Phylogenetics: Morphology and Partitioning in MrBayes

	EEB 349: Phylogenetics
	The goal of this lab is twofold. First, you will learn how to analyze discrete morphological character data in MrBayes. Second, you will learn how to combine morphological with molecular data in a partitioned analysis in which each data type is assigned an appropriate model of evolution.

The Nylander et al. study

The data for this lab comes from a paper by Nylander et al. (2004) that has already become a landmark study in combining data within a Bayesian framework. The full citation is:

Nylander, J., F. Ronquist, J. P. Huelsenbeck, and J. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67.

If you have access, you can download the pdf of this paper.

Downloading the data file

The data from the paper is available in TreeBase in the form of five separate files. While you can download these separately (search by Study Accession number for S970), putting them together into a single MrBayes data file is tricky (for one thing, the sequences are not in the same order in all five files!), so I have done that for you. Download the file by clicking here and save a copy to your local hard drive.