Minimum evolution

Minimum Evolution (ME) is a phylogenetic tree building method. It uses a pairwise distance matrix, calculated from a multiple sequence alignment, to generate a phylogenetic tree. ME evaluates different tree arrangements by estimating branch lengths that best fit the distance data, then selects the branching pattern with the smallest total branch length.

Phylogenetic tree of Acantobasidium created using Minimum Evolution

A simplified description of the Minimum Evolution algorithm

The modern minimum evolution framework was first used by Kenneth Kidd and Sgaramella-Zonta (1971), and later independently developed further by Andrey Rzhetsky and Masatoshi Nei (1992). This method should not be confused with the earlier minimum evolution, maximum parsimony-based method proposed by Edwards and Cavalli-Sforza (1964); while the methods both share goal of searching for a tree with the shortest total sum of branch lengths, the implementations differ, as ME has a statistical foundation that does not rely solely on Occam's razor reasoning, compared to its earlier predecessor.

Minimum evolution has helped establish several key ideas in phylogenetics:

• It reinforced the principle that the best phylogenetic tree may be the one that minimizes the total amount of inferred evolutionary change.
• It played a major role in shaping distance based phylogenetic algorithms, influencing the development of widely used algorithms such as neighbor joining.
• By framing tree reconstruction as an optimization theory problem solved using heuristic approaches, it also helped lay the groundwork for many modern fast heuristic tree search methods.