EEB 5348 – Population Genetics

Just in case you want to get an early start on Project #4, I’ve posted a link to it on the lecture detail page for tomorrow’s lecture.  It’s not due until the Tuesday after spring break, but Nora will be in Texas getting experiments for her postdoc started during spring break, and I’ll be (mostly) unavailable during spring break, so I encourage you to get started on it soon.

We shift gears on Tuesday and start our survey of molecular evolution. We’ll start with a review of the kinds of molecular variation that population geneticists have studied over the last 50 years, then we’ll discuss the neutral theory and some of the ways it’s been modified to fit our increasingly sophisticated understanding of molecular variation. After spring break Nora will talk about some of the ways we can detect selection on nucleotide sequences and about the evolution of multigene families. When I get back we’ll talk about how to use data from molecular markers to make inferences about the recent evolutionary history of individuals and populations, and we’ll finish with a very brief discussion of how the explosion of data that is coming with high-throughput sequencing is changing our approach to understanding evolutionary processes in populations.

I made some last-minute changes to the notes for tomorrow’s lecture, a short section on “genetic draft.” You read that right. It’s not a typo. Genetic draft is a thing – and we’ll discuss it briefly tomorrow. There’s still a permission problem with the notes, so follow the link with the PDF label on the lecture detail page, or click here.

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.