The past few years have seen the development of a plethora of new methods of population genetic analysis. Rather than just estimating genetic differentiation and diversity, these methods now allow the quantification of migration rates and time since divergence, identification of migrants, estimation of population sizes and even separation of samples into genetically homogenous groups. Furthermore, many of these methods go beyond the description of population structure to the explanation of mechanisms causing it. Although most of these new methods are computationally intensive, advances in PC computer power, together with a multitude of freely available programs, make their application on desktop computers feasible. The large number of approaches and easy availability of programs, however, adds further importance to the choice of the appropriate method for the biological question under study. The aim of this class is to provide an overview of the various methods, with a critical evaluation of their assumptions and their application to real world examples and hands-on experience with computer programs. This class is NOT a basic introduction to population genetic theory - for that I recommend Joe Felsenstein's courses Evolutionary Genetics (Genome 453) and Population Genetics (Genome 562).
I will assume that students have a basic understanding of population genetics, including microevolutionary forces (mutation, selection, drift, migration), Hardy-Weinberg equilibrium, linkage equilibrium, effective population size, the concepts of FST and genetic distance etc. I will also assume a basic knowledge of molecular markers, such as allozymes, microsatellites and sequencing (though I will quickly run through this in the first lecture).
For those who need to catch up, please check the website of my FISH 340 course, which also includes a glossary of terms. Also, if you are planning to take Conservation Genetics (which I highly recommend, FISH 444) you may want to buy Conservation and the Genetics of Populations by Fred Allendorf and Gordon Luikart. This book has an excellent appendix in basic analyses techniques.
Most importantly, don't be shy and ask. Asking about basic principles is fine, and will benefit the rest of the class. Youu can ask in class, or by using the message board. Also, please be active in explaining stuff to your class mates - there is no better way of learning than teaching!
The course will consist of three parts: (i) a lecture introducing specific methods and their assumptions, (ii) discussion of the relevant literature and (iii) a computer lab with demonstration and application of specific computer packages. Lecture and discussion will happen on Thursday and a computer lab on Friday.
Both literature surveys and the application of computer programs will require work outside normal class hours. I will expect that you read the assigned papers before class; to ensure that, an online message board has been established and you will be required to comment on the reading each week before class. In class, students will provide a brief (5 min) summary of the papers, which we will then discuss.
In the computer lab, we will use some analysis packages relevant to the respective theme. The computer lab time will probably be spent on demonstrating the computer package and explaining input and output files. You may have to run the full analyses at home - some of these programs are quite slow. At the beginning of the next class, we will discuss outcomes from these analyses - again, this may involve a presentation by a student.
If you have data sets you wish to analyze in the computer labs, you would be welcome to talk to me and do so, otherwise, I will supply appropriate data sets each week.
There is no specific textbook for this class - computer programs and statistical analyses develop too fast for that. Check the readings page for weekly readings and suggested additional literature.
There are several very good population genetics textbooks:
Hedrick (2004) Genetics of Populations. Third edition. Jones & Bartlett Publishers.
Hartl & Clark (2006) Principles of Population Genetics. Fourth Edition. Sinauer Associates
Balding et al. (2003) Handbook of Statistical Genetics. Second edition. Wiley. Like all handbooks, a fairly serious, two volume treatise.
There are several other course on campus which would be relevant for population geneticists. some examples: