Phylogeny for the faint of heart: a tutorial
Sandra L. Baldauf
Department of Biology, University of York, Box 373, York, UK YO10 5YW
Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.
Phylogenetics is the science of estimating the evolutionary past, in the case of molecular phylogeny, based on the comparison of DNA or protein sequences. The idea of representing these hypotheses as trees probably dates back to Darwin, but the numerical calculation of trees using quantitative methods is relatively recent, and their application to molecular data even more so. In the age of rapid and rampant gene sequencing, molecular phylogeny has truly come into its own, emerging as a major tool for making sense of a sometimes overwhelming amount information.
This tutorial aims to introduce the basic principles behind and programs for constructing evolutionary trees (phylogenetic analysis). It is intended primarily for those who want to read other people's trees, but also as a general introduction for those who might wish to begin to try building their own. In the latter case the reader is warned – phylogenetic analysis and evolutionary theory are not trivial pursuits; as with any new methodology, it is advisable to seek expert help before getting in too deep.