Characters used in phylogenetic inferrence

The first stage is to distinguish homologies from homoplasies.

Homologous characters

A homology is a character shared between two or more species that was present in their common ancestor; a homoplasy is a character shared between two or more species that was not present in their common ancestor. Homologous similarity reveals a phylogenetic relationship; homoplasious similarity does not.

Figure: a classic example of a homology; all tetrapods share a homologous five digit limb structure even though they perform different functions.