# Population Genetics notes

I’m releasing a draft of my population genetics notes from the graduate level course I teach in the population biology graduate core course here at UC Davis. I developed these notes in the last iteration of the course I taught, and so they are still full of typos etc. I hope they will be of use to others.

pdf of popgen notes (click on the “raw” button to download the pdf).

A html version of the notes generated by pandoc and github-pages. Thanks to Vince Buffalo for help setting these up.

I’m also releasing the latex, figures, and code for the figures so that these notes can be rewritten by others for other classes/purposes. All of this is available from our lab github page.

The code and data for the R exercises are available here.

Theses notes, code, and all of the figures are released under the Creative Commons Attribution 3.0 Unported License. So if you do reuse these you don’t need my permission, you just need to acknowledge me.

If they do prove helpful, it would be great if you also left a note here in the comments so that I get a sense of the uses that they are put to. Also typos, concerns, and corrections are welcome as comments on this page. The notes are not intended at the moment to be completely stand alone, and take a number of shortcuts in explaining concepts. My hope is eventually to turn them into xtml or a wiki where there could be links to expanded discussions of various topics. I will keep updating these notes overtime and in light of feedback, so hopefully they will develop into a useful resource.

These notes owe a debt to the huge literature of popgen papers and textbooks I’ve read over the years. I will also start to incorporate references etc in the notes to fill our my sources and resources, but I thought it good to get these notes out soon rather than later.

My notes aren’t the only popgen openly available online. Here’s a couple of other resources:

Kent Holsinger’s Notes on Figshare and webpage.

Joe Felsenstein’s book

I’m happy to add more to this list.

Graham

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Fantastic resource! Thanks, Graham.

Thanks Brian.

Thank you for the book

Graham, stumbled upon this resource from Haldane’s Sieve. This is fabulous. I’ve been doing something similar for microbial ecology and evolution (http://micropopbio.org) for several years, but not nearly as professionally or comprehensively as you have. I echo Felsenstein’s book.

I’m now even sadder not to be teaching molecular evolution or pop gen next fall, but will send this to my successor. Thank you!

Cheers

Dear Graham, just stumbled upon this fabulous resource from Haldane’s Sieve. Thank you very much! I’m now sadder that I’m not teaching molecular evolution / pop gen in the fall, but will send this resource to my successor.

I’ve been doing something similar for microbial ecology and evolution here at UNH (http://microopobio.org) for several years but in nowhere near the level of polish / detail that you’ve offered. And I second the value of Felsenstein’s book, which I send to all of my lab and students.

Thanks again!

Cheers

Vaughn

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Bruce Walsh’s homepage comes to mind, and under his “talks/notes” section he has a nice set of lectures on Evolutionary Quantitative Genetics (not to mention his book length draft of Evolution and Selection of Quantitative Traits with Lynch):

http://nitro.biosci.arizona.edu/workshops/Uppsala2012/Uppsala.html

Dear Graham,

This is a really great resource, perfect for brushing up on some difficult areas that aren’t covered that much in the usual texts e.g. Hartl and Clarke. I noticed in section 4.5.1, equation 90, I think the sign is wrong (should be negative on one side), giving

s\gamma(x)q(x)(1-q(x))=-\frac{\sigma^2}{2}\frac{d^2q(x)}{dx^2}

Also, I found it very slightly confusing that at the top of page 30 the sink location is described as receiving a contribution g(\Delta x) from the location x+\Delta x, when in fact it is receiving this contribution from x-\Delta x. Of course, due to the symmetry of the normal distribution, you get the same answer using g(-\Delta x).

I use your R codes in classes and your notes as an additional resource. Will give you feedback after the course (DNA analysis in population genetics, University of Oulu).

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This is really a rich source of information, I appreciate your work indeed