Month: December 2021

I just uploaded the final set of notes on genomic prediction. As you’ll see, there are some things you’ll need to be careful of if you want to use genomic prediction in your own work. Although I don’t mention this explicitly in the notes, the implication of the last caveat about genomic prediction is that GWAS may not be very useful in understanding the genetic basis of variation in a complicated trait beyond the population in which the analysis was done. A further leap is that even a traditional quantitative genetic analysis may not extrapolate well to other populations, even if the environmental conditions are similar.

In short, quantitative genetics provides some very powerful tools, but powerful tool can also cause a lot of damage. Be careful when you wield this one.

Congratulations! You still have a couple of lectures to survive, but you’ve almost joined the survivors of EEB 5348. I’ve now posted the last lab exercise for the semester. It builds on the locus-by-locus GWAS in last week’s lab and extends it to genomic prediction. We could easily spend several weeks, probably even an entire semester, exploring all of the ins and outs of GWAS and genomic prediction, but this is an overview course. My goal is to give you enough of an introduction to approaches like these that you not only know they exist but that you also can figure out how to use them on your own if it seems appropriate for your research.

• Genomic prediction in gypsy moths

If you downloaded the notes on genomic prediction before noon on Sunday, I suggest that you download them again. I’ve modified them a bit to reflect the new R notebook I put together on Saturday to illustrate the simple example that is discussed in the notes. I also suggest that you download the R notebook so that you can explore different simulated data sets and see how they perform.

I am working on the final lab exercise, and I’ve finished running nearly all of the analyses I want to run before typing it up and making it available. Since I have some non-teaching related things to attend to this afternoon, there’s a decent chance that the lab won’t be posted until some time on Monday, but I’ll do my best to have it posted before lecture on Tuesday.

• Exploring genomic prediction