Author: kent

If you’ve downloaded the book version of the notes or downloaded the PDF version of the notes for Thursday, you’ll find that there’s an error in the Stan code used to illustrate Bayesian inference for allele frequencies. The line that reads

p ~ dunif(0.0, 1.0);

should read

p ~ uniform(0.0, 1.0);

Sorry about that. I’ve corrected both the PDF and the HTML versions of the notes here. The book version of notes will include the correction after the semester is over (because I’m likely to find other errors that I want to correct).

I just posted details of the lectures for this Tuesday and this Thursday. You will also find information about this week’s laboratory exercise in the Lab Schedule tab. My plan is to have the lecture details and the lab exercises available by Sunday evening. In some cases, I may be able to post them even earlier. Even though the lecture detail pages, which you can get to by clicking on the lecture title from the Lecture schedule page, have links to the relevant lectures, that’s all they have for now.

I distributed a SurveyMonkey survey asking whether we should use Microsoft Teams or Slack for asynchronous communication this fall. There was nearly 100 percent response to the survey, and the results were clear. We’ll be using Slack. I’ll get the group set up and invite everyone who’s enrolled to join it. You should be receiving an invitation by the end of this week.

I posted the last set of notes for EEB 5348 over the weekend. Next weekend I’ll flesh out the schedule of project and lab assignments, but don’t expect to see those posted until the semester begins. My plan is to post assignments on Mondays. There will be weekly lab assignments that are relatively small that give you practice dealing with data for the longer projects. I won’t make lab assignments in the week when a project is assigned.

In addition to the lecture notes you’ll find on individual lecture detail pages, I’ve compiled all of them into a single PDF that you can download once. The PDF is structured in such a way that if you were to print it double-sided, you could have it bound into a reference volume. Here’s the link: https://figshare.com/articles/journal_contribution/Lecture_notes_in_population_genetics/100687.

• Evolution of quantitative traits (HTML) (PDF)
• Principles and applications of association mapping (HTML) (PDF)
• Genomic prediction (HTML)(PDF)

With any luck at all, I’ll post the last set of notes for the course next Monday. The notes today include a new lecture on admixture graphs and sparg, a powerful new approach to estimating dispersal distances and the geographical location of ancestors from genomic data. They also include the first two sets of notes on quantitative genetics.

• Statistical phylogeography: Migrate-N, IMa, and ABC (HTML) (PDF)
• Statistical phylogeography: Admixture graphs and sparg (HTML) (PDF)
• Population genomics (HTML) (PDF)
• Introduction to quantitative genetics (HTML) (PDF)
• Resemblance among relatives (HTML) (PDF)

I revised some notes last weekend and posted them to the lecture detail pages on the course website, but I didn’t make a note of that here. This weekend I revised some more. The result is that there’s a pretty long list of additions – all the way from the coalescent through AMOVA. With a little luck, the notes on statistical phylogeography and population genomics will be done by next week. Because I’ll be really busy once the semester begins, I’m doing my best to get all of the notes revised before the semester begins. That way I can focus on lab exercises once the semester starts.

• The coalescent (HTML) (PDF)
• Introduction to molecular evolution (HTML) (PDF)
• Patterns of nucleotide and amino acid substitution (HTML) (PDF)
• Detecting selection on nucleotide polymorphisms (HTML) (PDF)
• Analysis of molecular variance (AMOVA) (HTML) (PDF)

This set of notes covers estimating viabilities (relative and absolute) and the basic properties of genetic drift, including the inbreeding analogy to drift, inbreeding and variance effective population sizes, the interaction of mutation and drift, the interaction of migration and drift, and the interaction of natural selection (specifically viability selection) and drift.

• Estimating viability (HTML) (PDF)
• Genetic drift (HTML) (PDF)
• Mutation, migration, and drift (HTML) (PDF)
• Selection and drift (HTML) (PDF)

I have just posted revised notes on the analysis of population structure using individual assignment, focusing on STRUCTURE. I’ve also posted revised notes on the basic principles of natural selection, focusing on viability selection at one locus with two alleles. If you’ve seen earlier versions of either set of notes, you won’t find much new here – other than a few more lame jokes hidden in the footnotes.

• Analyzing the genetic structure of populations: individual assignment (HTML) (PDF)
• The genetics of natural selection (HTML) (PDF)

By the way, I haven’t mentioned this yet, but my goal is to finish revising these notes no later than mid-August, earlier if I can pull it off. When I’ve revised all of them, I’ll compile them into a single volume of notes and release a new version of Lecture notes in population genetics. I have to say that when I was looking up the URL for the last edition of my notes on Figshare, I was surprised to see that they’ve been seen nearly 11,000 times and been downloaded nearly 3400 times. I am pleased that so many people seem to find them useful. If you’re one of those people and you have suggestions on how to make them more useful, please let me know. I am especially interested in hearing from you if you find errors or discussions that are confusing.

If you follow me on Twitter or read Uncommon Ground, you may remember that I announced last September that I’d written a new version of Hickory (a C++ program that Paul Lewis and I wrote) using R and Stan for Bayesian analysis of Wright’s F-statistics. This set of notes outlines the basic principle behind the approach and provides an overview of using Hickory for analysis of F-statistics. Hickory can do more than is illustrated here. If you’re interested, visit the Github page. If you’re really interested, follow the instructions there to install it as a package in R.

• Analyzing the genetic structure of populations: a Bayesian approach (HTML) (PDF)

I uploaded notes on inbreeding, population structure (focusing on the Wahlund effect), and F-statistics this weekend. This set of notes includes a discussion of (and some of the math for) Nei’s G-statistics and Weir and Cockerham’s $\theta$ statistics. The next set of notes will outline a Bayesian approach to estimating F-statistics that is conceptually similar to Weir and Cockerham’s approach. It will also include an appendix describing how to load the package we’ll use into R, since it isn’t (yet) available on CRAN.

• Inbreeding and self-fertilization (HTML) (PDF)
• Analyzing the genetic structure of populations (HTML) (PDF)