Readings:  H&C pp. 349-377.

                2.  Short Essay: Read the following papers:

                     King, J. L., and Jukes, T. H.  1969.  Non-darwinian Evolution.  Science 164: 788-798.

                     Hughes, A. L., and Nei, M.  1988.  Pattern of nucleotide substitution at major
                            histocompatibility complex class I loci reveals overdominant selection.  Nature 335: 167-170.

                     McDonald, J. H., and Kreitman, M.  1991.  Adaptive protein evolution at the Adh locus in
                         Drosophila.  Nature 351: 552-554.

                    Write a short essay (2 pages) discussing how the work by Hughes and Nei and the work by
                            McDonald and Kreitman (a) supports, and (b) refutes the main thesis of the King and
                            Jukes paper.

For 31 October:

                1.  Text Readings:  H&C  pp. 209-220.

                2.  Short Essay:  Read the following papers:

                     Freeland, S. J., and Hurst, L. D.  1998.  The genetic code is one in a million.  J. Mol.
                            Evol. 47: 238-248.

                     Freeland, S. J., and Hurst, L. D.  Load minimization of the genetic code:  history does
                            not explain the pattern.  Proc. Royal Soc. B 265: 2111-2119.

                     Saks, M. E., Sampson, J. R., and Abelson, J.  1998.  Evolution of a transfer RNA gene
                            through a point mutation in the anticodon.  Science 279: 1665-1670.

                    Write a short essay (2 pages) proposing a mechanism whereby the genetic code could evolve.  Make
                            sure that you describe how all steps in the mechanism are permitted/favored by natural
                            selection.

For 5 November:

             1.  Text Readings:  Li  pp. 215-235,  pp. 419-432.

                2.   Begin exercise for12 November.

                3.   You should begin thinking about the topic for your long essay.
 

For 12 November:
 

             1.  Text Readings:  Li  pp. 59-78,  pp. 79-97.

                2.   Exercise:  Read the following papers:

                 Dykhuizen, D. E., and A. M. Dean.  1990.  Enzyme activity and fitness:  evolution in solution.
                        Trends in Ecology and Evolution 5:257-262.

                  Rausher, M. D., R. E. Miller, and P. Tiffin.  1999.  Patterns of evolutionary rate variation among
                        genes in the anthocyanin biosynthetic pathway.  Molecular Biology and Evolution 16: 266-274.
 

                Pick your favorite linear biochemical pathway (or you may use the lactose pathway described
                        by Dykhuizen and Dean) and, using GenBank, download sequences for pathway enzymes
                        for two organisms.  Using the degree of sequence difference between the two organisms,
                        calculate the rate of evolutionary divergence for each enzyme.  Describe any patterns in
                        evolutionary rate variation your analysis reveals (e.g. can you test any of the hypotheses
                        outlined in the two readings?)

                 NOTE:  You may  work together in groups on this exercise, but each individual must prepare
                        his/her own report.

                HELPFUL HINT:  The web address for GenBank is:

                                     http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
 
 
 
 

For 14 November:

                1.  Text Readings:  H&C  pp. 430-472 Part I,  Part II .
 
 
 

For 19 November:

                1.  Short Essay:  Read the following papers:

                 i. Orr, A. H., and J. A. Coyne.  1992.  The genetics of adaptation: a reassessment.
                        American Naturalist: 140: 725-742.

                    ii.  Bradshaw, H. D., S. M. Wilbert, K. G. Otto, and D. W. Schemske.  1995.  Genetic
                        mapping of floral traits associated with reproductive isolation in monkeyflowers
                        (Mimulus).  Nature 376: 762-765.

                    iii.  Long, A. D., S. L. Mullaney, L. A. Reid, J. D. Fry, C. H. Langley, and T. F. C.
                      Mackay.  1995.  High resolution mapping of genetic factors affecting abdominal bristle
                         number in Drosophila melanogaster.  Genetics 139: 1273-1291.

                Write a short essay (2 pages) discussing whether the results obtained by Bradshaw et al and
                        by Long et al. tend to support or not support the main thesis of Orr and Coyne's paper.
 

 For 21 November:

                1.  Text Readings:  H&C pp. 586-604.
 
 

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