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Course Material Readings 

Course readings may only be used for the University's educational purposes. You may print a copy for your own use, but you may not make a further copy for any other purpose. You may not copy or distribute any part of the reading to any other person. Failure to comply with these terms may expose you to legal action for copyright infringement and/or disciplinary action by the University.

Course Text:

Frankham, R., Ballou, J. D., Briscoe, D. A. (2002). Introduction to Conservation Genetics. Cambridge: Cambridge University Press.

Lectures by Dr. Shane Lavery - Gene Flow & Population Structure

• Shane's Simple Guide to F-statistics (PDF) - necessary reading*
  
  

• Hey, J., & Machado, C. A. (2003). The Study of Structured Populations - New Hope for a Difficult and Divided Science. Nature Reviews Genetics, 4(7), 535 -543.
  
  

• Knowles, L. L. (2004). The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17(1), 1-10. [You may need to scroll to find this article. Click on PDF for recommended viewing]
  
  

• Neigel, J. E. (2002). Is FST obsolete? Conservation Genetics, 3(2), 167-173.

• Neigel, J. E. (1997). A comparison of alternative strategies for estimating gene flow from genetic markers. Annual Review of Ecology and Systematics, 28, 105-128.
  
  

• Slatkin, M. (1985). Gene flow in natural populations. Annual Review Ecology and Systematics, 16, 393-430.

Lecture 3 - Drift, inbreeding depression and mutational load

• Ralls, K., Brugger, K., & Ballou, J. (1979). Inbreeding and juvenile mortality in small populations of ungulates. Science, 206, 1101-1103. [Choose Download to access a PDF of this article] 
  
  
• Arden, S. L., & Lambert, D. M. (1997). Is the black robin in genetic peril? Molecular Ecology, 6, 21-28. [Available only as a print journal] 
  
  
• Frankham, R. (1995). Inbreeding and extinction: a threshold effect. Conservation Biology, 9, 792-799. [Choose Download to access a PDF of this article] 
  
  
• Madsen, T., Shine, R., Olsson, M., & Wittzell, H. (1999). Restoration of an inbred adder population. Nature, 402, 34-35.
  
  
• O'Brien, S. J., Roelke, M. E., Marker, L., Newman, A., Winkler, C. A., Meltzer, D., et al. (1985). Genetic basis for species vulnerability in the cheetah. Science, 227, 1428-1434. [Choose Download to access a PDF of this article] 
  
  
• Lande, R. (1988). Genetics and demography in biological conservation. Science, 241, 1455-1460. [Choose Download to access a PDF of this article] 
  
  
• Eyre-Walker, A., & Keightley, P. D. (1999). High genomic deleterious mutation rates in hominids. Nature, 397, 344-347.

Lecture 2 by Dr Howard Ross

• Lewis, P. O. (2001). Phylogenetic systematics turns over a new leaf. Trends in Ecology and Evolution, 16, 30-37.
  
  
• Sanderson, M. J., & H. B. Shaffer (2002). Troubleshooting molecular phylogenetic analyses. Annual Review of Ecology and Systematics, 33, 49-72.
  
  
• Springer, M. S., Stanhope, M. J., Madsen, O., de Jong, W. W. (2004). Molecules consolidate the placental mammal tree. Trends in Ecology and Evolution, 19, 430-438.

Lecture for 8 April

• Messier, W., & Stewart, C. B. (1997). Episodic adaptive evolution of primate lysozymes. Nature, 385, 151-154.
  
  
• Nielsen, R., & Yang, Z. (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929-936.

  Additional References:
  

• Sharp, P. M. (1997). In search of molecular darwinism. Nature, 385, 111-112.
  
  
• Yang, Z., & Nielsen, R. (2002). Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular biology and evolution, 19(6), 908-917.
  
  
• Krietman, M. (2000). Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539-559.

Lectures by Associate Professor Brian Murray 

• Bailey, R.J., Rees, H., Jones, L.M. (1976). Interchange heterozygotes versus homozygotes.  Heredity, 37, 109-112.

• Butlin, R.K. (2005). Recombination and speciation. Molecular Ecology 14, 2621-2635

• Levin, D.A. (2002). The Role of Chromosomal Change in Plant Evolution, New York: Oxford University Press.
  (a) Pages 23-44 provide very basic information on the types of chromosome mutation and (b) 72-76 introduce the concept of chromosome change forming a barrier to gene exchange.
  
  

• Rieseberg, L. H. (2001). Chromosome rearrangements and speciation.  Trends in Ecology and Evolution, 16, 351-358.
  
  
• Reeves, G., Francis, D., Davies, M.S., Rogers, H.J., & T.R. Hodgkinson, (1998). Genome size is negatively correlated with altitude in natural populations of Dactylis glomerata. Annals of Botany, 82 (suppl. 1): 99-105.
  
  
• Stefansson, H., Helgason, A., Thorleifsson, G., Steinthorsdottir, V., Masson, G., Barnard, J., et al. (2005). A common inversion under selection in Europeans.  Nature genetics, 37, 129.
  
  
• Wolfe, K. (2003). Speciation reversal.  Nature, 422, 25-26.  Provides a commentary on the paper by Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis EJ, Oliver SG (2003) Engineering evolution to study speciation in yeasts.  Nature, 422, 68-72.
  
  
• Wendel, J., & Wessler, S.R. (2000). Retrotransposon-mediated genome evolution on a local ecological scale.  Proceedings of the National Academy of Sciences of the United States of America, 97, 6250-6252.