Chapter 1 About this workshop

The evolutionary tree of life is fundamental to our understanding of the natural world. This workshop will go through all of the steps of research in understanding the evolutionary history of several groups of Andean plants. We will participate in field collections of plants and processing of samples for collections. In real research projects, the species and collections should be considered carefully with an expectation of the potential for phylogenetic results and evolutionary hypotheses. Researchers should create voucher specimens to preserve the samples long-term, as well as appropriate samples for DNA extraction. Samples should be recorded and given a unique identifier, in order to connect the specimen to the sequencing data.

In this workshop we will not have an opportunity to experience the expected next step of sample processing, DNA extraction, or sequencing. Contemporary sequencing is often completed by an outside facility, although we will discuss options as part of this workshop. We will continue with the analysis of sequence data, particularly target-capture data from genome sequencing. As part of this we will learn basic computing on the command line and some approaches to writing code in the bash shell and R. This will allow us to conduct data analysis that can apply to larger scale work than can be conducted on a laptop. As part of the analysis of different datasets, we will see how in many cases we draw different conclusions from different datasets and how we examine phylogenies. We will then use these phylogenies to conduct comparative analyses to understand how phylogenies inform our understanding of trait evolution. Finally, we will ask you to present the results of your analyses.