A knowledge of the phylogenetic relations among species is essential for many other inferences in biology, and a proportionally large effort has been put into reconstructing the tree of life. We look at the techniques used on the morphology of organisms, and then those mainly used with molecular sequences. We consider why different techniques have been used with morphological and molecular evidence, and finish with two case studies in which different kinds of evidence have come into conflict.

Key Questions:

• How do we infer phylogeny?
• How do we analyze the characters used in phylogenetic inference?
• How do we distinguish ancestral from derived homologies?
• How is molecular evidence used?
• What are the different molecular methods?
• What happens when morphological and molecular methods clash?
• Summary