Suggested readings relevant to wheat SNP data interpretation and analytical methods

(Assembled by Peter Morrell, Clegg Lab, UC Irvine, updated 1/30/2007)

Introduction to evolutionary genetics:

Nei M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press. Oxford UK. pp 333.
ISBN 0-19-513584-9.
Chapter 5 Phylogenetic Trees (introduces methods of phylogenetic estimation)
Chapter 12 Genetic Polymorphism and Evolution (introduces measures of genetic diversity)

Sampling:

What can we learn from SNP data?

Brumfield, R.T., P. Beerli, D.A. Nickerson, and S.V. Edwards. 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology & Evolution 18:249-256.

More genes, more individuals, or longer sequenced fragmens?

Pluzhnikov, A. and P. Donnelly. 1996. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144:1247-1262.
http://www.genetics.org/cgi/reprint/144/3/1247?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Pluzhnikov&searchid=1123643813323_429&stored_search=&FIRSTINDEX=0&journalcode=genetics

Molecular population genetics:

How do we make use of intraspecific nucleotide sequence data?

Posada, D. and K.A. Crandall. 2001. Intraspecific gene genealogies: Tree grafting into networks. Trends in Ecology and Evolution 16:37-45.

How can we analyze the geographic distribution of allelic diversity in populations?

Hey, J. and C.A. Machado. 2003. The study of structured populations—new hope for a difficult and divided science. Nat Rev Genet 4:535-43.

This paper provides an excellent introduction to coalescent theory.

Hudson, R.R. 1990. Gene genealogies and the coalescent process. p. 1-44 in R. Dawkins and M. Ridley, eds. Oxford Survey of Evolutionary Biology, vol. 7. Oxford University Press, Oxford, UK. http://home.uchicago.edu/~rhudson1/popgen356/OxfordSurveysEvolBiol7_1-44.pdf

What is linkage disequilibrium? If you don’t understand everything, read one of the other versions of the manuscript available online. As one of the authors says, you can ‘Collect them all’.

Nordborg, M., and S. Tavaré. 2002. Linkage disequilibrium: What history has to tell us. Trends in Genetics 18:83-90. (Paper #9 in the list at http://walnut.usc.edu/~magnus/papers/)

Further reading

An upcoming book that provides an introduction to coalescent theory. Sample chapters are available at the link below.

Wakeley, J. 200?. Coalescent Theory: An Introduction. Roberts & Company Publishers
http://www.roberts-publishers.com/wakeley/chapt.html

A nice review of molecular population genetics research on plants.

Wright, S.I. and B.S. Gaut. 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506-519.

Identifying genes targeted by selection in maize.

Wright, S.I., I.V. Bi, S.G. Schroeder, M. Yamasaki, J.F. Doebley, M.D. McMullen, and B.S. Gaut. 2005. The effects of artificial selection on the maize genome. Science 308:1310-1314.

Another approach to identifying genes impacted by selection.

Voight, B.F., S. Kudaravalli, X. Wen, and J.K. Pritchard. 2006. A map of recent positive selection in the human genome. PLoS Biol 4:e72.

Commentary on the use of haplotypes in candidate gene studies.

Clark, A.G., 2004. The role of haplotypes in candidate gene studies. Genetic Epidemiology 27:321-333.

An example of work from the Clegg lab; How much do mutation, recombination, and homologous gene conversion contribute to haplotype diversity?

Morrell, P.L., D.M. Toleno, K.E. Lundy, and M.T. Clegg. 2006. Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173:1705-1723.