Case study exercise: Neanderthal ancestry trajectory

In this case study exercise, you will be reproducing a critical result from my 2018 study on the limits of selection against Neanderthal introgression, which turned into a study on the importance of model assumptions on the robustness of inferences with \(f_4\) statistics and \(D\) statistics.

I chose this paper for several reasons:

1. This study would’ve been absolutely impossible to carry out without computer simulations.

2. The limitations of tools I had available at the time required me to write hundreds of lines of code spread across shell scripts, Python scripts, and R scripts.

3. Thanks to slendr, a project which required months of work and lots of coding is possible to reduce to a handful of lines of R.

4. It provides an excellent educational example of how slendr simulations can help you navigate any conceivable population genomic scenario, gain confidence in your results, and aid in their interpretation.

The outcome of