Statistical phylogeography – notes are updated an R Shiny application will follow

I just updated notes on AMOVA, statistical phylogeography, and population genomics. There will be an R Shiny application on shinyapps.io (I hope). It’s the one I referred to on the 27th. It’s written and it runs on my computer (it will run on yours if you download it and follow the instructions). I’m working with R Studio support to sort out the problem, and I hope it will be fixed before long.

As usual, you can find the notes from the Lecture notes page or from the lecture detail page on the Lecture schedule.

The genealogy of the coalescent at one locus in two populations with migration and mutation

I just posted another R Shiny application illustrating properties of the coalescent in two populations with mutation and migration. Unfortunately, to see this one, you’ll have to download the source from Github (app.R) and run it in your local version of R. It’s not difficult, but it’s less convenient than running it on shinyapps.io. The problem arises because I use ggtree() to plot and color the tree. ggtree() is a BioConductor package, and I’m running into an error installing it in the application package. If I can’t figure it out, I may install a version of R Studio Server here and host it locally.

Here’s how to run the application in your local version of R:

    • Follow the link to Github and download app.R (click on the button labeled “Raw” at the right side of the screen and use “File->Save” to save it somewhere convenient on your hard drive.
    • Make sure your version of R has the libraries mentioned at the top of app.R installed. They are: ggplot2, shiny, cowplot, plotly, coala, ggtree, and ape. (Actually, I think you can delete cowplot and plotly from the list of libraries that are loaded. They’re leftover from some earlier experiments. To install ggtree(), you’ll first have to make sure that you have BiocManager installed. Then you can simply BiocManager::install("ggtree").
    • Launch R and make sure your working directory contains the source for app.R.
    • Then runApp() and enjoy the ride!

Updated notes – the interaction of genetic drift with mutation, migration, and selection and a new R Shiny application

I’ve updated notes on the interaction of genetic drift with mutation, and to complement the notes, I’ve written a new simulation in R Shiny and Plotly to illustrate both the dynamics of allele frequency changes within populations and the distribution of allele frequencies among populations. I’ve also updated notes on the interaction of genetic drift and natural selection. I’m having some kind of a weird permission problem with my server. A copy of the PDF that I just linked to with the original name (selection-drift.pdf) and the same permissions (at least so far as I can tell) keeps giving me a permission error when I try to download it. I’ll leave temp.pdf on the server, but I hope to fix the permission problem, so it would be best not to link to that file until I get it fixed.

Estimating viability, principles of genetic drift, and an R Shiny application illustrating genetic drift

I’ve posted the last set of notes on selection, outlining the principles of estimating viability components of fitness from observations on genotypes before and after selection. I’ve also posted notes on basic principles of genetic drift, including the concept of effective population size. In addition, I’ve written an application in R Shiny that lets you explore the properties of genetic drift. You can pick the initial allele frequency, the number of different populations subject to drift (from one to ten), the (effective) population size of each population, and the number of generations for the simulation to run.

An R Shiny application to illustrate F-statistics

I posted notes on the Wahlund effect and F-statistics a while ago. I’ve now posted an R Shiny application to illustrate the difference between Nei’s GST and Weir and Cockerham’s FST. The application simulates a sample of 25 diploid genotypes from 10 different populations. The genotypes are a multinomial sample from genotype frequencies calculated from Hardy-Weinberg expectations within each population, given the population allele frequency. That’s statistical sampling. The allele frequencies in each population are sampled from a Beta distribution with a mean of p = 0.5 and a variance of FSTp(1-p). That’s evolutionary sampling (or genetic sampling). Just as the individuals we sampled within each population are a sample of all individuals we could have sampled, the populations we sampled are a sample of all populations we could have sampled.

If you keep the parametric FST the same and just keep hitting “Go”, you’ll see that the genotype counts change every time. That’s the evolutionary sampling. You’ll find a link to the application on the lecture detail page, or you can link directly to the application on shinyapps.io.

As a reminder, if you’re interested in the source code for this or other R Shiny applications I develop for this course, they’ll all be available on Github.

Adding R Shiny applications to illustrate concepts

I started learning R Shiny this afternoon. It will take me a while to become fluent with it, but when I do, I’ll be able to construct a variety of web applications to illustrate principles of population genetics. I just finished the first one. It illustrates how the EM algorithm works, following the example in the notes accompanying the lecture for 24 January. You’ll find a link to the web application there, but if you’d like to save yourself a click, here’s the direct link: https://keholsinger.shinyapps.io/EM-algorithm-for-allele-frequencies/ . I expect to add other web applications over the next month or two. You’ll find the code for them in a new Github repository (https://kholsinger.github.io/PopGen-Shiny/). I hope you find the applications useful. If you have suggestions or requests, please drop me a line. I can’t promise that I’ll follow through, but I promise to consider any requests I receive.