Practical 1 Methods in Macroecology and Macroevolution

These practicals were designed for a module on the MSc Taxonomy and Biodiversity run by Natural History Museum and Imperial College London. Please feel free to use and share.

1.1 Module Aims

The aim of this module is to introduce you to some of the cutting-edge methods being used in macroecology and macroevolution, with particular focus on work being done right now at the Museum. Rather than concentrating on learning theory through lectures, the module will introduce you to various ways we collect, analyse and interpret macro-scale data with a large emphasis on practical work, mostly using R.

1.2 Datasets and practical handouts

All datasets and practical handouts are available on GitHub at [https://github.com/nhcooper123/macro-methods-module]. You can download the whole repository. Scripts as .Rmd files and the data are all available in the MacroModule folder.

1.3 How to use these materials

It is possible to use these materials in a number of ways.

  1. Follow this book, copy pasting code into an R script and then running it in the R console.
  2. Open the .Rmd file for each practical in RStudio and use it as an RNotebook. This allows you to run chunks of code in the script and for the results to appear below the code. This is a good way to learn/teach these materials. See here for more details.

Some knowledge of R is required, but this is mostly covered in the first chapter of this book.

1.4 Module outline

These practicals fit into a broader module as follows.

  • What are macroecology and macroevolution?
  • Diversity indices in R. [practical]
  • Visualising phylogenies in R. [practical]
  • Using Big Data in conservation with the PREDICTS project. (Andy Purvis)
  • Using the paleobiology database (PBDB) to get data on fossil species for macroecological and macroevolutionary analyses. (Terri Cleary)
  • The comparative method, dealing with phylogenetic non-independence in comparative analyses.* PGLS in R. [practical]
  • Macroevolutionary patterns.
  • Models of evolution in R. [practical]
  • Using museum specimen data in macroecological and macroevolutionary analyses.
  • Geometric morphometrics. [practical]
  • Case study using Foraminifera. (Isabel Fenton)
  • Diversification rates.
  • BAMM [practical]
  • Critical thinking: Do you trust your methods?

Links to some of the lectures are also available here.