Population Genetics / Molecular Evolution Journal Club

Spring 2004

When and where
Fridays @ 1 PM, Jan 30 - May 7, 4151 VLSB (Slatkin Lab).

The plan
With a number of Slatkin lab and other journal club members taking quals this semester, we decided to depart from our usual casual format and to adopt a format that would progress through an admittedly limited set of "classic" papers. The first eight weeks attempt to move chronologically through some important papers in the history of population genetics and molecular evolution, mainly focusing on the history of the field's ideas regarding what forces explain most observable genetic variation. We'll take spring break off and then in the remaining seven weeks read classics and reviews regarding a few assorted topics that reflect a portion of the research interests of the students taking their quals.

Web resources
Mark Ridley's text Evolution has some classic papers available online at http://www.blackwellpublishing.com/ridley/classictexts/
MIT has a website called Perspectives on Molecular Evolution at http://hrst.mit.edu/hrs/evolution/public/
Most of the older papers can be found on one of the above websites.  If you have any trouble obtaining pdf files of any of the other papers, please just email us at novembre at socrates berkeley edu and we will be happy to provide assistance.

Reading schedule

• Jan 30
  Fisher, R.A. 1930. "The genetical theory of natural selection" Chapter 1: "The nature of inheritance" pp 1-21.  (link to Blackwell Publishing site)
   
• Feb 6
  Wright, S. 1932. "The roles of mutation, inbreeding, crossbreeding and selection in evolution" Proceedings of the VI International Congress of Genetrics: 1. pp 356-366.  (link to Blackwell)
   
• Feb 13
  Haldane, J.B.S. 1957. The cost of natural selection. J. Genet.  55:511-524.  (link to Blackwell)
   
• Feb 20
  Kimura, M. 1968. Evolutionary rate at the molecular level. Nature 217:624-626.  (link to MIT)
  
  Excerpts pp. 19-31 from the chapter "The Struggle to Measure Variation" in R.C. Lewontin's "The Genetic Basis of Evolutionary Change" 1974.  (link to MIT site)
   
• Feb 27
  Kimura, M. and Crow. J.F. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-738.  (link to MIT)
   
• March 5
  R. C. Lewontin and J. L. Hubby, "A Molecular Approach to the Study of Genic Heterozygosity in Natural Populations. II. Amount of Variation
  and Degree of Heterozygosity in Natural Populations of Drosophila pseudoobscura," Genetics 54 (1966): 595-609.  (link to MIT)
  
  Ohta and Gillespie. 1996. "Development of Neutral and Nearly Neutral Theories" TPB 49:128-142.  (link to TPB via Science Direct)
  (You may want to check out other articles in this issue of TPB, which is devoted to Motoo Kimura's lifework.)
   
• March 12
  A. L. Hughes and M. Nei, "Pattern of nucleotide substitutions at major histocompatibility complex class I loci reveals overdominant selection," Nature 335 (1988), 167-170.  (the abstract is online at the Nature Archives, but the PDF doesn't seem to download, so look in our pdf directory [ie, add pdf to the url in your browser])
  
  J. H. McDonald and M. Kreitman, "Adaptive protein evolution at the ADH locus in Drosophila," Nature 351 (1991), 652-654.  (link to article at Nature Archive)
   
• March 19
  Smith, NG, A Eyre-Walker. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024.  (link to article at Nature)
  
  Fay, JC, GJ Wyckoff, CI Wu. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila Nature 415:1024 - 1026.  (link to article at Nature)
   
• March 26
  
  SPRING BREAK
   
• April 2   Topic: Population Expansions
  Slatkin, M and RR Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562.  (link to article at Genetics)
   
• April 9   Topic: LD / Measuring Recombination
  
  Lewontin, RC and K Kojima. 1960. The evolutionary dynamics of complex polymorphisms. Evolution 14:458-472.  (link to article at JStor)
  
  Stumpf, MPH and GAT McVean. 2003. Estimating recombination rates from population genetic data. Nature Reviews Genetics 4:959-968.  (link to article at Nature)
   
• April 16   Topic: Human genetic history
  
  Nei M, Roychoudhury AK. 1974. Genic variation within and between the three major races of man, Caucasoids, Negroids, and Mongoloids. Am J Hum Genet 26:421-43.  (Not available online - check our pdf folder!)
  
  Rosenberg, N.A. et al. Genetic structure of human populations. Science 298, 2381-2385 (2002).  (link to article at Science)
   
• April 23   Topic: Association based studies
  
  KT Zondervan and LR Cardon. The complex interplay among factors that influence allelic association. Nature Reviews Genetics 5:89-100. 2004.  (link to article at Nature)
  
  Terwillger, J.D. and Weiss, K.M. Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotechnol 9:578-594. 1998.  (link to journal at Science Direct)
   
• April 30   Topic: Viral studies
  
  Allen G. Rodrigo, Eugene G. Shpaer, Eric L. Delwart, Astrid K. N. Iversen, Michael V. Gallo, Jürgen Brojatsch, Martin S. Hirsch, Bruce D. Walker, and James I. Mullins. Coalescent estimates of HIV-1 generation time in vivo. PNAS 1999; 96: 2187-2191.  (link to article at PNAS)
  
  KA Crandall, CR Kelsey, H Imamichi, HC Lane, and NP Salzman. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol 1999 16: 372-382.  (link to article at MBE)
  
   
• May 7
  
  Final meeting. Reading TBA.