The character-state data model used in evolutionary comparative analysis. The character-state data model is illustrated here with an example showing members of a protein family, with a single set of labels for Operational Taxonomic Units, 2 phylogenies, and 3 types of characters (modified from ). The biological entities to be compared— whether genes, species, individuals, or some other unit— are known as “OTUs” or “Taxa”. Each OTU may be characterized as having a “state” for a given “character”, e.g., the OTU C_elegans_17537797 has the state “A” (Alanine) for the 2nd amino acid character. Phylogenetic trees (typically, directional, acyclic, singly-linked graphs in which no node has more than one ancestor) connect all the OTUs, representing their descent from a common ancestor.