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Textbook and supplementary texts
*Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland MA.
Freeman, S., and Herron, J.C. 2001. Evolutionary Analysis, 2nd Edition. Prentice Hall, Upper Saddle River, NJ.
Hillis, D.M., Moritz, C., and Mable, B.K. 1996. Molecular Systematics, 2nd Edition. Sinauer Associates, Sunderland MA.
Lee, W.-H. 1997. Molecular Evolution. Sinauer Associates, Sunderland MA.
Page, R.D.M., and Holmes, E.C. 1998. Molecular Evolution, a Phylogenetic Approach. Blackwell Science, Oxford.
Required Reading
Baldauf SL (2003) The deep roots of eukaryotes. Science 300:1703-1706
Stewart CB (1993) The Powers and Pitfalls of Parsimony. Nature 361:603-607
Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theoret. Biol. 8:357-366.
Delwiche, C. F. 2004. The genomic palimpsest: Genomics in evolution and ecology. Bioscience 54:991-1001.
Felsenstein Chapters 2 & 3
Eisen, J. A., and C. M. Fraser. 2003. Phylogenomics: Intersection of evolution and genomics. Science 300:1706-1707.
Felsenstein Chapters 4 & 5
Felsenstein, J. 1978. Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading. Systematic Zoology 27:401-410. Available from jstor
Felsenstein Chapters 13 & 16
Homework
Due 2/13/2006, review: Fitz-Gibbon, S.T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Research 27: 4218-4222.
Supplementary Reading
Reeck, G. R., et al. 1987. "Homology" in proteins and nucleic acids: a terminological muddle and a way out of it. Cell 50:667.
Riedl, R. 1978. Order in Living Organisms (Translated by R.P.S. Jefferies). John Wiley & Sons, Chichester. Pp. 32-40.