Difference between revisions of "Reading"
Peter Beerli (talk | contribs) (Created page with "== General== Yang, Ziheng 2006. Computational Molecular Evolution (Oxford Series in Ecology and Evolution) Read: +text necessary reading, if there is a reference with + this...") |
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== Effective population size == | == Effective population size == | ||
| − | Alter, S. E., E. Rynes, and S. R. Palumbi. DNA evidence for historic population size and past | + | 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. |
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Ewens, W. J. 2004.Mathematical Population Genetics. Springer, New York. | Ewens, W. J. 2004.Mathematical Population Genetics. Springer, New York. | ||
| − | Roman, J. and S. R. Palumbi. 2003.Whales before whaling in the north atlantic. | + | Roman, J. and S. R. Palumbi. 2003.Whales before whaling in the north atlantic. Science, 301:508–510. |
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== Coalescence theory == | == Coalescence theory == | ||
Revision as of 17:42, 30 August 2013
Contents
General
Yang, Ziheng 2006. Computational Molecular Evolution (Oxford Series in Ecology and Evolution)
Read: +text necessary reading, if there is a reference with + this means that only those chapters, all other in the section will be not mandatory; -text = not necessary to read for class [but I suggest to browse it anyway, because Yang makes important points.]
- Models of nucleotide substitution (- chapter 1.6)
- Models of amino acid and codon substitution (+2.2, +2.5)
- Maximum likelihood methods (-4.4, -4.5, -4.6, -4.7 [comes later])
- Bayesian methods (this chapter contains about the same content as Paul Lewis’ lecture)
- Molecular clock +7.2
- 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.
