I presume you’ve all heard by now that the University will be closed tomorrow (Thursday, 9 February). The notes for lecture have been posted on the lecture detail page since last weekend. Tomorrow morning (probably by 9:00am, possibly earlier, and certainly by noon) I’ll be posting some short exercises you can do to test your understanding of what’s covered in the lecture notes. I’ll post my answers to the exercises on Sunday. The exercise won’t be graded, and you may find the questions a little simple, but I encourage you to think about them and to try your hand at the calculations. It’s a good way to make sure you understand the concepts.
We’ll start the lecture on Tuesday by discussing any questions you have about the exercise. So if there’s anything confusing or if there’s simply something you’d like to hear explained out loud, come prepared to ask a question. If you don’t ask a question, I’ll barrel on and assume that you have it all mastered, which you may regret in the future.
I’ve posted notes for the week of 6 February. On Tuesday we’ll complete our discussion of F-statistics. Then we’ll move on to a very different approach to analysis of genetic structure – individual assignment. You’ll be using Structure for your analysis of genetic structure in Project #2, and Nora will introduce you to it in lab. Depending on how things go, we may start our discussion of the principles of natural selection towards the end of the lecture on Tuesday. In any case, we’ll be deep into the weeds on understanding it on Thursday so that we’re ready to understand how to go about estimating it next week.
If you’re interested in getting an early start, I’ve posted Project #2. You’ll find links to the description of the project, the data files, and the R and JAGS scripts you’ll need for the project on the lecture detail page for Tuesday. You’ll be using JAGS this time, but you won’t have to write any of your own code. Structure will be unfamiliar to you until we cover it in lecture on Tuesday. Those notes will be going up later tonight.
The Prunier et al. paper that provides background on the data was just accepted in <em>American Journal of Botany</em>.
I’ve posted notes on estimating F-statistics. The notes for Tuesday’s lecture are identical to the ones for last Thursday’s lecture. The lecture detail page on both of those days links to the same PDF.
On Tuesday we’ll go over Weir & Cockerham’s approach to estimating F-statistics, and I’ll introduce to a form of stochastic variation that you probably haven’t thought about before. I think you’ll be surprised when you discover how important it can be.
On Thursday (possibly late on Tuesday if we move through Tuesday’s material quickly), we’ll discuss a Bayesian approach to estimating <em>F</em>-statistics. I’ll give you the JAGS code you need, so long as you’re dealing with only two alleles per locus. You can find the code on Thursday’s lecture detail page.
Enjoy the rest of your weekend. I’ll see you bright and early on Tuesday morning.
If you happened to log onto the course website this afternoon between about 4:30 and 5:30, you may have noticed that the lecture schedule and readings pages weren’t working. Not that you should care, but I upgraded the WordPress theme, and I forgot to save a copy of the code that I had to write for those. Luckily, having reconstructed the code once before, it wasn’t too hard to reconstruct it again (and now I have it backed up in two places). I think everything’s back to normal. Let me know if you encounter any problems.
Tonight I was going over the notes on genetic that I posted over the weekend, and I found a couple of small changes I wanted to make. If you’ve already downloaded the older version and printed them, don’t worry about downloading again. I’ll point out the one small error in lecture. The other just changes the heading on a table.
The notes for this week’s lectures are now posted. As usual, you’ll find them linked on the lecture detail page. As a reminder, the Project #1 assignment is also posted. You’ll find it (and a link to a paper you’ll want to refer to) on the lecture detail page for Tuesday.
I’ve posted Project #1. You can find it on the lecture detail page for next Tuesday. If you take a look at it before lab on Tuesday, please try not to freak out. It may look a little daunting, but it should look a little less daunting after lecture and after Nora gives you a little more background (and a few hints). It still won’t be easy, but at least it should be a little less daunting.
The lecture schedule is (finally!) complete. We may tweak it a little bit as the semester goes along, but any changes will be minor.
I have also posted lecture notes for the first week of class. They’re available from the lecture detail page associated with each lecture. As a reminder, to get to the lecture detail page, simply click on the lecture title on the Lecture Schedule page. Once you’re there, you’ll see a brief description of the lecture and you’ll find a link to the associated notes (and sometimes some other resources).
See you bright and early Tuesday morning. Enjoy the rest of your weekend.
I (Nora) have finally figured out how to semi-operate the WordPress page, now all I have to do is actually come up with the lab schedule (with Kent’s help, of course). The lab schedule will not only tell you what we’re doing every week, it will also have links to example data and code, and I’ll be updating it with any presentations I give after the lab as well.