Phylogenies are based on
monophyletic groups. The taxonomic theory of phylogenetic systematics is organized around the principles that organisms are related through descent from a common ancestor, that there are natural groups of monophyletic taxa, and that unique changes or modifications shared by members of a taxon are evidence of their evolutionary history.
Although monophyletic taxa exist in nature whether they are discovered or not, the goal of phylogenetic systematics is to reveal natural groups of taxa. The main principle of phylogenetic systematics is that natural groups are defined by uniquely shared evolutionary novelties, or homologous characters. A character is a heritable feature (one that is passed from an ancestor to its descendants) of an organism that can be described, measured, or otherwise compared to other organisms. To be considered homologous, a character must be not only heritable, but also independent from any other characters in an organism. The different forms a character may take are called the character states.
Similarities and Phenetic Systems
Systems of classification that are based on overall similarity are called phenetic systems. Phenetic classification schemes do not distinguish between homologous characters (where taxa share a similar characteristic because they inherited it from a common ancestor) and analogous characters (where the characteristic shared by taxa was not inherited from a common ancestor).
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