If for some strange reason you logged onto the website after about 5:45pm last Wednesday, you will have noticed that I posted the last two sets of lecture notes – on genome-wide association mapping and on genomic prediction. I didn’t say this in the notes, but what I’m presenting is a very high level overview. People who know GWAS and genomic prediction could easily teach an entire course on them. We’ll just cover enough in this course so that you have a sense of how to read and interpret papers that use GWAS or genomic prediction and a sense of the things you have to be careful about in interpreting and applying the results.
The final set of notes on molecular population genetics has been uploaded. You’ll find a link on the lecture detail page for Tuesday, Population genomics. You’ll also find a link to the first set of notes on quantitative genetics on the lecture detail page for Thursday. As noted there, understanding some key ideas in quantitative genetics involves a lot of math. I’ll do my best to continually remind you where we’re going and why what we’re doing matters, but please remember to ask me “WGAD? – Who gives a damn?” whenever you’re feeling lost. If you’re too confused even to ask a question to clarify, just ask “WGAD?” and I’ll do my best to back up and explain things another way. If I can demonstrate why you should GAD, the light bulb that shows how things connect might suddenly go off.
I will be out of town on Halloween. (My mother is celebrating her 92nd birthday, and I’ll be in Idaho visiting her.) As a result, I’m getting notes posted well ahead of time. You’ll find notes for lectures on 24, 26, and 31 October as well as 2 November on the corresponding lecture detail page.
I’ll mention this again next week, and I will probably send an email about it to everyone too, but as a heads up, although I will not be with you in person on Halloween, I will record a lecture for 31 October. Nick and I will be going over the technology before I leave, and if all goes well, he’ll be able to broadcast in McHugh 206 on the 31st at 8:00am. I encourage all of you to be there. I anticipate that the recording will be 45 minutes long or less. That will give you half an hour or so to ask Nick questions about the lecture. If he doesn’t know the answer, he can at least write them down so that I can address them when I’m back on the 2nd of November.
UPDATE: I finished recording the lecture, and I’ll add the link to the lecture detail page for 31 October in a few minutes. The recording is just over 38 minutes long.
I just added links to an R notebook and the corresponding HTML file illustrating basic properties of the Jukes-Cantor model of nucleotide sequence evolution to the lecture detail page for Tuesday. I’ll illustrate the properties during lecture, but feel free to download the notebook ahead of time and play around with it if you’re so inclined.
I’m posting Project #2 a bit earlier than usual because it’s a bit different from any of the projects you’ve seen before. Instead of having you analyze data or interpret simulations, I’m asking you to read a paper and respond to questions about it using what you’ve learned about population genetics so far, and especially what you’ve learned about drift and selection.
That means that the lab meeting on Tuesday will be a bit different from usual too. Rather than figuring out how to download R packages and run R code, I suggest that you use the time to discuss the paper and to think about how you will answer the questions. That also means that you’ll need to read the paper before you get to lab on Tuesday morning. That’s why I’m posting this now. I want to make sure you have time to read the paper before Tuesday morning. (I am not trying to destroy your weekend. You’ll have plenty of time to read the paper on Monday. I just wanted you to be prepared to set aside some time on Monday to read it. If you want to read the paper over the weekend, that’s fine, but it isn’t at all necessary for you to do so.)
I’ve posted the lab exercise for the week of 9 October on the lab schedule page. Once again you’ll be doing simulations, but you’ll be using a coalescent approach to simulating genetic drift instead of the forward simulation approach you’ve used for the past couple of weeks. If you don’t know what that means, don’t worry. We’ll discuss the coalescent in lecture on Tuesday and Thursday.
I’ve also posted notes for the first several lectures on molecular evolution. When we get there, we’ll be moving into the second thematic block of lectures. We’ll start to connect population genetic principles much more directly with data. We’ll start by focusing on how to understand the evolution of molecules themselves.
Next Tuesday we’ll start by reviewing what we’ve learned about genetic drift so far. Please come prepared to ask any questions you have about the basic process, effective population size, or the interaction of drift with mutation, migration, or selection. We’ll revisit some of the results we’ve already seen, but through a different lens. We’ll be looking backwards to develop the conceptual tools we need to make inferences about population history from the data we collect rather than looking forwards as we’ve done so far in the course. The lecture detail page includes a link to an HTML page and the corresponding R markdown file. There’s no need to play with the R markdown before lecture, but if you have a chance to download it, you might want to use it to follow along in lecture on Tuesday.
I’ve added the recording of yesterday’s lecture to the lecture detail page for 5 October. Unfortunately, none of the slides are there, only my voice. You may remember that I said that the rear monitor wasn’t on. Apparently whatever technical malfunction caused it not to be on also caused recording of slides not to work. I’m really sorry about that. You would think that by the time we’re nearing the halfway point in the semester I’d have the technology figured out. Now I know that if the rear monitor isn’t working I need either to get it working myself or find someone who can get it working for me.
I’ve posted revised versions of the notes for this week’s lectures. I also posted a link to the video recording of Thursday’s lecture, and I posted links to the lab exercise for this week. I think I’m caught up. Let me know if I’m missing anything.
Also, please come prepared with questions about effective population size. It’s an important and difficult concept. We’ll take as much time as we need at the start of lecture on Tuesday to clear up confusion.
I’ve posted the notes on genetic drift. We’ll be covering a lot of pretty complicated stuff this week. I encourage you to take a look at the notes beforehand. There’s a good chance that many parts of them won’t make a lot of sense, but if you’ve reviewed them before we get to lecture, you’ll be in a better position to ask questions in class.
I also have to apologize for Thursday’s lecture. The video is now linked from the lecture detail page, but I forgot to turn the microphone on. As a result, you see all of the slides, but there isn’t any audio. I deeply regret the error. I’ll do my best not to repeat it in the future.