Perfect Phylogeny - Building A Phylogenetic Tree

Building A Phylogenetic Tree

Main Article: Computational phylogenetics

In general there are two different data types that are used in the construction of a phylogenetic tree. In distance-based computations a phylogenetic tree is created by analyzing relationships among the distance between species and the edge lengths of a corresponding tree. Using a character-based approach employs character states across species as an input in an attempt to find the most "perfect" phylogenetic tree.

The statistical components of a perfect phylogenetic tree can best be described as follows:

A perfect phylogeny for an n x m character state matrix M is a rooted tree T with n leaves satisfying:
i. Each row of M labels exactly one leaf of T
ii. Each column of M labels exactly one edge of T
iii. Every interior edge of T is labeled by at least one column of M
iv. The characters associated with the edges along the unique path from root to a leaf v exactly specify the character vector of v, i.e. the character vector has a 1 entry in all columns corresponding to characters associated to path edges and a 0 entry otherwise.

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It is worth noting that it is very rare to find actual phylognetic data that adheres to the concepts and limitations detailed here. Therefore, it is often the case that researchers are forced to compromise by developing trees that simply try to minimalize homoplasy, finding a maximum-cardinality set of compatible characters, or constructing phylogenies that match as closely as possible to the partitions implied by the characters.