The reconstruction of phylogeny - How do we analyze the characters used in phylogenetic inference?
Characters used in phylogenetic inferrence
The first stage is to distinguish homologies from homoplasies.
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.