No book is required for this class!
But if you want to to check out a book anyway I suggest to read
Yang, Ziheng 2006. Computational Molecular Evolution (Oxford Series in Ecology and Evolution)

  1. Models of nucleotide substitution (- chapter 1.6)
  2. Models of amino acid and codon substitution (+2.2, +2.5)
  3. Maximum likelihood methods (-4.4, -4.5, -4.6, -4.7 [comes later])
  4. Bayesian methods (this chapter contains about the same content as Paul Lewis’ lecture)
  5. Molecular clock +7.2
  6. Simulating molecular evolution +9.5.1

Population models

Ewens, W. J. 2004. Mathematical Population Genetics. Springer, New York.

Effective population size

Alter, S. E., E. Rynes, and S. R. Palumbi. DNA evidence for historic population size and past ecosystem impacts of gray whales. Proceedings of the National Academy of Sciences U.S.A., 104(38):15162–15167, Jan 2007.

Ewens, W. J. 2004.Mathematical Population Genetics. Springer, New York.

Roman, J. and S. R. Palumbi. 2003.Whales before whaling in the north atlantic. Science, 301:508–510.

Coalescence theory

Fu, Y. X. 2006. Exact coalescent for the Wright-Fisher model. Theoretical Population Biology, 69:385–394.

Hein, J., M. H. Schierup, and C. Wiuf. 2005. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford University Press, Oxford.

Hudson, R. R. 1991. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7:1–44.

Kingman, J. F. C. 2000. Origins of the Coalescent: 1974-1982. Genetics, 156(4):1461–1463.

Rosenberg, N. A. and M. Nordborg. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics, 3(5):380–390.

Wakeley, J.. 2008. Coalescent theory. Roberts & Company Publishers, Greenwood Village, Colorado. pp 326.

Mutation models

Ewens, W. J. 2004. Mathematical Population Genetics. Springer, New York.

Moler, C. and C. V. Loan. 2003. Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later. SIAM REVIEW, 45(1):1–46.