Detecting and dating admixture using GLOBETROTTER/fastGLOBETROTTER

GLOBETROTTER, and an updated version fastGLOBETROTTER appropriate for larger datasets, are widely used software to identify and date admixture events, particularly in humans. However, the programs come with a variety of parameter options and require multiple steps, including preparatory applications of the software ChromoPainter, making them complicated to use in practice. Here we outline how to run these programs to infer ancestry and admixture events in target populations. We describe the input files, provide intuition and some simple equations underlying key steps of the analysis pipeline, and discuss how to interpret output and assess reliability of findings. We also highlight some of the main limitations of these approaches, and point out some common issues that can hinder analyses. Throughout we use a simulated example that is provided alongside the software, so that the reader can follow each step. Overall we relay the best practice usage of the method, hopefully enabling easier application of these software going forward.