## Software used in the course

R – An open-source environment for statistical computing and graphics. It is enormously flexible, widely used, and freely available (including source code), and installable binary versions are available for Linux (Debian, Redhat, Suse, and Ubuntu), Mac OS X, and Windows.

JAGS (**J**ust **A**nother **G**ibbs **S**ampler) – An open-source program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo. (If you don’t understand what any of that means, don’t worry about it. We’ll cover it in due course.) Rather than using JAGS as a standalone program, we’ll use the R2jags package in R. If you’re not familiar with installing packages in R, we (i.e., Nora) will cover that when it becomes necessary.

Structure – A program that uses a Bayesian clustering algorithm to group genotyped individuals into clusters. Structure is very computationally intensive. For large datasets, teraStructure is a promising alternative. Installable binaries are available for Structure (Linux, Mac OS X, and Windows), but you will have to compile teraStructure from source. If we use teraStructure in the course, we will make it available to you on a University computer cluster.

easyGWAS – easyGWAS is a web-based tool for **G**enome **W**ide **A**ssociation **S**tudies. Registration (free) is required to use the resources at the site.

TextWrangler – TextWrangler is a nice text editor for Mac users.

## Other resources

The January 2017 issue of *Molecular Ecology Resources* describes a series of packages for R that are useful for analysis of population genetic data.

The Statistical Genetics Task View on the Comprehensive R Archive Network (CRAN) lists more than 30 packages for analysis of genetic data in R.

The Population Genetics in R site provides tutorials for several kinds of population genetic analysis in R.

## Selected books on population genetics

This is not a comprehensive bibliography. It is a list of books that provide alternative ways of approaching some of the topics we cover in the course (e.g., Christiansen and Feldman 1986; Crow and Kimura 1970; Falconer and Mackay 1996) or that delve into particular topics in much greater detail (e.g., Hein et al. 2005; Lynch and Walsh 1998; Wakeley 2008).

Bulmer, M. G. 1985. *The Mathematical Theory of Quantitative Genetics*. Clarendon Press, Oxford.

Cavalli-Sforza, L. L., and W. F. Bodmer. 1971. *The Genetics of Human Populations*. W. H. Freeman and Co., San Francisco, CA.

Christiansen, F. B., and M. W. Feldman. 1986. *Population Genetics*. Blackwell Scientific Publications, Palo Alto, CA.

Crow, J. F. 1986. *Basic Concepts in Population, Quantitative, and Evolutionary Genetics*. W. H. Freeman and Co., San Francisco, CA.

Crow, J. F., and M. Kimura. 1970. *An Introduction to Population Genetics Theory*. Harper & Row, New York, NY.

Doolittle, D. P. 1987. *Population Genetics: Basic Principles*. Springer-Verlag, Berlin.

Durrett, R. 2002. *Probability Models for DNA sequence evolution*. Springer-Verlag, Berlin.

Edwards, A. W. F. 2000. *Foundations of Mathematical Genetics*. Cambridge University Press, Cambridge, UK.

Ewens, W. J. 2004. *Mathematical Population Genetics. I. Theoretical Introduction*, 2nd ed. Springer-Verlag, Berlin.

Falconer, D. S., and T. F. C. Mackay. 1996. *Introduction to Quantitative Genetics*, 4th ed. Longman, London.

Fisher, R. A. 1958. *The Genetical Theory of Natural Selection*, 2nd revised ed. Dover Publications, Inc., New York, NY.

Gale, J. S. 1990. *Theoretical Population Genetics*. Unwin Hyman, London.

Gillespie, J. H. 1991. *The Causes of Molecular Evolution*. Oxford University Press, New York, NY.

Gillespie, J. H. 1998. *Population Genetics: A Concise Guide*. Johns Hopkins University Press, Baltimore, MD.

Haldane, J. B. S. 1932. *The Causes of Evolution*. Longmans, Green, \& Co., Ltd., London.

Hartl, D. L., and A. G. Clark. 1997. *Principles of Population Genetics*, 3rd ed. Sinauer Associates, Sunderland, MA.

Hedrick, P. W. 2000. *Genetics of Populations*, 2nd ed. Jones and Bartlett Publishers, Sudbury, MA.

Hein, J., M. H. Schierup, and C. Wiuf. 2005. *Gene Genealogies, Variation, and Evolution*. Oxford University Press, New York, NY.

Kearsey, M. J., and H. S. Pooni. 1996. *The Genetical Analysis of Quantitative Traits*. Chapman & Hall, London.

Kimura, M. 1983. *The Neutral Theory of Molecular Evolution*. Cambridge University Press, Cambridge.

Lewontin, R. C. 1974. *The Genetic Basis of Evolutionary Change*. Columbia University Press, New York, NY.

Li, C. C. 1955. *Population Genetics*. University of Chicago Press, Chicago, IL.

Li, W.-H., and D. Graur. 1991. *Fundamentals of Molecular Evolution*. Sinauer Associates, Sunderland, MA.

Li, W.-H. 1997. *Molecular Evolution*. Sinauer Associates, Sunderland, MA.

Lynch, M., and B. Walsh. 1998. *Genetics and Analysis of Quantitative Traits*. Sinauer Associates, Sunderland, MA.

Mather, K., and J. L. Jinks. 1982. *Biometrical Genetics*, 3rd ed. Chapman and Hall, London.

Maynard Smith, J. 1989. *Evolutionary Genetics*. Oxford University Press, New York, NY.

Nei, M. 1987. *Molecular Evolutionary Genetics*. Columbia University Press, New York, NY.

Nielsen, R., ed. 2005. *Statistical Methods in Molecular Evolution*. Springer-Verlag, Berlin.

Rice, S. H. 2004. *Evolutionary Theory: Mathematical and Conceptual Foundations*. Sinauer Associates, Sunderland, MA.

Roff, D. A. 1997. *Evolutionary Quantitative Genetics*. Chapman & Hall, New York, NY.

Sorensen, D., and D. Gianola. 2002. *Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics*. Springer-Verlag, Berlin.

Spiess, E. B. 1989. *Genes in Populations*, 2nd edition. John Wiley & Sons, New York, NY.

Wakeley, J. 2008. *Coalescent Theory: An Introduction*, W.H. Freeman & Co., San Francisco, CA.

Weir, B. S. 1996. *Genetic Data Analysis II*. Sinauer Associates, Sunderland, MA.

Wright, S. 1968-1978. *Evolution and the Genetics of Populations*, 4 vols. University of Chicago Press, Chicago, IL.