I’ve posted notes for Tuesday (drift and selection) and Thursday (the coalescent). Something strange is happening with the permissions on my server. For some reason I can’t get the regular link from the detail page to the PDF notes for Tuesday to work. Use this link instead. I’ve also posted the link on the lecture detail page for Tuesday. I think I know where the permission problem is, but I may not have time to fix it until next weekend.
I’ve posted the notes for Thursday’s discussion of mutation, migration, and genetic drift. Notes on effective population size are included in the notes from last Thursday on genetic drift. Of course, the notes are always available from the lecture detail page.
If you visit the lecture detail page for Tuesday’s lecture, you’ll also find a link to Project #3. Nora will go over it in lab on Tuesday, but I encourage you to take a look at it ahead of time so that you have questions ready.
I’ve posted notes for this week’s lectures. Since snow prevented us from meeting in person last Thursday, we’ll devote the first part of Tuesday’s lecture to discussing any questions that arose from the practice exercise. (You did take my advice, and try it, didn’t you?) We’ll take as much time as we need to discuss any questions you have before moving on to discuss how to estimate viabilities from data. If there’s time, we’ll close by discussing how the dynamics of viability selection with multiple alleles differ from those with only two alleles present and how fertility selection differs from viability selection.
I hope that you had a chance to look at the Practice Exercise I posted on Thursday. I’ve now posted answers to the questions in the exercise. In addition to following the posted answers link in this post, you can also find links to the exercise and answers on the lecture detail page for last Thursday.
I expect to have notes for this week (estimating viabilities, an introduction to genetic drift) posted by this evening. Enjoy the snow!
As promised (or threatened) last night, I’ve posted a practice exercise that you can use to test your understanding of the concepts we would have covered in lecture today had classes not been canceled because of snow. The practice exercise link in this sentence and the last one will take you directly to the PDF. You will also find the link on the lecture detail page for today.
I will post my answers to the questions on Sunday night. Please take time between now and then to work through the questions on your own. Bring any questions you have about the exercise or about today’s lecture notes to class on Tuesday. We’ll discuss your questions before we dive into estimating viabilities.
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.