Full-text access

I just learned something. Most of you apparently haven't tried to read the full text of any of the readings I suggested. How do I know this? I just heard from one of you that if you follow the link you get to pages that ask for payment. Well, I've fixed that now, or at least I think I fixed it.

The University now uses a proxy server to authenticate IPs for access to full-text resources. I had to add a little "magic" to the PHP script that serves up the links to run the links through the proxy server. Let me know if you run into any more problems. (And take a look at the papers before lecture, if you have a chance.)

On a related note, there are only 5 responses to the SurveyMonkey questionnaire so far. That means 2/3 of you haven't responded.

Snow day

Snow is falling gently as I type this at 8:30pm Monday evening, but all of the forecasts say that they heaviest snow will begin to fall later tonight. If you have power (and if Darwin doesn't go down), you'll be able to read this Tuesday morning. If you see it, please look over the notes for last Thursday and today. Actually, don't look them over, study them. When you think you have a good understanding of what's going on, head over to this link at SurveyMonkey https://www.surveymonkey.com/s/H9C6JXK for a short quiz on a few key concepts. You'll only be able to take the quiz once (unless you switch computers), and SurveyMonkey won't tell you how you did. I'll collect the answers on Wednesday and use them to identify points of confusion that we need to revisit at the beginning of Thursday's lecture.

If possible, I'd like to spend no more than 10-15 minutes reviewing what's in the notes from these two lectures, but it's critical that you have a good understanding of inbreeding, so if it takes longer than 15 minutes so be it. We'll make up the time somewhere else.

Genetic drift

I've posted notes on genetic drift, effective population size, and the interactions between mutation, migration, and drift. We won't get to these topics until the end of February, but I wanted you to know that I am making progress. I am hopeful that all of the notes will be revised by mid-February so that you can print an updated copy of the one-volume version of these notes for reference if you're so inclined.

Winter storm watch

The National Weather Service has issued a winter storm watch for our area:

URGENT - WINTER WEATHER MESSAGE
NATIONAL WEATHER SERVICE TAUNTON MA
352 AM EST SUN JAN 25 2015

...A MAJOR WINTER STORM WILL IMPACT THE REGION MONDAY NIGHT
THROUGH TUESDAY NIGHT WITH 1 TO 2 FEET OF SNOW AND BLIZZARD
CONDITIONS POSSIBLE...

If this forecast holds, I expect that the University will be closed on Tuesday. I think I've successfully added UConn's alert banner to all of the web pages on this site, so if you were to log directly onto the web site Tuesday morning, you'd see the alert message if there is one. It will link you to http://alert.uconn.edu/, so you might simply want to head there first. If you haven't already done so, you might also want to register your cell phone to receive text message alerts.

If the University is closed on Tuesday, please stop by the course website Tuesday morning after 8:00am. I will post instructions describing how we can cover most of the material I was planning to cover in person. It will require you to do a bit more work on your own, but I think we can manage.

Lab 1

Hi all,

I've uploaded the brief presentation from today's lab as a pdf, and corrected the extra parantheses in the R Tutorial as well. Try and get JAGS and R2jags running before next week when we'll be using them more extensively. Note: MAC users install JAGS v3.3 and then the rjags and R2jags libraries--we had some issues with v3.4. Feel free to email me if you run into more issues!

More complicated forms of selection

I've posted notes on more complicated forms of selection, and I also found a couple of minor errors in the notes for testing Hardy-Weinberg that I've fixed. I had hoped to have notes for the entire semester updated before Tuesday, but that's clearly not going to happen, but at least I made it to mid-February.


Enjoy the rest of your weekend. I look forward to seeing you bright and early on Tuesday morning in TLS 301. By the way, there are a couple of you who are signed up for EEB 5348 but not EEB 5895 section 9. I'll be e-mailing you with permission numbers for EEB 5895 section 9 as soon as I finish this entry, so if you happen to see this post before you check your e-mail, check your e-mail and register for EEB 5895, section 9.

Estimating viabilities

I've just posted the notes on estimating viaibility. If you go to the detail page for that lecture, you'll see that I have to be in Hartford that morning - a commitment that was scheduled in December and can't be moved. Nora hasn't heard this yet, but since that's a day when (a) we have a lab and (b) you'll be working on Project #2, I'll let you and Nora decide whether you'd like to have her illustrate how to estimate viabilities in JAGS for the first part of the day or if you'd prefer simply to spend the whole time working on Project #2.

The genetics of natural selection

I just posted notes on the genetics of natural selection. I won't be posting notes tomorrow, but I hope to have the notes on estimating viability selection posted by Tuesday night. I may not get all of the notes revised before the semester starts,1 but I will have a lot of them revised.

Individual assignment

Individual assignment methods have become very important tools for analyzing genetic structure in the last 15 years. The mathematical details behind how they work is fairly complicated, so we'll barely scratch the surface of how they are implemented.1 We'll spend most of our time discussing three examples, both the data from which they were derived and how to interpret the results.

Bayesian F-statistics

I've updated my notes on using a Bayesian approach to estimate F-statistics. You'll see that I've included both an R script to automate the analysis (once you have your data in the right format) and the JAGS scripts that run the actual analysis. If you look at the code you'll realize that as currently written it will only work for co-dominant, bi-allelic markers in diploids, e.g., SNPs. It would be trivial to extend it to dominant, bi-allelic markers. Extending it to allow for multliple alleles should be possible, but the indexing will get a little messy.