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 (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 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.