Selection and drift

I just realized that I didn't include a link to the notes on selection and drift for Thursday's lecture. I've added links to both the HTML and PDF versions now.

Resemblance among relatives

I've posted notes on resemblance among relatives. They are for the lecture on March 12th. Unfortunately, I'll be leaving town that morning for a trip to Arizona, and the notes involve a lot more math than I can ask anyone else to try and cover. So I've done the next best thing.

I wrote a simple simulation in R that generates data from a full-sib, half-sib crossing design and JAGS code that will analyse the data. Nora will walk you through how the code works, and she'll suggest a simple in-class experiment that will illustrate some of the important principles associated with these analyses.

It's not so important that you understand the math for this lecture, but it's really important that you understand the idea that (a) we can partition phenotypic variation into different components based on the experimental design (in this case among sires, among dams within sires, and among offspring within dams) and (b) we can relate those observational components of variance to the causal components of variance that we're trying to learn about (additive, dominance, and environmental). Because of that, we finally have the tools to explore the genetic basis of variation and evolution in quantitative traits.

Introductory notes on quantitative genetics posted

I've just posted notes for the first two lectures on quantitative genetics. Be forewarned. There is a lot of algebra in these notes. It is unavoidable. There's no way you can possibly understand what additive and dominance variance are without seeing at least some of these details. Even if you use quantitative genetics extensively in your own research, you'll probably never need to refer to it again, but I don't know of a better way for you to develop your intuition about how to interpret quantitative genetic data and to understand the promises and limitations of a quantitative genetic approach to understanding the inheritance and evolution of quantitative traits.

Notes on the coalescent posted

I found a little time to update some more notes. I've now updated notes on the coalescent, which finishes the notes associated with genetic drift. Quantitative genetics is up next.

Running Structure for Project #2

Just a reminder that your Structure runs for K of 1 to 16 is due to me by next Thursday, 2/12. Please use a burnin of 50,000 reps and then 250,000 post-burnin. This should only take a few hours (depending on your machine), and won't need to be run overnight (though you still can if you want)!


Genes, geography, and phonemes

There's a very interesting paper from the most recent issue of Proceedings of the National Academy of Sciences that I encourage you to read:  "A comparison of worldwide phonemic and genetic variation in human populations" (http://10.1073/pnas.1424033112) Here's the abstract:

Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes--sound units that distinguish meaning between words in languages--to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.

And take a close look at the author list. Marc Feldman will be giving a seminar in EEB's Distinguished Ecologist and Evolutionary Biologist Seminar Series on March 10, and Sohini Ramachandaran is tentatively scheduled to give us a guest lecture on April 28.

See you at 8:00am

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I hope that you made good use of your time during yesterday's snow day. As you can see from the Alert banner that I clipped from a few minutes ago, all UConn campuses are following a normal schedule today. That means that we'll continue our discussion of F-statistics bright and early at 8:00am.

Please drive carefully on your way to campus. Many roads are still covered with snow and ice. You'll want to allow some extra time for travel and parking. The sidewalks on campus seem to have been cleared, but they are covered with snowpack and ice, so walking may be a little treacherous too. Be careful, and I'll see you soon.

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 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.