Note: This brief tutorial is written for UNR’s NRES 721 as a basic introduction to the utility of full-genome data. Students, if you wish to follow along, you can download all of the data we’ll use by typing the svn checkout https://github.com/twpierson/nres721_genome/trunk/data command in your working directory, from the /data directory in the Github repository here, or from Dropbox by clicking on the link here.

Introduction

In this tutorial, we’re going to introduce full-genome assemblies and briefly discuss how they can be useful in population genetic and phylogenetic studies. For practical reasons, we have to move away from salamanders (☹️), because the only chromosome-level reference genome is 32 Gb! Nobody wants to deal with that for a tutorial.

Instead, we’ll use some real data from the pygmy rabbit (Brachylagus idahoensis). This is a small, endangered species found in the western United States.